Starting phenix.real_space_refine on Tue Jul 29 05:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_9935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_9935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_9935.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_9935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7j_9935/07_2025/6k7j_9935.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.58, per 1000 atoms: 0.62 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.12 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: 3.90 Time building geometry restraints manager: 2.89 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: 6367 32.36 - 64.72: 203 64.72 - 97.08: 14 97.08 - 129.43: 0 129.43 - 161.79: 2 Dihedral angle restraints: 6586 sinusoidal: 2760 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 6583 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 15.542 161.793 4109 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.004 TRP A 927 HIS 0.009 0.002 HIS A 323 PHE 0.045 0.004 PHE C 304 TYR 0.025 0.003 TYR C 122 ARG 0.017 0.001 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.01348 ( 3) link_NAG-ASN : angle 3.46508 ( 9) link_ALPHA1-4 : bond 0.00166 ( 1) link_ALPHA1-4 : angle 5.91237 ( 3) link_BETA1-4 : bond 0.00281 ( 1) link_BETA1-4 : angle 3.46805 ( 3) hydrogen bonds : bond 0.12000 ( 467) hydrogen bonds : angle 6.95869 ( 1344) SS BOND : bond 0.01231 ( 3) SS BOND : angle 5.01963 ( 6) covalent geometry : bond 0.01290 (10852) covalent geometry : angle 1.22913 (14737) *********************** 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 : 1.171 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: 0.7983 (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: 0.7336 (ttt-90) cc_final: 0.6916 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2624 time to fit residues: 47.3880 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 : 1.123 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.6980 chunk 98 optimal weight: 0.0470 chunk 54 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.196080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.166487 restraints weight = 10152.312| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.55 r_work: 0.3292 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10860 Z= 0.140 Angle : 0.685 8.841 14758 Z= 0.351 Chirality : 0.045 0.197 1684 Planarity : 0.006 0.084 1835 Dihedral : 10.394 162.572 1622 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 1.48 % Allowed : 11.29 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.21), residues: 1301 helix: -1.03 (0.20), residues: 587 sheet: -1.06 (0.38), residues: 161 loop : -2.58 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.016 0.001 PHE A 368 TYR 0.017 0.001 TYR C 121 ARG 0.006 0.000 ARG A 538 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 2.96785 ( 9) link_ALPHA1-4 : bond 0.00282 ( 1) link_ALPHA1-4 : angle 4.51856 ( 3) link_BETA1-4 : bond 0.00427 ( 1) link_BETA1-4 : angle 2.25552 ( 3) hydrogen bonds : bond 0.04984 ( 467) hydrogen bonds : angle 5.25443 ( 1344) SS BOND : bond 0.01875 ( 3) SS BOND : angle 2.20228 ( 6) covalent geometry : bond 0.00300 (10852) covalent geometry : angle 0.67579 (14737) *********************** 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 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.8531 (mttt) cc_final: 0.8073 (mmtt) REVERT: A 730 ASP cc_start: 0.7558 (p0) cc_final: 0.7348 (p0) REVERT: A 778 LYS cc_start: 0.8178 (mptt) cc_final: 0.7970 (mmtp) REVERT: A 904 ASN cc_start: 0.8364 (m110) cc_final: 0.8059 (m110) REVERT: A 1059 ARG cc_start: 0.6819 (tmt-80) cc_final: 0.6593 (ttt-90) outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 0.2764 time to fit residues: 51.4498 Evaluate side-chains 108 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 124 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.193272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.158027 restraints weight = 10344.459| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.15 r_work: 0.3293 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10860 Z= 0.176 Angle : 0.676 9.053 14758 Z= 0.345 Chirality : 0.046 0.216 1684 Planarity : 0.006 0.090 1835 Dihedral : 9.903 158.167 1621 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.46 % Favored : 93.39 % Rotamer: Outliers : 2.52 % Allowed : 13.73 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1301 helix: -0.43 (0.21), residues: 577 sheet: -0.82 (0.38), residues: 172 loop : -2.33 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.022 0.002 PHE C 304 TYR 0.013 0.001 TYR C 121 ARG 0.003 0.000 ARG C 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 3) link_NAG-ASN : angle 2.42647 ( 9) link_ALPHA1-4 : bond 0.00065 ( 1) link_ALPHA1-4 : angle 4.07586 ( 3) link_BETA1-4 : bond 0.00368 ( 1) link_BETA1-4 : angle 3.17094 ( 3) hydrogen bonds : bond 0.05134 ( 467) hydrogen bonds : angle 5.04929 ( 1344) SS BOND : bond 0.00417 ( 3) SS BOND : angle 2.63206 ( 6) covalent geometry : bond 0.00416 (10852) covalent geometry : angle 0.66774 (14737) *********************** 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: 29 poor density : 103 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 645 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: A 665 LYS cc_start: 0.8685 (mttt) cc_final: 0.8214 (mmtm) REVERT: A 691 MET cc_start: 0.4040 (ttt) cc_final: 0.3581 (ttt) REVERT: A 904 ASN cc_start: 0.8460 (m110) cc_final: 0.7955 (m110) REVERT: A 1059 ARG cc_start: 0.6760 (tmt-80) cc_final: 0.6289 (ttt-90) REVERT: C 185 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8708 (mp) outliers start: 29 outliers final: 16 residues processed: 128 average time/residue: 0.2449 time to fit residues: 44.9923 Evaluate side-chains 111 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 764 LEU Chi-restraints excluded: chain A residue 1058 LYS 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 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 4 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** 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 = 0.4033 r_free = 0.4033 target = 0.191676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158867 restraints weight = 10254.592| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.15 r_work: 0.3241 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10860 Z= 0.222 Angle : 0.699 9.655 14758 Z= 0.356 Chirality : 0.048 0.235 1684 Planarity : 0.006 0.083 1835 Dihedral : 9.726 155.040 1621 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.46 % Favored : 93.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1301 helix: -0.41 (0.20), residues: 585 sheet: -0.54 (0.40), residues: 172 loop : -2.28 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 927 HIS 0.005 0.001 HIS A 124 PHE 0.023 0.002 PHE C 304 TYR 0.015 0.002 TYR C 297 ARG 0.004 0.000 ARG C 215 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 3) link_NAG-ASN : angle 2.55411 ( 9) link_ALPHA1-4 : bond 0.00150 ( 1) link_ALPHA1-4 : angle 4.39971 ( 3) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 3.04188 ( 3) hydrogen bonds : bond 0.05407 ( 467) hydrogen bonds : angle 5.03889 ( 1344) SS BOND : bond 0.00442 ( 3) SS BOND : angle 2.98201 ( 6) covalent geometry : bond 0.00540 (10852) covalent geometry : angle 0.68958 (14737) *********************** 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 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.6520 (p) REVERT: A 665 LYS cc_start: 0.8518 (mttt) cc_final: 0.8191 (mmtm) REVERT: A 1059 ARG cc_start: 0.7027 (tmt-80) cc_final: 0.6721 (ttt-90) REVERT: C 185 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8696 (mp) outliers start: 35 outliers final: 20 residues processed: 129 average time/residue: 0.2379 time to fit residues: 44.7955 Evaluate side-chains 116 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 864 VAL 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 88 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4080 r_free = 0.4080 target = 0.196390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.163816 restraints weight = 10238.062| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.72 r_work: 0.3201 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1990 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= 0.119 Angle : 0.596 7.922 14758 Z= 0.306 Chirality : 0.044 0.179 1684 Planarity : 0.005 0.078 1835 Dihedral : 9.268 151.159 1621 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 2.61 % Allowed : 15.55 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1301 helix: 0.10 (0.21), residues: 583 sheet: -0.31 (0.40), residues: 171 loop : -2.10 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.012 0.001 TYR C 121 ARG 0.002 0.000 ARG A 901 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 3) link_NAG-ASN : angle 1.60086 ( 9) link_ALPHA1-4 : bond 0.00013 ( 1) link_ALPHA1-4 : angle 3.92855 ( 3) link_BETA1-4 : bond 0.00486 ( 1) link_BETA1-4 : angle 2.98892 ( 3) hydrogen bonds : bond 0.04311 ( 467) hydrogen bonds : angle 4.66441 ( 1344) SS BOND : bond 0.00284 ( 3) SS BOND : angle 2.05736 ( 6) covalent geometry : bond 0.00263 (10852) covalent geometry : angle 0.58943 (14737) *********************** 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 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6467 (p) REVERT: A 589 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7363 (mt) REVERT: A 665 LYS cc_start: 0.8566 (mttt) cc_final: 0.8208 (mmtm) REVERT: A 738 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6403 (tt) REVERT: A 1059 ARG cc_start: 0.6920 (tmt-80) cc_final: 0.6551 (ttt-90) outliers start: 30 outliers final: 19 residues processed: 128 average time/residue: 0.2509 time to fit residues: 46.3927 Evaluate side-chains 114 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU 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 129 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 122 optimal weight: 0.2980 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.197959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.165592 restraints weight = 10206.531| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.78 r_work: 0.3233 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10860 Z= 0.112 Angle : 0.576 7.437 14758 Z= 0.295 Chirality : 0.043 0.179 1684 Planarity : 0.005 0.077 1835 Dihedral : 8.926 146.618 1621 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.47 % Rotamer: Outliers : 2.61 % Allowed : 16.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1301 helix: 0.40 (0.22), residues: 580 sheet: -0.33 (0.39), residues: 181 loop : -1.96 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 473 PHE 0.015 0.001 PHE A 368 TYR 0.012 0.001 TYR C 121 ARG 0.005 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 3) link_NAG-ASN : angle 1.57701 ( 9) link_ALPHA1-4 : bond 0.00236 ( 1) link_ALPHA1-4 : angle 3.46943 ( 3) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 2.88843 ( 3) hydrogen bonds : bond 0.04023 ( 467) hydrogen bonds : angle 4.50709 ( 1344) SS BOND : bond 0.00325 ( 3) SS BOND : angle 1.84500 ( 6) covalent geometry : bond 0.00247 (10852) covalent geometry : angle 0.56990 (14737) *********************** 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 127 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7019 (mmt-90) cc_final: 0.6787 (mmt180) REVERT: A 270 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6564 (p) REVERT: A 589 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 665 LYS cc_start: 0.8555 (mttt) cc_final: 0.8189 (mmtm) REVERT: A 685 LYS cc_start: 0.7182 (mttp) cc_final: 0.5950 (mmmt) REVERT: A 1059 ARG cc_start: 0.6784 (tmt-80) cc_final: 0.6463 (ttt-90) REVERT: C 115 GLU cc_start: 0.8197 (pt0) cc_final: 0.7978 (pt0) outliers start: 30 outliers final: 17 residues processed: 126 average time/residue: 0.2289 time to fit residues: 41.5823 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 : 1.063 ------------------------------------------------------------------------------- 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 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 589 LEU 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 849 TYR 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 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 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 = 0.4073 r_free = 0.4073 target = 0.195772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166001 restraints weight = 10417.586| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.70 r_work: 0.3306 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2262 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= 0.145 Angle : 0.601 8.249 14758 Z= 0.306 Chirality : 0.045 0.178 1684 Planarity : 0.005 0.080 1835 Dihedral : 8.895 142.995 1621 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 2.69 % Allowed : 16.68 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1301 helix: 0.34 (0.21), residues: 579 sheet: -0.31 (0.40), residues: 181 loop : -1.92 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 PHE 0.018 0.001 PHE C 304 TYR 0.013 0.001 TYR C 121 ARG 0.004 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 3) link_NAG-ASN : angle 1.76016 ( 9) link_ALPHA1-4 : bond 0.00106 ( 1) link_ALPHA1-4 : angle 3.53097 ( 3) link_BETA1-4 : bond 0.00276 ( 1) link_BETA1-4 : angle 3.12419 ( 3) hydrogen bonds : bond 0.04382 ( 467) hydrogen bonds : angle 4.53028 ( 1344) SS BOND : bond 0.00484 ( 3) SS BOND : angle 2.11436 ( 6) covalent geometry : bond 0.00339 (10852) covalent geometry : angle 0.59446 (14737) *********************** 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: 31 poor density : 97 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6786 (t0) REVERT: A 197 ARG cc_start: 0.7031 (mmt-90) cc_final: 0.6794 (mmt180) REVERT: A 270 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6605 (p) REVERT: A 589 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7718 (mt) REVERT: A 665 LYS cc_start: 0.8486 (mttt) cc_final: 0.8208 (mmtm) REVERT: A 685 LYS cc_start: 0.7426 (mttp) cc_final: 0.6269 (mmmt) REVERT: A 738 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6614 (tt) REVERT: A 1059 ARG cc_start: 0.6907 (tmt-80) cc_final: 0.6575 (ttt-90) outliers start: 31 outliers final: 21 residues processed: 127 average time/residue: 0.2379 time to fit residues: 43.6172 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 589 LEU 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 849 TYR Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 151 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 71 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 16 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** 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 = 0.4093 r_free = 0.4093 target = 0.197708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163827 restraints weight = 10128.899| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.77 r_work: 0.3173 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2443 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= 0.119 Angle : 0.575 8.567 14758 Z= 0.293 Chirality : 0.043 0.177 1684 Planarity : 0.005 0.076 1835 Dihedral : 8.761 141.085 1621 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 2.09 % Allowed : 17.90 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1301 helix: 0.44 (0.22), residues: 581 sheet: -0.44 (0.39), residues: 191 loop : -1.83 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.002 0.001 HIS A 456 PHE 0.012 0.001 PHE A 368 TYR 0.011 0.001 TYR C 121 ARG 0.004 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 3) link_NAG-ASN : angle 1.53063 ( 9) link_ALPHA1-4 : bond 0.00092 ( 1) link_ALPHA1-4 : angle 3.54292 ( 3) link_BETA1-4 : bond 0.00384 ( 1) link_BETA1-4 : angle 2.98989 ( 3) hydrogen bonds : bond 0.04041 ( 467) hydrogen bonds : angle 4.42160 ( 1344) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.81190 ( 6) covalent geometry : bond 0.00268 (10852) covalent geometry : angle 0.56891 (14737) *********************** 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 121 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6680 (t0) REVERT: A 197 ARG cc_start: 0.7025 (mmt-90) cc_final: 0.6812 (mmt180) REVERT: A 270 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6540 (p) REVERT: A 665 LYS cc_start: 0.8558 (mttt) cc_final: 0.8122 (mmtm) REVERT: A 685 LYS cc_start: 0.7227 (mttp) cc_final: 0.5979 (mmmt) REVERT: A 738 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6200 (tt) REVERT: A 1058 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7049 (ttmt) REVERT: A 1059 ARG cc_start: 0.6779 (tmt-80) cc_final: 0.6416 (ttt-90) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.2344 time to fit residues: 39.9442 Evaluate side-chains 118 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 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 849 TYR Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 151 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 96 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.197450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162390 restraints weight = 10268.075| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.85 r_work: 0.3174 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2517 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= 0.117 Angle : 0.573 8.207 14758 Z= 0.292 Chirality : 0.043 0.175 1684 Planarity : 0.005 0.077 1835 Dihedral : 8.716 140.323 1621 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.26 % Allowed : 17.72 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1301 helix: 0.47 (0.22), residues: 582 sheet: -0.36 (0.39), residues: 191 loop : -1.76 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 53 PHE 0.012 0.001 PHE C 304 TYR 0.012 0.001 TYR C 121 ARG 0.004 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 1.63096 ( 9) link_ALPHA1-4 : bond 0.00140 ( 1) link_ALPHA1-4 : angle 3.44065 ( 3) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 3.00326 ( 3) hydrogen bonds : bond 0.04029 ( 467) hydrogen bonds : angle 4.37169 ( 1344) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.79121 ( 6) covalent geometry : bond 0.00264 (10852) covalent geometry : angle 0.56697 (14737) *********************** 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 125 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6634 (t0) REVERT: A 197 ARG cc_start: 0.7054 (mmt-90) cc_final: 0.6843 (mmt180) REVERT: A 270 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6511 (p) REVERT: A 665 LYS cc_start: 0.8582 (mttt) cc_final: 0.8101 (mmtm) REVERT: A 685 LYS cc_start: 0.7305 (mttp) cc_final: 0.5978 (mmmt) REVERT: A 738 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6126 (tt) REVERT: A 1059 ARG cc_start: 0.6744 (tmt-80) cc_final: 0.6382 (ttt-90) outliers start: 26 outliers final: 19 residues processed: 123 average time/residue: 0.2383 time to fit residues: 42.0356 Evaluate side-chains 117 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 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 864 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 810 GLN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.193382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.155075 restraints weight = 10263.406| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.31 r_work: 0.3231 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10860 Z= 0.196 Angle : 0.651 9.524 14758 Z= 0.329 Chirality : 0.047 0.210 1684 Planarity : 0.005 0.078 1835 Dihedral : 8.999 142.490 1621 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 2.26 % Allowed : 18.07 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1301 helix: 0.20 (0.21), residues: 581 sheet: -0.48 (0.39), residues: 190 loop : -1.84 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 876 HIS 0.005 0.001 HIS A 124 PHE 0.024 0.002 PHE C 304 TYR 0.015 0.002 TYR C 122 ARG 0.003 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 3) link_NAG-ASN : angle 2.13798 ( 9) link_ALPHA1-4 : bond 0.00023 ( 1) link_ALPHA1-4 : angle 3.83124 ( 3) link_BETA1-4 : bond 0.00372 ( 1) link_BETA1-4 : angle 3.20690 ( 3) hydrogen bonds : bond 0.04942 ( 467) hydrogen bonds : angle 4.60852 ( 1344) SS BOND : bond 0.00637 ( 3) SS BOND : angle 2.43991 ( 6) covalent geometry : bond 0.00474 (10852) covalent geometry : angle 0.64395 (14737) ********************** 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 124 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6465 (t0) REVERT: A 222 GLU cc_start: 0.3278 (OUTLIER) cc_final: 0.3058 (tt0) REVERT: A 270 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6147 (p) REVERT: A 372 TYR cc_start: 0.8307 (m-80) cc_final: 0.8095 (m-10) REVERT: A 665 LYS cc_start: 0.8673 (mttt) cc_final: 0.8187 (mmtm) REVERT: A 685 LYS cc_start: 0.6956 (mttp) cc_final: 0.5622 (mmmt) REVERT: A 1059 ARG cc_start: 0.6795 (tmt-80) cc_final: 0.6303 (ttt-90) REVERT: C 115 GLU cc_start: 0.8408 (pt0) cc_final: 0.8187 (pt0) REVERT: C 347 ASN cc_start: 0.7284 (t0) cc_final: 0.7064 (t0) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 0.2507 time to fit residues: 43.3208 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP 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 261 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 426 ILE 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 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 864 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4065 r_free = 0.4065 target = 0.194594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160091 restraints weight = 10148.616| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10860 Z= 0.160 Angle : 0.623 9.574 14758 Z= 0.314 Chirality : 0.045 0.191 1684 Planarity : 0.005 0.077 1835 Dihedral : 8.937 141.091 1621 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 2.17 % Allowed : 18.25 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1301 helix: 0.28 (0.21), residues: 581 sheet: -0.50 (0.39), residues: 190 loop : -1.77 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.019 0.001 PHE C 304 TYR 0.012 0.001 TYR C 297 ARG 0.003 0.000 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 3) link_NAG-ASN : angle 1.93703 ( 9) link_ALPHA1-4 : bond 0.00042 ( 1) link_ALPHA1-4 : angle 3.85374 ( 3) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 3.11276 ( 3) hydrogen bonds : bond 0.04569 ( 467) hydrogen bonds : angle 4.51362 ( 1344) SS BOND : bond 0.00531 ( 3) SS BOND : angle 2.19341 ( 6) covalent geometry : bond 0.00382 (10852) covalent geometry : angle 0.61605 (14737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.14 seconds wall clock time: 97 minutes 0.96 seconds (5820.96 seconds total)