Starting phenix.real_space_refine on Fri Sep 11 18:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2026/6k7j_9935.cif" } resolution = 3.08 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= 0.000 sd= 0.005 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 3 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6863 2.51 5 N 1757 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10602 At special positions: 0 Unit cell: (73.87, 116.2, 166.83, 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 56 16.00 P 3 15.00 Mg 1 11.99 O 1922 8.00 N 1757 7.00 C 6863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 386.7 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.985A pdb=" N TYR A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 123 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.825A pdb=" N MET A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.266A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.810A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 559 through 565 removed outlier: 3.606A pdb=" N ASP A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 5.120A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 4.635A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.545A pdb=" N LEU A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 730 through 738 removed outlier: 4.143A pdb=" N TYR A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 762 through 778 removed outlier: 4.191A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.337A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 866 removed outlier: 4.313A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.134A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.756A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.115A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1035 through 1062 removed outlier: 4.145A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.196A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.919A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.736A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 removed outlier: 4.019A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.688A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 removed outlier: 4.339A pdb=" N GLN A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 158 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.904A pdb=" N CYS A 181 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.542A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.620A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.516A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 518 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.881A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.291A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.291A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 468 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1885 1.32 - 1.45: 2830 1.45 - 1.57: 6044 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10852 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.607 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.606 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CD LYS C 308 " pdb=" CE LYS C 308 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.28e+01 ... (remaining 10847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 14376 3.46 - 6.91: 323 6.91 - 10.37: 31 10.37 - 13.82: 5 13.82 - 17.28: 2 Bond angle restraints: 14737 Sorted by residual: angle pdb=" N ASP A 672 " pdb=" CA ASP A 672 " pdb=" C ASP A 672 " ideal model delta sigma weight residual 113.18 120.61 -7.43 1.33e+00 5.65e-01 3.12e+01 angle pdb=" C PRO A 91 " pdb=" N ASP A 92 " pdb=" CA ASP A 92 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" CA LEU A 738 " pdb=" CB LEU A 738 " pdb=" CG LEU A 738 " ideal model delta sigma weight residual 116.30 133.58 -17.28 3.50e+00 8.16e-02 2.44e+01 angle pdb=" C LYS A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta sigma weight residual 121.97 130.59 -8.62 1.80e+00 3.09e-01 2.30e+01 angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 111.91 107.98 3.93 8.90e-01 1.26e+00 1.95e+01 ... (remaining 14732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 6193 32.36 - 64.72: 191 64.72 - 97.08: 11 97.08 - 129.43: 0 129.43 - 161.79: 2 Dihedral angle restraints: 6397 sinusoidal: 2571 harmonic: 3826 Sorted by residual: dihedral pdb=" CA ALA A1020 " pdb=" C ALA A1020 " pdb=" N PRO A1021 " pdb=" CA PRO A1021 " ideal model delta harmonic sigma weight residual 180.00 -120.56 -59.44 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA THR A 511 " pdb=" C THR A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta harmonic sigma weight residual 180.00 128.89 51.11 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA LEU C 243 " pdb=" C LEU C 243 " pdb=" N ASP C 244 " pdb=" CA ASP C 244 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 6394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1313 0.081 - 0.162: 321 0.162 - 0.243: 46 0.243 - 0.324: 1 0.324 - 0.405: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.13 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 964 " pdb=" CB LEU A 964 " pdb=" CD1 LEU A 964 " pdb=" CD2 LEU A 964 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1681 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.351 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.270 2.00e-02 2.50e+03 2.29e-01 6.58e+02 pdb=" C7 NAG C 402 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.230 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG C 401 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 479 2.71 - 3.26: 9883 3.26 - 3.80: 17417 3.80 - 4.35: 22588 4.35 - 4.90: 37953 Nonbonded interactions: 88320 Sorted by model distance: nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1202 " model vdw 2.159 2.170 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.245 3.040 nonbonded pdb=" O GLU A 222 " pdb=" OH TYR A 269 " model vdw 2.263 3.040 nonbonded pdb=" O CYS A 50 " pdb=" OG1 THR A 270 " model vdw 2.278 3.040 ... (remaining 88315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.013 0.125 10860 Z= 0.529 Angle : 1.239 17.279 14758 Z= 0.647 Chirality : 0.071 0.405 1684 Planarity : 0.014 0.300 1835 Dihedral : 15.300 161.793 3920 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 0.17 % Allowed : 9.12 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.08 % 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: -3.98 (0.18), residues: 1301 helix: -2.61 (0.16), residues: 577 sheet: -1.21 (0.39), residues: 156 loop : -3.03 (0.21), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 898 TYR 0.025 0.003 TYR C 122 PHE 0.045 0.004 PHE C 304 TRP 0.022 0.004 TRP A 927 HIS 0.009 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.01290 / 0.53 (10852) covalent geometry : angle 1.22913 / 0.64 (14737) SS BOND : bond 0.01231 / 0.61 ( 3) SS BOND : angle 5.01963 / 2.74 ( 6) hydrogen bonds : bond 0.12000 / 7.55 ( 467) hydrogen bonds : angle 6.95869 / 5.00 ( 1344) link_ALPHA1-4 : bond 0.00166 / 0.09 ( 1) link_ALPHA1-4 : angle 5.91237 / 3.12 ( 3) link_BETA1-4 : bond 0.00281 / 0.15 ( 1) link_BETA1-4 : angle 3.46805 / 1.83 ( 3) link_NAG-ASN : bond 0.01348 / 0.64 ( 3) link_NAG-ASN : angle 3.46508 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.373 Fit side-chains REVERT: A 155 ASP cc_start: 0.5940 (m-30) cc_final: 0.5620 (m-30) REVERT: A 178 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 419 MET cc_start: 0.7777 (mtt) cc_final: 0.7516 (mtt) REVERT: A 645 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6531 (mt-10) REVERT: A 665 LYS cc_start: 0.7853 (mttt) cc_final: 0.7102 (mmtt) REVERT: A 904 ASN cc_start: 0.8244 (m110) cc_final: 0.8016 (m110) REVERT: A 1058 LYS cc_start: 0.6492 (mmmt) cc_final: 0.6280 (mtpt) REVERT: A 1059 ARG cc_start: 0.6166 (tmt-80) cc_final: 0.5784 (ttt-90) REVERT: C 49 THR cc_start: 0.8321 (m) cc_final: 0.8093 (p) REVERT: C 215 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6997 (mmp-170) REVERT: C 290 ARG cc_start: 0.7335 (ttt-90) cc_final: 0.6916 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.1083 time to fit residues: 19.9589 Evaluate side-chains 102 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 78 ASN A 124 HIS A 128 ASN A 136 GLN A 225 ASN A 256 GLN A 381 HIS A 453 GLN A 679 ASN ** C 249 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 = 0.4071 r_free = 0.4071 target = 0.195542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.165955 restraints weight = 10268.211| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.64 r_work: 0.3309 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10860 Z= 0.142 Angle : 0.700 9.255 14758 Z= 0.358 Chirality : 0.046 0.206 1684 Planarity : 0.006 0.085 1835 Dihedral : 8.904 164.373 1433 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.54 % Rotamer: Outliers : 1.48 % Allowed : 11.03 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.21), residues: 1301 helix: -1.04 (0.19), residues: 585 sheet: -1.06 (0.38), residues: 161 loop : -2.62 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 538 TYR 0.016 0.001 TYR C 121 PHE 0.017 0.001 PHE A 368 TRP 0.020 0.001 TRP A 927 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10852) covalent geometry : angle 0.69047 / 0.36 (14737) SS BOND : bond 0.01385 / 0.66 ( 3) SS BOND : angle 2.76734 / 1.42 ( 6) hydrogen bonds : bond 0.05115 / 3.33 ( 467) hydrogen bonds : angle 5.30341 / 3.76 ( 1344) link_ALPHA1-4 : bond 0.00145 / 0.08 ( 1) link_ALPHA1-4 : angle 4.05599 / 2.16 ( 3) link_BETA1-4 : bond 0.00308 / 0.16 ( 1) link_BETA1-4 : angle 2.35748 / 1.23 ( 3) link_NAG-ASN : bond 0.00437 / 0.22 ( 3) link_NAG-ASN : angle 3.06716 / 1.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.8535 (mttt) cc_final: 0.8129 (mmtt) REVERT: A 778 LYS cc_start: 0.8215 (mptt) cc_final: 0.7984 (mmtp) REVERT: A 874 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: A 1059 ARG cc_start: 0.6842 (tmt-80) cc_final: 0.6580 (ttt-90) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 0.1089 time to fit residues: 19.2807 Evaluate side-chains 108 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.193240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.159722 restraints weight = 10350.379| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.08 r_work: 0.3358 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10860 Z= 0.182 Angle : 0.680 9.021 14758 Z= 0.347 Chirality : 0.047 0.211 1684 Planarity : 0.006 0.089 1835 Dihedral : 8.582 160.744 1432 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 2.61 % Allowed : 13.38 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.96 (0.22), residues: 1301 helix: -0.46 (0.21), residues: 577 sheet: -0.81 (0.38), residues: 172 loop : -2.35 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.013 0.002 TYR C 121 PHE 0.023 0.002 PHE C 304 TRP 0.020 0.002 TRP A 927 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (10852) covalent geometry : angle 0.67140 / 0.35 (14737) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 2.69883 / 1.34 ( 6) hydrogen bonds : bond 0.05177 / 3.35 ( 467) hydrogen bonds : angle 5.09012 / 3.59 ( 1344) link_ALPHA1-4 : bond 0.00060 / 0.03 ( 1) link_ALPHA1-4 : angle 3.92154 / 2.09 ( 3) link_BETA1-4 : bond 0.00385 / 0.20 ( 1) link_BETA1-4 : angle 2.98719 / 1.56 ( 3) link_NAG-ASN : bond 0.00452 / 0.22 ( 3) link_NAG-ASN : angle 2.62607 / 1.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.8433 (mttt) cc_final: 0.8180 (mmtm) REVERT: A 772 MET cc_start: 0.7770 (tmm) cc_final: 0.7362 (ttp) REVERT: A 874 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: A 1059 ARG cc_start: 0.6952 (tmt-80) cc_final: 0.6718 (ttt-90) REVERT: C 185 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8644 (mp) outliers start: 30 outliers final: 18 residues processed: 129 average time/residue: 0.1079 time to fit residues: 19.8995 Evaluate side-chains 113 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.192303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.156226 restraints weight = 10289.993| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.24 r_work: 0.3233 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10860 Z= 0.194 Angle : 0.675 9.195 14758 Z= 0.344 Chirality : 0.047 0.212 1684 Planarity : 0.005 0.080 1835 Dihedral : 8.403 158.122 1432 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Rotamer: Outliers : 3.04 % Allowed : 14.60 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.70 (0.22), residues: 1301 helix: -0.26 (0.21), residues: 580 sheet: -0.50 (0.40), residues: 173 loop : -2.29 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 215 TYR 0.013 0.002 TYR C 297 PHE 0.021 0.002 PHE C 304 TRP 0.019 0.002 TRP A 927 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (10852) covalent geometry : angle 0.66697 / 0.34 (14737) SS BOND : bond 0.01283 / 0.61 ( 3) SS BOND : angle 2.65445 / 1.33 ( 6) hydrogen bonds : bond 0.05163 / 3.34 ( 467) hydrogen bonds : angle 4.96923 / 3.50 ( 1344) link_ALPHA1-4 : bond 0.00076 / 0.04 ( 1) link_ALPHA1-4 : angle 3.95269 / 2.11 ( 3) link_BETA1-4 : bond 0.00255 / 0.13 ( 1) link_BETA1-4 : angle 2.87711 / 1.52 ( 3) link_NAG-ASN : bond 0.00497 / 0.24 ( 3) link_NAG-ASN : angle 2.61119 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6428 (OUTLIER) cc_final: 0.6088 (p) REVERT: A 665 LYS cc_start: 0.8692 (mttt) cc_final: 0.8207 (mmtm) REVERT: A 691 MET cc_start: 0.4206 (ttt) cc_final: 0.3942 (ttp) REVERT: A 874 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: A 1059 ARG cc_start: 0.6799 (tmt-80) cc_final: 0.6337 (ttt-90) REVERT: C 185 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (mp) outliers start: 35 outliers final: 22 residues processed: 130 average time/residue: 0.1017 time to fit residues: 19.5102 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 98 optimal weight: 0.0010 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.195874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.159535 restraints weight = 10255.725| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.22 r_work: 0.3235 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10860 Z= 0.123 Angle : 0.598 7.872 14758 Z= 0.306 Chirality : 0.044 0.179 1684 Planarity : 0.005 0.078 1835 Dihedral : 8.073 155.771 1432 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.87 % Allowed : 15.12 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.29 (0.23), residues: 1301 helix: 0.15 (0.21), residues: 579 sheet: -0.45 (0.39), residues: 181 loop : -2.11 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 538 TYR 0.012 0.001 TYR C 121 PHE 0.014 0.001 PHE A 368 TRP 0.018 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10852) covalent geometry : angle 0.59112 / 0.30 (14737) SS BOND : bond 0.00438 / 0.21 ( 3) SS BOND : angle 2.14147 / 1.08 ( 6) hydrogen bonds : bond 0.04337 / 2.81 ( 467) hydrogen bonds : angle 4.67610 / 3.28 ( 1344) link_ALPHA1-4 : bond 0.00149 / 0.08 ( 1) link_ALPHA1-4 : angle 3.65672 / 1.95 ( 3) link_BETA1-4 : bond 0.00410 / 0.22 ( 1) link_BETA1-4 : angle 2.91060 / 1.51 ( 3) link_NAG-ASN : bond 0.00259 / 0.13 ( 3) link_NAG-ASN : angle 1.90351 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6072 (p) REVERT: A 589 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6498 (mt) REVERT: A 665 LYS cc_start: 0.8669 (mttt) cc_final: 0.8184 (mmtm) REVERT: A 738 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5803 (tt) REVERT: A 874 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: A 1058 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6904 (ttmt) REVERT: A 1059 ARG cc_start: 0.6713 (tmt-80) cc_final: 0.6266 (ttt-90) REVERT: C 185 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 202 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8471 (mttt) outliers start: 33 outliers final: 18 residues processed: 133 average time/residue: 0.1048 time to fit residues: 20.2363 Evaluate side-chains 119 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.195166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.162121 restraints weight = 10312.966| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.76 r_work: 0.3177 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10860 Z= 0.138 Angle : 0.608 8.252 14758 Z= 0.309 Chirality : 0.044 0.176 1684 Planarity : 0.005 0.078 1835 Dihedral : 7.970 154.482 1432 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 2.78 % Allowed : 16.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.17 (0.23), residues: 1301 helix: 0.23 (0.21), residues: 579 sheet: -0.40 (0.39), residues: 181 loop : -2.03 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 133 TYR 0.013 0.001 TYR C 121 PHE 0.016 0.001 PHE C 304 TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10852) covalent geometry : angle 0.60110 / 0.31 (14737) SS BOND : bond 0.00456 / 0.22 ( 3) SS BOND : angle 2.18969 / 1.09 ( 6) hydrogen bonds : bond 0.04454 / 2.89 ( 467) hydrogen bonds : angle 4.63780 / 3.25 ( 1344) link_ALPHA1-4 : bond 0.00192 / 0.10 ( 1) link_ALPHA1-4 : angle 3.50313 / 1.87 ( 3) link_BETA1-4 : bond 0.00373 / 0.20 ( 1) link_BETA1-4 : angle 2.86602 / 1.50 ( 3) link_NAG-ASN : bond 0.00371 / 0.18 ( 3) link_NAG-ASN : angle 2.06399 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7072 (mmt-90) cc_final: 0.6848 (mmt180) REVERT: A 225 ASN cc_start: 0.6453 (t0) cc_final: 0.6191 (t0) REVERT: A 270 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6545 (p) REVERT: A 665 LYS cc_start: 0.8554 (mttt) cc_final: 0.8190 (mmtm) REVERT: A 738 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6408 (tt) REVERT: A 874 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: A 1059 ARG cc_start: 0.6885 (tmt-80) cc_final: 0.6507 (ttt-90) outliers start: 32 outliers final: 21 residues processed: 125 average time/residue: 0.1028 time to fit residues: 18.7972 Evaluate side-chains 116 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 87 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.196668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136463 restraints weight = 10238.430| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.80 r_work: 0.2994 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10860 Z= 0.122 Angle : 0.589 7.695 14758 Z= 0.300 Chirality : 0.044 0.178 1684 Planarity : 0.005 0.077 1835 Dihedral : 7.825 152.789 1432 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Rotamer: Outliers : 2.43 % Allowed : 17.12 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.05 (0.23), residues: 1301 helix: 0.34 (0.21), residues: 581 sheet: -0.31 (0.40), residues: 181 loop : -1.99 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.011 0.001 TYR C 121 PHE 0.014 0.001 PHE A 368 TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10852) covalent geometry : angle 0.58323 / 0.30 (14737) SS BOND : bond 0.00375 / 0.18 ( 3) SS BOND : angle 1.89503 / 0.95 ( 6) hydrogen bonds : bond 0.04197 / 2.72 ( 467) hydrogen bonds : angle 4.51697 / 3.16 ( 1344) link_ALPHA1-4 : bond 0.00193 / 0.10 ( 1) link_ALPHA1-4 : angle 3.46587 / 1.85 ( 3) link_BETA1-4 : bond 0.00369 / 0.19 ( 1) link_BETA1-4 : angle 2.82748 / 1.47 ( 3) link_NAG-ASN : bond 0.00275 / 0.14 ( 3) link_NAG-ASN : angle 1.80206 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6231 (OUTLIER) cc_final: 0.5923 (p) REVERT: A 665 LYS cc_start: 0.8525 (mttt) cc_final: 0.7941 (mmtm) REVERT: A 685 LYS cc_start: 0.6576 (mttp) cc_final: 0.5313 (mmmt) REVERT: A 738 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5546 (tt) REVERT: A 874 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: A 904 ASN cc_start: 0.8222 (m110) cc_final: 0.7943 (m110) REVERT: A 1059 ARG cc_start: 0.6467 (tmt-80) cc_final: 0.5985 (ttt-90) REVERT: C 115 GLU cc_start: 0.8302 (pt0) cc_final: 0.8068 (pt0) REVERT: C 185 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 202 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8329 (mttt) outliers start: 28 outliers final: 22 residues processed: 127 average time/residue: 0.1100 time to fit residues: 20.1619 Evaluate side-chains 122 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 50 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.192498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160589 restraints weight = 10267.638| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.16 r_work: 0.3245 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10860 Z= 0.218 Angle : 0.672 9.933 14758 Z= 0.338 Chirality : 0.047 0.212 1684 Planarity : 0.005 0.081 1835 Dihedral : 7.890 147.731 1432 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 3.21 % Allowed : 16.59 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.32 (0.23), residues: 1301 helix: -0.03 (0.21), residues: 590 sheet: -0.49 (0.39), residues: 191 loop : -1.97 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.016 0.002 TYR C 297 PHE 0.023 0.002 PHE C 304 TRP 0.016 0.002 TRP A 927 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (10852) covalent geometry : angle 0.66374 / 0.34 (14737) SS BOND : bond 0.00676 / 0.33 ( 3) SS BOND : angle 2.61380 / 1.29 ( 6) hydrogen bonds : bond 0.05163 / 3.35 ( 467) hydrogen bonds : angle 4.74383 / 3.34 ( 1344) link_ALPHA1-4 : bond 0.00043 / 0.02 ( 1) link_ALPHA1-4 : angle 3.76381 / 2.01 ( 3) link_BETA1-4 : bond 0.00233 / 0.12 ( 1) link_BETA1-4 : angle 2.83928 / 1.51 ( 3) link_NAG-ASN : bond 0.00582 / 0.28 ( 3) link_NAG-ASN : angle 2.55558 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6294 (p) REVERT: A 665 LYS cc_start: 0.8636 (mttt) cc_final: 0.8166 (mmtm) REVERT: A 738 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5804 (tt) REVERT: A 874 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: A 1059 ARG cc_start: 0.6823 (tmt-80) cc_final: 0.6322 (ttt-90) outliers start: 37 outliers final: 27 residues processed: 130 average time/residue: 0.1062 time to fit residues: 20.0244 Evaluate side-chains 125 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.197241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.163643 restraints weight = 10253.136| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.84 r_work: 0.3187 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10860 Z= 0.116 Angle : 0.584 8.149 14758 Z= 0.298 Chirality : 0.043 0.180 1684 Planarity : 0.005 0.076 1835 Dihedral : 7.559 143.105 1432 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 1.91 % Allowed : 18.16 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.97 (0.23), residues: 1301 helix: 0.36 (0.21), residues: 586 sheet: -0.46 (0.39), residues: 191 loop : -1.85 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.014 0.001 TYR C 121 PHE 0.014 0.001 PHE A 368 TRP 0.019 0.001 TRP A 927 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10852) covalent geometry : angle 0.57813 / 0.30 (14737) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.75825 / 0.89 ( 6) hydrogen bonds : bond 0.04055 / 2.62 ( 467) hydrogen bonds : angle 4.46594 / 3.13 ( 1344) link_ALPHA1-4 : bond 0.00130 / 0.07 ( 1) link_ALPHA1-4 : angle 3.59454 / 1.92 ( 3) link_BETA1-4 : bond 0.00433 / 0.23 ( 1) link_BETA1-4 : angle 2.84960 / 1.48 ( 3) link_NAG-ASN : bond 0.00139 / 0.07 ( 3) link_NAG-ASN : angle 1.70413 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6895 (OUTLIER) cc_final: 0.6569 (p) REVERT: A 665 LYS cc_start: 0.8556 (mttt) cc_final: 0.8195 (mmtm) REVERT: A 685 LYS cc_start: 0.7305 (mttp) cc_final: 0.6014 (mmmt) REVERT: A 738 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6310 (tt) REVERT: A 874 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: A 1059 ARG cc_start: 0.6849 (tmt-80) cc_final: 0.6456 (ttt-90) REVERT: C 115 GLU cc_start: 0.8166 (pt0) cc_final: 0.7935 (pt0) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 0.1086 time to fit residues: 18.6176 Evaluate side-chains 113 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 810 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.196802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.161408 restraints weight = 10157.660| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.87 r_work: 0.3129 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10860 Z= 0.121 Angle : 0.588 7.769 14758 Z= 0.299 Chirality : 0.044 0.179 1684 Planarity : 0.005 0.077 1835 Dihedral : 7.477 141.022 1432 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 1.74 % Allowed : 18.42 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1301 helix: 0.39 (0.21), residues: 586 sheet: -0.40 (0.39), residues: 191 loop : -1.80 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.010 0.001 TYR C 121 PHE 0.012 0.001 PHE C 304 TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10852) covalent geometry : angle 0.58195 / 0.30 (14737) SS BOND : bond 0.00389 / 0.19 ( 3) SS BOND : angle 1.89278 / 0.95 ( 6) hydrogen bonds : bond 0.04149 / 2.68 ( 467) hydrogen bonds : angle 4.46523 / 3.13 ( 1344) link_ALPHA1-4 : bond 0.00214 / 0.11 ( 1) link_ALPHA1-4 : angle 3.36666 / 1.79 ( 3) link_BETA1-4 : bond 0.00489 / 0.26 ( 1) link_BETA1-4 : angle 2.86058 / 1.49 ( 3) link_NAG-ASN : bond 0.00271 / 0.13 ( 3) link_NAG-ASN : angle 1.87219 / 0.88 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6536 (p) REVERT: A 583 GLN cc_start: 0.6000 (tp-100) cc_final: 0.5779 (pt0) REVERT: A 665 LYS cc_start: 0.8590 (mttt) cc_final: 0.8183 (mmtm) REVERT: A 685 LYS cc_start: 0.7283 (mttp) cc_final: 0.5979 (mmmt) REVERT: A 738 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6163 (tt) REVERT: A 874 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: A 1059 ARG cc_start: 0.6786 (tmt-80) cc_final: 0.6397 (ttt-90) outliers start: 20 outliers final: 17 residues processed: 114 average time/residue: 0.1050 time to fit residues: 17.4130 Evaluate side-chains 114 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.164187 restraints weight = 10216.070| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.92 r_work: 0.3167 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10860 Z= 0.112 Angle : 0.572 7.553 14758 Z= 0.291 Chirality : 0.043 0.177 1684 Planarity : 0.005 0.076 1835 Dihedral : 7.329 138.668 1432 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.00 % Allowed : 18.16 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.79 (0.23), residues: 1301 helix: 0.50 (0.22), residues: 585 sheet: -0.39 (0.40), residues: 190 loop : -1.74 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.013 0.001 TYR C 121 PHE 0.013 0.001 PHE A 368 TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10852) covalent geometry : angle 0.56633 / 0.29 (14737) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 1.66549 / 0.84 ( 6) hydrogen bonds : bond 0.03905 / 2.52 ( 467) hydrogen bonds : angle 4.38749 / 3.08 ( 1344) link_ALPHA1-4 : bond 0.00199 / 0.10 ( 1) link_ALPHA1-4 : angle 3.28966 / 1.75 ( 3) link_BETA1-4 : bond 0.00578 / 0.30 ( 1) link_BETA1-4 : angle 2.83145 / 1.47 ( 3) link_NAG-ASN : bond 0.00242 / 0.12 ( 3) link_NAG-ASN : angle 1.62086 / 0.76 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.43 seconds wall clock time: 47 minutes 13.96 seconds (2833.96 seconds total)