Starting phenix.real_space_refine on Wed Sep 17 20:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7j_9935/09_2025/6k7j_9935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7j_9935/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2025/6k7j_9935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2025/6k7j_9935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2025/6k7j_9935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7j_9935/09_2025/6k7j_9935.map" } 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-2.0-5805/lib/python3.9/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 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: 2.42, per 1000 atoms: 0.23 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: 1.03 Conformation dependent library (CDL) restraints added in 460.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.43 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: 1.50 Time building geometry restraints manager: 1.35 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: 1.130 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01290 (10852) covalent geometry : angle 1.22913 (14737) SS BOND : bond 0.01231 ( 3) SS BOND : angle 5.01963 ( 6) hydrogen bonds : bond 0.12000 ( 467) hydrogen bonds : angle 6.95869 ( 1344) 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) link_NAG-ASN : bond 0.01348 ( 3) link_NAG-ASN : angle 3.46508 ( 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 : 0.412 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: 0.7336 (ttt-90) cc_final: 0.6916 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.1184 time to fit residues: 21.3400 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 : 0.248 ------------------------------------------------------------------------------- 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... 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 = 0.4068 r_free = 0.4068 target = 0.195400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.164443 restraints weight = 10261.071| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.65 r_work: 0.3258 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10860 Z= 0.143 Angle : 0.686 8.870 14758 Z= 0.352 Chirality : 0.045 0.189 1684 Planarity : 0.006 0.084 1835 Dihedral : 10.418 162.663 1622 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 1.48 % Allowed : 11.21 % Favored : 87.32 % 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 aren not related in a simple way. whole: -2.56 (0.21), residues: 1301 helix: -1.04 (0.19), residues: 587 sheet: -1.06 (0.38), residues: 161 loop : -2.58 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 538 TYR 0.017 0.001 TYR C 121 PHE 0.016 0.001 PHE A 368 TRP 0.020 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00311 (10852) covalent geometry : angle 0.67711 (14737) SS BOND : bond 0.02016 ( 3) SS BOND : angle 2.15372 ( 6) hydrogen bonds : bond 0.05058 ( 467) hydrogen bonds : angle 5.27673 ( 1344) link_ALPHA1-4 : bond 0.00115 ( 1) link_ALPHA1-4 : angle 4.45809 ( 3) link_BETA1-4 : bond 0.00408 ( 1) link_BETA1-4 : angle 2.26105 ( 3) link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 2.95149 ( 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 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.8567 (mttt) cc_final: 0.8165 (mmtm) REVERT: A 778 LYS cc_start: 0.8171 (mptt) cc_final: 0.7946 (mmtp) REVERT: A 1059 ARG cc_start: 0.6819 (tmt-80) cc_final: 0.6549 (ttt-90) outliers start: 17 outliers final: 8 residues processed: 127 average time/residue: 0.1054 time to fit residues: 18.9553 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 : 0.441 ------------------------------------------------------------------------------- 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 234 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 52 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.192985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158973 restraints weight = 10347.082| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.20 r_work: 0.3312 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1499 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= 0.190 Angle : 0.687 9.365 14758 Z= 0.351 Chirality : 0.047 0.223 1684 Planarity : 0.006 0.092 1835 Dihedral : 9.936 157.954 1621 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.22), residues: 1301 helix: -0.47 (0.21), residues: 577 sheet: -0.82 (0.38), residues: 173 loop : -2.38 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 215 TYR 0.013 0.002 TYR C 121 PHE 0.023 0.002 PHE C 304 TRP 0.019 0.002 TRP A 876 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00453 (10852) covalent geometry : angle 0.67816 (14737) SS BOND : bond 0.00492 ( 3) SS BOND : angle 2.66425 ( 6) hydrogen bonds : bond 0.05261 ( 467) hydrogen bonds : angle 5.08966 ( 1344) link_ALPHA1-4 : bond 0.00262 ( 1) link_ALPHA1-4 : angle 4.23175 ( 3) link_BETA1-4 : bond 0.00596 ( 1) link_BETA1-4 : angle 3.17200 ( 3) link_NAG-ASN : bond 0.00585 ( 3) link_NAG-ASN : angle 2.57378 ( 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 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.8487 (mttt) cc_final: 0.8199 (mmtm) REVERT: A 772 MET cc_start: 0.7815 (tmm) cc_final: 0.7435 (ttp) REVERT: A 1059 ARG cc_start: 0.6953 (tmt-80) cc_final: 0.6690 (ttt-90) REVERT: C 185 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8639 (mp) outliers start: 29 outliers final: 17 residues processed: 127 average time/residue: 0.1093 time to fit residues: 19.8475 Evaluate side-chains 114 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.192375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158876 restraints weight = 10295.219| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.16 r_work: 0.3232 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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= 0.195 Angle : 0.671 9.258 14758 Z= 0.342 Chirality : 0.047 0.225 1684 Planarity : 0.005 0.082 1835 Dihedral : 9.625 154.446 1621 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 3.04 % Allowed : 15.03 % Favored : 81.93 % 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 aren not related in a simple way. whole: -1.73 (0.22), residues: 1301 helix: -0.31 (0.21), residues: 584 sheet: -0.47 (0.40), residues: 172 loop : -2.31 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 270 TYR 0.013 0.001 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 covalent geometry : bond 0.00469 (10852) covalent geometry : angle 0.66301 (14737) SS BOND : bond 0.00694 ( 3) SS BOND : angle 2.65729 ( 6) hydrogen bonds : bond 0.05137 ( 467) hydrogen bonds : angle 4.97529 ( 1344) link_ALPHA1-4 : bond 0.00140 ( 1) link_ALPHA1-4 : angle 4.27970 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 3.04498 ( 3) link_NAG-ASN : bond 0.00503 ( 3) link_NAG-ASN : angle 2.33466 ( 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 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6514 (OUTLIER) cc_final: 0.6168 (p) REVERT: A 665 LYS cc_start: 0.8699 (mttt) cc_final: 0.8218 (mmtm) REVERT: A 691 MET cc_start: 0.4297 (ttt) cc_final: 0.4024 (ttp) REVERT: A 1059 ARG cc_start: 0.6849 (tmt-80) cc_final: 0.6318 (ttt-90) REVERT: C 185 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8771 (mp) outliers start: 35 outliers final: 20 residues processed: 131 average time/residue: 0.1087 time to fit residues: 20.5539 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 : 0.501 ------------------------------------------------------------------------------- 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 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 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 248 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.196988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.165232 restraints weight = 10270.629| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.74 r_work: 0.3209 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2063 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= 0.115 Angle : 0.588 7.887 14758 Z= 0.302 Chirality : 0.044 0.184 1684 Planarity : 0.005 0.078 1835 Dihedral : 9.157 149.915 1621 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 2.35 % Allowed : 15.73 % Favored : 81.93 % 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 aren not related in a simple way. whole: -1.21 (0.23), residues: 1301 helix: 0.22 (0.21), residues: 579 sheet: -0.41 (0.39), residues: 181 loop : -2.08 (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 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00250 (10852) covalent geometry : angle 0.58187 (14737) SS BOND : bond 0.00319 ( 3) SS BOND : angle 1.95702 ( 6) hydrogen bonds : bond 0.04190 ( 467) hydrogen bonds : angle 4.61952 ( 1344) link_ALPHA1-4 : bond 0.00023 ( 1) link_ALPHA1-4 : angle 3.79824 ( 3) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 2.98132 ( 3) link_NAG-ASN : bond 0.00250 ( 3) link_NAG-ASN : angle 1.49745 ( 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 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6803 (OUTLIER) cc_final: 0.6477 (p) REVERT: A 665 LYS cc_start: 0.8543 (mttt) cc_final: 0.8199 (mmtm) REVERT: A 738 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6408 (tt) REVERT: A 1058 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7038 (ttmt) REVERT: A 1059 ARG cc_start: 0.6849 (tmt-80) cc_final: 0.6505 (ttt-90) outliers start: 27 outliers final: 17 residues processed: 127 average time/residue: 0.1125 time to fit residues: 20.4281 Evaluate side-chains 110 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 87 optimal weight: 0.0570 chunk 56 optimal weight: 10.0000 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.194373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157576 restraints weight = 10325.719| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.29 r_work: 0.3227 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10860 Z= 0.156 Angle : 0.622 8.642 14758 Z= 0.316 Chirality : 0.045 0.192 1684 Planarity : 0.005 0.079 1835 Dihedral : 9.155 149.306 1621 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 2.87 % Allowed : 16.16 % Favored : 80.97 % 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 aren not related in a simple way. whole: -1.20 (0.23), residues: 1301 helix: 0.16 (0.21), residues: 585 sheet: -0.39 (0.39), residues: 181 loop : -2.00 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.012 0.001 TYR C 121 PHE 0.020 0.001 PHE C 304 TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00371 (10852) covalent geometry : angle 0.61537 (14737) SS BOND : bond 0.00500 ( 3) SS BOND : angle 2.28206 ( 6) hydrogen bonds : bond 0.04588 ( 467) hydrogen bonds : angle 4.67392 ( 1344) link_ALPHA1-4 : bond 0.00077 ( 1) link_ALPHA1-4 : angle 3.77855 ( 3) link_BETA1-4 : bond 0.00324 ( 1) link_BETA1-4 : angle 3.10585 ( 3) link_NAG-ASN : bond 0.00422 ( 3) link_NAG-ASN : angle 1.95438 ( 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 124 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.6139 (p) REVERT: A 665 LYS cc_start: 0.8650 (mttt) cc_final: 0.8194 (mmtm) REVERT: A 738 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5820 (tt) REVERT: A 1059 ARG cc_start: 0.6787 (tmt-80) cc_final: 0.6323 (ttt-90) outliers start: 33 outliers final: 20 residues processed: 121 average time/residue: 0.1163 time to fit residues: 20.1145 Evaluate side-chains 113 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 764 LEU 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 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 128 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.196678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.161501 restraints weight = 10238.963| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.78 r_work: 0.3136 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2284 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= 0.118 Angle : 0.585 7.675 14758 Z= 0.299 Chirality : 0.044 0.181 1684 Planarity : 0.005 0.077 1835 Dihedral : 8.925 146.974 1621 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.26 % Allowed : 17.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.23), residues: 1301 helix: 0.30 (0.21), residues: 588 sheet: -0.31 (0.40), residues: 181 loop : -1.94 (0.26), residues: 532 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 0.015 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 covalent geometry : bond 0.00262 (10852) covalent geometry : angle 0.57869 (14737) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.85340 ( 6) hydrogen bonds : bond 0.04119 ( 467) hydrogen bonds : angle 4.51443 ( 1344) link_ALPHA1-4 : bond 0.00102 ( 1) link_ALPHA1-4 : angle 3.65883 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 2.98559 ( 3) link_NAG-ASN : bond 0.00249 ( 3) link_NAG-ASN : angle 1.53698 ( 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 122 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6434 (p) REVERT: A 645 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7051 (mp0) REVERT: A 665 LYS cc_start: 0.8595 (mttt) cc_final: 0.8197 (mmtm) REVERT: A 685 LYS cc_start: 0.7158 (mttp) cc_final: 0.5853 (mmmt) REVERT: A 738 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6203 (tt) REVERT: A 865 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8138 (p0) REVERT: A 1059 ARG cc_start: 0.6774 (tmt-80) cc_final: 0.6386 (ttt-90) REVERT: C 115 GLU cc_start: 0.8214 (pt0) cc_final: 0.7977 (pt0) outliers start: 26 outliers final: 19 residues processed: 121 average time/residue: 0.1122 time to fit residues: 19.4282 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 : 0.382 ------------------------------------------------------------------------------- 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 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 865 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 0.0030 chunk 85 optimal weight: 5.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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 131 HIS ** 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 = 0.4061 r_free = 0.4061 target = 0.194679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.161268 restraints weight = 10223.613| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.20 r_work: 0.3234 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10860 Z= 0.165 Angle : 0.617 8.724 14758 Z= 0.314 Chirality : 0.045 0.192 1684 Planarity : 0.005 0.079 1835 Dihedral : 9.003 147.249 1621 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 2.43 % Allowed : 17.29 % Favored : 80.28 % 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 aren not related in a simple way. whole: -1.10 (0.23), residues: 1301 helix: 0.26 (0.21), residues: 579 sheet: -0.47 (0.39), residues: 191 loop : -1.93 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.013 0.001 TYR C 297 PHE 0.019 0.001 PHE C 304 TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00396 (10852) covalent geometry : angle 0.60989 (14737) SS BOND : bond 0.00522 ( 3) SS BOND : angle 2.23197 ( 6) hydrogen bonds : bond 0.04574 ( 467) hydrogen bonds : angle 4.60093 ( 1344) link_ALPHA1-4 : bond 0.00015 ( 1) link_ALPHA1-4 : angle 3.68927 ( 3) link_BETA1-4 : bond 0.00297 ( 1) link_BETA1-4 : angle 3.12501 ( 3) link_NAG-ASN : bond 0.00414 ( 3) link_NAG-ASN : angle 1.89876 ( 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 125 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.6286 (p) REVERT: A 665 LYS cc_start: 0.8650 (mttt) cc_final: 0.8199 (mmtm) REVERT: A 685 LYS cc_start: 0.6953 (mttp) cc_final: 0.5668 (mmmt) REVERT: A 738 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5843 (tt) REVERT: A 1059 ARG cc_start: 0.6824 (tmt-80) cc_final: 0.6327 (ttt-90) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.1142 time to fit residues: 20.1334 Evaluate side-chains 119 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 1058 LYS Chi-restraints excluded: chain C residue 94 CYS 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: 7.9990 chunk 56 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.195334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.161640 restraints weight = 10276.867| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.11 r_work: 0.3273 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2330 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= 0.144 Angle : 0.602 8.253 14758 Z= 0.306 Chirality : 0.045 0.180 1684 Planarity : 0.005 0.076 1835 Dihedral : 8.963 146.299 1621 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 2.35 % Allowed : 17.46 % 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 aren not related in a simple way. whole: -1.04 (0.23), residues: 1301 helix: 0.29 (0.21), residues: 581 sheet: -0.44 (0.39), residues: 191 loop : -1.87 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.012 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 covalent geometry : bond 0.00339 (10852) covalent geometry : angle 0.59506 (14737) SS BOND : bond 0.00471 ( 3) SS BOND : angle 2.11171 ( 6) hydrogen bonds : bond 0.04396 ( 467) hydrogen bonds : angle 4.54006 ( 1344) link_ALPHA1-4 : bond 0.00018 ( 1) link_ALPHA1-4 : angle 3.73960 ( 3) link_BETA1-4 : bond 0.00357 ( 1) link_BETA1-4 : angle 3.06506 ( 3) link_NAG-ASN : bond 0.00338 ( 3) link_NAG-ASN : angle 1.77979 ( 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 124 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6515 (OUTLIER) cc_final: 0.6191 (p) REVERT: A 665 LYS cc_start: 0.8654 (mttt) cc_final: 0.8193 (mmtm) REVERT: A 685 LYS cc_start: 0.6845 (mttp) cc_final: 0.5553 (mmmt) REVERT: A 1059 ARG cc_start: 0.6747 (tmt-80) cc_final: 0.6269 (ttt-90) REVERT: C 115 GLU cc_start: 0.8354 (pt0) cc_final: 0.8145 (pt0) outliers start: 27 outliers final: 24 residues processed: 121 average time/residue: 0.1158 time to fit residues: 19.9968 Evaluate side-chains 121 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 742 VAL Chi-restraints excluded: chain A residue 764 LEU 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 1058 LYS Chi-restraints excluded: chain C residue 83 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.197310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.162660 restraints weight = 10161.846| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.80 r_work: 0.3187 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2490 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= 0.117 Angle : 0.586 9.934 14758 Z= 0.298 Chirality : 0.043 0.177 1684 Planarity : 0.005 0.076 1835 Dihedral : 8.831 145.375 1621 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 2.09 % Allowed : 17.72 % 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 aren not related in a simple way. whole: -0.89 (0.23), residues: 1301 helix: 0.40 (0.21), residues: 583 sheet: -0.39 (0.39), residues: 191 loop : -1.77 (0.26), residues: 527 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 covalent geometry : bond 0.00262 (10852) covalent geometry : angle 0.58042 (14737) SS BOND : bond 0.00348 ( 3) SS BOND : angle 1.80313 ( 6) hydrogen bonds : bond 0.04066 ( 467) hydrogen bonds : angle 4.44019 ( 1344) link_ALPHA1-4 : bond 0.00122 ( 1) link_ALPHA1-4 : angle 3.55543 ( 3) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 2.95134 ( 3) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.62278 ( 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 122 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6505 (p) REVERT: A 645 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6906 (mp0) REVERT: A 665 LYS cc_start: 0.8558 (mttt) cc_final: 0.8183 (mmtm) REVERT: A 685 LYS cc_start: 0.7302 (mttp) cc_final: 0.6012 (mmmt) REVERT: A 1059 ARG cc_start: 0.6799 (tmt-80) cc_final: 0.6427 (ttt-90) outliers start: 24 outliers final: 20 residues processed: 120 average time/residue: 0.1108 time to fit residues: 19.2919 Evaluate side-chains 116 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 331 ASN A 810 GLN C 131 HIS C 144 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.196974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.162811 restraints weight = 10225.951| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.86 r_work: 0.3171 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2546 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= 0.125 Angle : 0.592 8.957 14758 Z= 0.300 Chirality : 0.044 0.175 1684 Planarity : 0.005 0.076 1835 Dihedral : 8.812 146.205 1621 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 2.43 % Allowed : 17.72 % 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 aren not related in a simple way. whole: -0.84 (0.23), residues: 1301 helix: 0.43 (0.21), residues: 583 sheet: -0.38 (0.39), residues: 190 loop : -1.73 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.012 0.001 TYR C 121 PHE 0.013 0.001 PHE C 304 TRP 0.016 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00285 (10852) covalent geometry : angle 0.58651 (14737) SS BOND : bond 0.00389 ( 3) SS BOND : angle 1.88849 ( 6) hydrogen bonds : bond 0.04126 ( 467) hydrogen bonds : angle 4.41812 ( 1344) link_ALPHA1-4 : bond 0.00010 ( 1) link_ALPHA1-4 : angle 3.52361 ( 3) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 3.00071 ( 3) link_NAG-ASN : bond 0.00315 ( 3) link_NAG-ASN : angle 1.68964 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.41 seconds wall clock time: 48 minutes 19.19 seconds (2899.19 seconds total)