Starting phenix.real_space_refine on Fri Sep 11 18:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7m_9941/09_2026/6k7m_9941.map" } resolution = 2.95 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= 0.004 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6871 2.51 5 N 1745 2.21 5 O 1912 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7827 Classifications: {'peptide': 983} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 298} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' MG': 1, 'ALF': 1, 'D39': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.12, per 1000 atoms: 0.20 Number of scatterers: 10591 At special positions: 0 Unit cell: (73.87, 106.24, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 56 16.00 P 1 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1912 8.00 N 1745 7.00 C 6871 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=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 512.5 milliseconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 47.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.717A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 208 through 214 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 324 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.681A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 357 through 376 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.847A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.651A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.526A pdb=" N ILE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 3.577A pdb=" N THR A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 617 removed outlier: 5.511A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 741 through 752 removed outlier: 4.304A pdb=" N TYR A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 778 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 790 through 796 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.354A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 866 removed outlier: 3.833A pdb=" N ASN A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.890A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.548A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 984 removed outlier: 3.785A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1012 removed outlier: 3.791A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 3.925A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.368A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.783A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.690A pdb=" N CYS C 157 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 158 " --> pdb=" O LYS C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.517A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.958A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 349 removed outlier: 3.551A pdb=" N LYS C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.549A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 198 removed outlier: 3.773A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.081A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP A 730 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 696 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 425 removed outlier: 5.289A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 638 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 596 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG A 546 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 528 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.946A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.344A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1392 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: 1.84 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1849 1.32 - 1.45: 2835 1.45 - 1.57: 6062 1.57 - 1.70: 1 1.70 - 1.82: 89 Bond restraints: 10836 Sorted by residual: bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.786 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.787 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.786 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O3 D39 A1304 " pdb=" P D39 A1304 " ideal model delta sigma weight residual 1.639 1.540 0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 10831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.70: 14692 13.70 - 27.40: 6 27.40 - 41.10: 0 41.10 - 54.80: 0 54.80 - 68.51: 2 Bond angle restraints: 14700 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 177.19 -68.51 3.00e+00 1.11e-01 5.21e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 178.11 -68.48 3.00e+00 1.11e-01 5.21e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 89.21 20.38 3.00e+00 1.11e-01 4.61e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.91 19.78 3.00e+00 1.11e-01 4.35e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.02 89.36 19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 14695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.87: 6194 29.87 - 59.73: 204 59.73 - 89.60: 17 89.60 - 119.47: 1 119.47 - 149.33: 3 Dihedral angle restraints: 6419 sinusoidal: 2605 harmonic: 3814 Sorted by residual: dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N GLU C 164 " pdb=" CA GLU C 164 " ideal model delta harmonic sigma weight residual -180.00 -139.55 -40.45 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 158.33 -65.33 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA PRO A 477 " pdb=" C PRO A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta harmonic sigma weight residual 180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1339 0.080 - 0.159: 301 0.159 - 0.239: 32 0.239 - 0.318: 6 0.318 - 0.398: 1 Chirality restraints: 1679 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 3.96e+00 chirality pdb=" C1 MAN B 3 " pdb=" O4 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.19e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1676 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.209 2.00e-02 2.50e+03 1.74e-01 3.77e+02 pdb=" C7 NAG C 402 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.286 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.137 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.193 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.131 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG C 401 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.170 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.023 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 83 2.58 - 3.16: 8126 3.16 - 3.74: 16563 3.74 - 4.32: 24339 4.32 - 4.90: 40170 Nonbonded interactions: 89281 Sorted by model distance: nonbonded pdb=" F2 ALF A1301 " pdb="MG MG A1303 " model vdw 2.002 2.120 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1303 " model vdw 2.045 2.170 nonbonded pdb=" OD1 ASN A 331 " pdb=" OH TYR C 160 " model vdw 2.229 3.040 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP A 409 " pdb=" F2 ALF A1301 " model vdw 2.284 2.990 ... (remaining 89276 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: 1.760 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: 0.040 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.011 0.105 10844 Z= 0.479 Angle : 1.426 68.506 14721 Z= 0.669 Chirality : 0.066 0.398 1679 Planarity : 0.010 0.174 1831 Dihedral : 15.445 149.334 3950 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 0.61 % Allowed : 7.41 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.19), residues: 1297 helix: -2.41 (0.16), residues: 573 sheet: -0.57 (0.39), residues: 151 loop : -2.49 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.030 0.004 TYR A 849 PHE 0.032 0.004 PHE C 214 TRP 0.017 0.003 TRP A 990 HIS 0.007 0.002 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.01143 / 0.48 (10836) covalent geometry : angle 1.42103 / 0.67 (14700) SS BOND : bond 0.00328 / 0.16 ( 3) SS BOND : angle 1.20718 / 0.65 ( 6) hydrogen bonds : bond 0.13687 / 8.62 ( 486) hydrogen bonds : angle 7.31126 / 5.16 ( 1392) link_ALPHA1-4 : bond 0.00852 / 0.45 ( 1) link_ALPHA1-4 : angle 5.78413 / 3.06 ( 3) link_BETA1-4 : bond 0.00223 / 0.12 ( 1) link_BETA1-4 : angle 2.90925 / 1.52 ( 3) link_NAG-ASN : bond 0.01030 / 0.50 ( 3) link_NAG-ASN : angle 3.41353 / 1.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.397 Fit side-chains REVERT: A 58 LYS cc_start: 0.8082 (mttt) cc_final: 0.7588 (mtmm) REVERT: A 74 ARG cc_start: 0.7297 (tmm160) cc_final: 0.7081 (ttm-80) REVERT: A 485 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 742 VAL cc_start: 0.6947 (OUTLIER) cc_final: 0.6698 (p) REVERT: A 749 LEU cc_start: 0.8106 (tp) cc_final: 0.7868 (tp) REVERT: A 754 LYS cc_start: 0.7180 (mttt) cc_final: 0.6210 (mmtm) REVERT: A 776 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 1023 MET cc_start: 0.7541 (ttm) cc_final: 0.7313 (ttm) REVERT: C 337 PHE cc_start: 0.7248 (t80) cc_final: 0.6715 (m-80) outliers start: 7 outliers final: 3 residues processed: 151 average time/residue: 0.5979 time to fit residues: 96.6732 Evaluate side-chains 110 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 784 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 333 ASN A 487 GLN A 580 HIS A 744 GLN A 789 ASN C 36 GLN C 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.187197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145569 restraints weight = 11006.826| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.66 r_work: 0.3127 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10844 Z= 0.145 Angle : 0.659 9.519 14721 Z= 0.342 Chirality : 0.045 0.184 1679 Planarity : 0.006 0.056 1831 Dihedral : 9.151 113.247 1481 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.44 % Allowed : 11.77 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.22), residues: 1297 helix: -0.80 (0.20), residues: 577 sheet: 0.04 (0.42), residues: 151 loop : -1.95 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.014 0.001 TYR C 297 PHE 0.015 0.002 PHE A 968 TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10836) covalent geometry : angle 0.65248 / 0.34 (14700) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 0.95154 / 0.53 ( 6) hydrogen bonds : bond 0.05010 / 3.16 ( 486) hydrogen bonds : angle 5.65934 / 3.96 ( 1392) link_ALPHA1-4 : bond 0.00154 / 0.08 ( 1) link_ALPHA1-4 : angle 4.07261 / 2.20 ( 3) link_BETA1-4 : bond 0.00232 / 0.12 ( 1) link_BETA1-4 : angle 3.03334 / 1.57 ( 3) link_NAG-ASN : bond 0.00329 / 0.16 ( 3) link_NAG-ASN : angle 2.38593 / 1.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8179 (mttt) cc_final: 0.7655 (mtmm) REVERT: A 74 ARG cc_start: 0.7739 (tmm160) cc_final: 0.7446 (ttm-80) REVERT: A 184 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: A 541 MET cc_start: 0.6519 (tpp) cc_final: 0.5815 (tmm) REVERT: A 744 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.6953 (mp-120) REVERT: A 754 LYS cc_start: 0.7231 (mttt) cc_final: 0.6228 (mmtm) REVERT: A 776 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 1023 MET cc_start: 0.7969 (ttm) cc_final: 0.7660 (ttm) REVERT: C 215 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7380 (mmp-170) REVERT: C 337 PHE cc_start: 0.7374 (t80) cc_final: 0.6946 (m-80) outliers start: 28 outliers final: 10 residues processed: 137 average time/residue: 0.5452 time to fit residues: 80.9688 Evaluate side-chains 116 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN A 352 ASN A 353 ASN A 487 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142207 restraints weight = 11082.467| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.48 r_work: 0.3153 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10844 Z= 0.199 Angle : 0.661 9.152 14721 Z= 0.339 Chirality : 0.047 0.231 1679 Planarity : 0.005 0.056 1831 Dihedral : 8.851 116.109 1474 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.05 % Allowed : 13.69 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1297 helix: -0.23 (0.21), residues: 579 sheet: 0.24 (0.42), residues: 158 loop : -1.85 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.017 0.002 TYR A 817 PHE 0.016 0.002 PHE C 304 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (10836) covalent geometry : angle 0.65386 / 0.34 (14700) SS BOND : bond 0.00151 / 0.07 ( 3) SS BOND : angle 0.82022 / 0.45 ( 6) hydrogen bonds : bond 0.05104 / 3.24 ( 486) hydrogen bonds : angle 5.40126 / 3.80 ( 1392) link_ALPHA1-4 : bond 0.00164 / 0.09 ( 1) link_ALPHA1-4 : angle 4.24398 / 2.28 ( 3) link_BETA1-4 : bond 0.00530 / 0.28 ( 1) link_BETA1-4 : angle 3.36514 / 1.74 ( 3) link_NAG-ASN : bond 0.00500 / 0.24 ( 3) link_NAG-ASN : angle 2.53260 / 1.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8271 (mttt) cc_final: 0.7775 (mtmm) REVERT: A 74 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7569 (ttm-80) REVERT: A 184 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6502 (tt0) REVERT: A 541 MET cc_start: 0.6563 (tpp) cc_final: 0.5941 (tmm) REVERT: A 612 GLN cc_start: 0.4963 (OUTLIER) cc_final: 0.4631 (mp10) REVERT: A 742 VAL cc_start: 0.6872 (OUTLIER) cc_final: 0.6638 (p) REVERT: A 754 LYS cc_start: 0.7277 (mttt) cc_final: 0.6286 (mmtm) REVERT: A 776 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 1023 MET cc_start: 0.8037 (ttm) cc_final: 0.7739 (ttm) REVERT: C 60 ILE cc_start: 0.8479 (tp) cc_final: 0.8190 (tt) REVERT: C 86 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: C 337 PHE cc_start: 0.7425 (t80) cc_final: 0.7033 (m-80) outliers start: 35 outliers final: 15 residues processed: 137 average time/residue: 0.5156 time to fit residues: 76.5385 Evaluate side-chains 118 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 487 GLN A 674 GLN C 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.185464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139278 restraints weight = 11135.919| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.97 r_work: 0.3016 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10844 Z= 0.182 Angle : 0.641 9.096 14721 Z= 0.328 Chirality : 0.046 0.211 1679 Planarity : 0.005 0.057 1831 Dihedral : 8.450 115.012 1474 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.57 % Allowed : 13.86 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1297 helix: 0.11 (0.22), residues: 569 sheet: 0.26 (0.42), residues: 161 loop : -1.73 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.015 0.002 TYR A 817 PHE 0.015 0.002 PHE A 968 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (10836) covalent geometry : angle 0.63377 / 0.33 (14700) SS BOND : bond 0.00150 / 0.07 ( 3) SS BOND : angle 0.77640 / 0.43 ( 6) hydrogen bonds : bond 0.04877 / 3.10 ( 486) hydrogen bonds : angle 5.21552 / 3.67 ( 1392) link_ALPHA1-4 : bond 0.00268 / 0.14 ( 1) link_ALPHA1-4 : angle 4.10341 / 2.20 ( 3) link_BETA1-4 : bond 0.00384 / 0.20 ( 1) link_BETA1-4 : angle 3.25986 / 1.68 ( 3) link_NAG-ASN : bond 0.00453 / 0.22 ( 3) link_NAG-ASN : angle 2.46222 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7971 (mttt) cc_final: 0.7403 (mtmm) REVERT: A 74 ARG cc_start: 0.7983 (tmm160) cc_final: 0.7466 (ttm-80) REVERT: A 134 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: A 184 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6349 (tt0) REVERT: A 258 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6946 (mmt90) REVERT: A 468 MET cc_start: 0.6853 (mtm) cc_final: 0.6550 (mtt) REVERT: A 541 MET cc_start: 0.6242 (tpp) cc_final: 0.5806 (tmm) REVERT: A 599 ILE cc_start: 0.3112 (OUTLIER) cc_final: 0.2697 (pp) REVERT: A 612 GLN cc_start: 0.4674 (OUTLIER) cc_final: 0.4350 (mp10) REVERT: A 742 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6595 (p) REVERT: A 754 LYS cc_start: 0.7125 (mttt) cc_final: 0.6058 (mmtm) REVERT: A 776 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 1023 MET cc_start: 0.8338 (ttm) cc_final: 0.8014 (ttm) REVERT: C 60 ILE cc_start: 0.8399 (tp) cc_final: 0.8115 (tt) REVERT: C 86 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: C 337 PHE cc_start: 0.7308 (t80) cc_final: 0.6855 (m-80) outliers start: 41 outliers final: 18 residues processed: 143 average time/residue: 0.5614 time to fit residues: 86.9264 Evaluate side-chains 125 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 50.0000 chunk 105 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.184024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140065 restraints weight = 11054.960| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.01 r_work: 0.3061 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10844 Z= 0.233 Angle : 0.672 9.129 14721 Z= 0.344 Chirality : 0.048 0.232 1679 Planarity : 0.005 0.060 1831 Dihedral : 8.414 118.620 1474 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.40 % Allowed : 14.47 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1297 helix: 0.10 (0.22), residues: 575 sheet: 0.16 (0.41), residues: 167 loop : -1.70 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 525 TYR 0.018 0.002 TYR A1010 PHE 0.017 0.002 PHE A 968 TRP 0.016 0.002 TRP A 927 HIS 0.017 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (10836) covalent geometry : angle 0.66444 / 0.34 (14700) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 0.79096 / 0.43 ( 6) hydrogen bonds : bond 0.05197 / 3.31 ( 486) hydrogen bonds : angle 5.22596 / 3.68 ( 1392) link_ALPHA1-4 : bond 0.00509 / 0.27 ( 1) link_ALPHA1-4 : angle 4.28708 / 2.29 ( 3) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 3.26525 / 1.69 ( 3) link_NAG-ASN : bond 0.00577 / 0.28 ( 3) link_NAG-ASN : angle 2.61737 / 1.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7995 (mttt) cc_final: 0.7433 (mtmm) REVERT: A 74 ARG cc_start: 0.7961 (tmm160) cc_final: 0.7489 (ttm-80) REVERT: A 134 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: A 184 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: A 258 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6970 (mmt90) REVERT: A 541 MET cc_start: 0.6192 (tpp) cc_final: 0.5736 (tmt) REVERT: A 596 VAL cc_start: 0.5374 (OUTLIER) cc_final: 0.4937 (m) REVERT: A 612 GLN cc_start: 0.4671 (OUTLIER) cc_final: 0.4393 (mp10) REVERT: A 742 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6567 (p) REVERT: A 754 LYS cc_start: 0.7136 (mttt) cc_final: 0.6122 (mmtm) REVERT: A 776 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 1023 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7897 (ttm) REVERT: C 45 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 60 ILE cc_start: 0.8463 (tp) cc_final: 0.8183 (tt) REVERT: C 86 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: C 96 SER cc_start: 0.8201 (m) cc_final: 0.7967 (p) REVERT: C 337 PHE cc_start: 0.7354 (t80) cc_final: 0.6897 (m-80) outliers start: 39 outliers final: 17 residues processed: 142 average time/residue: 0.5682 time to fit residues: 87.5151 Evaluate side-chains 130 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 487 GLN C 36 GLN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.189176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147145 restraints weight = 11094.209| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.58 r_work: 0.3079 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10844 Z= 0.123 Angle : 0.589 9.267 14721 Z= 0.302 Chirality : 0.044 0.197 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.875 109.708 1474 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.31 % Allowed : 15.43 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1297 helix: 0.47 (0.22), residues: 568 sheet: 0.32 (0.41), residues: 167 loop : -1.44 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 525 TYR 0.014 0.001 TYR A1010 PHE 0.012 0.001 PHE A 968 TRP 0.017 0.001 TRP A 927 HIS 0.018 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10836) covalent geometry : angle 0.58240 / 0.30 (14700) SS BOND : bond 0.00138 / 0.07 ( 3) SS BOND : angle 0.68787 / 0.39 ( 6) hydrogen bonds : bond 0.04343 / 2.75 ( 486) hydrogen bonds : angle 4.95608 / 3.49 ( 1392) link_ALPHA1-4 : bond 0.00045 / 0.02 ( 1) link_ALPHA1-4 : angle 3.71825 / 1.99 ( 3) link_BETA1-4 : bond 0.00480 / 0.25 ( 1) link_BETA1-4 : angle 3.07708 / 1.58 ( 3) link_NAG-ASN : bond 0.00295 / 0.15 ( 3) link_NAG-ASN : angle 2.21001 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8084 (mttt) cc_final: 0.7511 (mtmm) REVERT: A 74 ARG cc_start: 0.7968 (tmm160) cc_final: 0.7488 (ttm-80) REVERT: A 134 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: A 184 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6286 (tt0) REVERT: A 258 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6963 (mmt90) REVERT: A 541 MET cc_start: 0.6215 (tpp) cc_final: 0.5791 (tmt) REVERT: A 596 VAL cc_start: 0.5341 (OUTLIER) cc_final: 0.4707 (m) REVERT: A 612 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4398 (mp10) REVERT: A 742 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6678 (p) REVERT: A 754 LYS cc_start: 0.7143 (mttt) cc_final: 0.6065 (mmtm) REVERT: A 776 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8072 (tm-30) REVERT: A 1023 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: C 45 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 60 ILE cc_start: 0.8432 (tp) cc_final: 0.8152 (tt) REVERT: C 86 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6237 (pm20) REVERT: C 156 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 337 PHE cc_start: 0.7323 (t80) cc_final: 0.6950 (m-80) outliers start: 38 outliers final: 13 residues processed: 140 average time/residue: 0.5613 time to fit residues: 85.0586 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 487 GLN C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.188495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144787 restraints weight = 11056.361| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.74 r_work: 0.3076 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10844 Z= 0.147 Angle : 0.595 9.096 14721 Z= 0.304 Chirality : 0.044 0.199 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.826 109.882 1474 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.05 % Allowed : 16.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1297 helix: 0.57 (0.22), residues: 568 sheet: 0.41 (0.41), residues: 166 loop : -1.35 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.017 0.001 TYR A 99 PHE 0.015 0.001 PHE A 968 TRP 0.027 0.001 TRP A 990 HIS 0.003 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10836) covalent geometry : angle 0.58861 / 0.30 (14700) SS BOND : bond 0.00159 / 0.08 ( 3) SS BOND : angle 0.71460 / 0.39 ( 6) hydrogen bonds : bond 0.04476 / 2.83 ( 486) hydrogen bonds : angle 4.90504 / 3.45 ( 1392) link_ALPHA1-4 : bond 0.00060 / 0.03 ( 1) link_ALPHA1-4 : angle 3.75427 / 2.01 ( 3) link_BETA1-4 : bond 0.00493 / 0.26 ( 1) link_BETA1-4 : angle 3.15505 / 1.62 ( 3) link_NAG-ASN : bond 0.00375 / 0.18 ( 3) link_NAG-ASN : angle 2.26525 / 1.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8053 (mttt) cc_final: 0.7501 (mtmm) REVERT: A 74 ARG cc_start: 0.7956 (tmm160) cc_final: 0.7474 (ttm-80) REVERT: A 134 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: A 184 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: A 214 ARG cc_start: 0.7626 (mpt-90) cc_final: 0.7404 (mmt-90) REVERT: A 222 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 258 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6952 (mmt90) REVERT: A 541 MET cc_start: 0.6191 (tpp) cc_final: 0.5779 (tmt) REVERT: A 596 VAL cc_start: 0.5096 (OUTLIER) cc_final: 0.4666 (m) REVERT: A 754 LYS cc_start: 0.7080 (mttt) cc_final: 0.6028 (mmtm) REVERT: A 776 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 1023 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (ttm) REVERT: C 36 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: C 45 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 60 ILE cc_start: 0.8448 (tp) cc_final: 0.8162 (tt) REVERT: C 86 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6271 (pm20) REVERT: C 156 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 337 PHE cc_start: 0.7303 (t80) cc_final: 0.6942 (m-80) outliers start: 35 outliers final: 14 residues processed: 137 average time/residue: 0.5912 time to fit residues: 87.4032 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 487 GLN C 36 GLN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.186028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143136 restraints weight = 11092.191| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.90 r_work: 0.3088 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10844 Z= 0.158 Angle : 0.609 9.885 14721 Z= 0.310 Chirality : 0.045 0.199 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.812 110.404 1474 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.23 % Allowed : 16.65 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1297 helix: 0.59 (0.22), residues: 569 sheet: 0.39 (0.41), residues: 164 loop : -1.32 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.019 0.002 TYR A1010 PHE 0.015 0.002 PHE A 968 TRP 0.025 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10836) covalent geometry : angle 0.60291 / 0.31 (14700) SS BOND : bond 0.00170 / 0.08 ( 3) SS BOND : angle 0.72334 / 0.40 ( 6) hydrogen bonds : bond 0.04500 / 2.86 ( 486) hydrogen bonds : angle 4.90371 / 3.45 ( 1392) link_ALPHA1-4 : bond 0.00155 / 0.08 ( 1) link_ALPHA1-4 : angle 3.79277 / 2.03 ( 3) link_BETA1-4 : bond 0.00450 / 0.24 ( 1) link_BETA1-4 : angle 3.16566 / 1.63 ( 3) link_NAG-ASN : bond 0.00398 / 0.19 ( 3) link_NAG-ASN : angle 2.29164 / 1.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8003 (mttt) cc_final: 0.7455 (mtmm) REVERT: A 74 ARG cc_start: 0.7853 (tmm160) cc_final: 0.7396 (ttm-80) REVERT: A 134 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: A 184 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6175 (tt0) REVERT: A 214 ARG cc_start: 0.7589 (mpt-90) cc_final: 0.7349 (mmt-90) REVERT: A 222 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 258 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6908 (mmt90) REVERT: A 541 MET cc_start: 0.6148 (tpp) cc_final: 0.5751 (tmt) REVERT: A 596 VAL cc_start: 0.5084 (OUTLIER) cc_final: 0.4610 (m) REVERT: A 754 LYS cc_start: 0.7040 (mttt) cc_final: 0.5964 (mmtm) REVERT: A 776 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 1023 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7935 (ttm) REVERT: C 45 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8105 (mp) REVERT: C 60 ILE cc_start: 0.8430 (tp) cc_final: 0.8150 (tt) REVERT: C 86 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6250 (pm20) REVERT: C 156 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 337 PHE cc_start: 0.7258 (t80) cc_final: 0.6878 (m-80) outliers start: 37 outliers final: 18 residues processed: 136 average time/residue: 0.5970 time to fit residues: 87.5287 Evaluate side-chains 130 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN A 744 GLN C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.187309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145330 restraints weight = 11078.397| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.70 r_work: 0.3077 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10844 Z= 0.138 Angle : 0.589 9.471 14721 Z= 0.299 Chirality : 0.044 0.198 1679 Planarity : 0.004 0.061 1831 Dihedral : 7.619 108.217 1474 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.79 % Allowed : 17.26 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1297 helix: 0.74 (0.22), residues: 568 sheet: 0.32 (0.40), residues: 176 loop : -1.20 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 525 TYR 0.018 0.001 TYR A 99 PHE 0.014 0.001 PHE A 968 TRP 0.026 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10836) covalent geometry : angle 0.58270 / 0.30 (14700) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.71290 / 0.39 ( 6) hydrogen bonds : bond 0.04296 / 2.72 ( 486) hydrogen bonds : angle 4.81635 / 3.38 ( 1392) link_ALPHA1-4 : bond 0.00009 / 0.00 ( 1) link_ALPHA1-4 : angle 3.66129 / 1.96 ( 3) link_BETA1-4 : bond 0.00445 / 0.23 ( 1) link_BETA1-4 : angle 3.09379 / 1.59 ( 3) link_NAG-ASN : bond 0.00336 / 0.17 ( 3) link_NAG-ASN : angle 2.15830 / 1.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5670 (mp) REVERT: A 58 LYS cc_start: 0.7994 (mttt) cc_final: 0.7429 (mtmm) REVERT: A 74 ARG cc_start: 0.7906 (tmm160) cc_final: 0.7433 (ttm-80) REVERT: A 184 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6221 (tt0) REVERT: A 214 ARG cc_start: 0.7582 (mpt-90) cc_final: 0.7308 (mmt-90) REVERT: A 222 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 258 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6946 (mmt90) REVERT: A 541 MET cc_start: 0.6144 (tpp) cc_final: 0.5747 (tmt) REVERT: A 596 VAL cc_start: 0.5164 (OUTLIER) cc_final: 0.4657 (m) REVERT: A 754 LYS cc_start: 0.7082 (mttt) cc_final: 0.6009 (mmtm) REVERT: A 776 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 1023 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7960 (ttm) REVERT: C 45 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8119 (mp) REVERT: C 60 ILE cc_start: 0.8457 (tp) cc_final: 0.8178 (tt) REVERT: C 86 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: C 156 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7668 (mm-30) REVERT: C 337 PHE cc_start: 0.7276 (t80) cc_final: 0.6896 (m-80) outliers start: 32 outliers final: 17 residues processed: 136 average time/residue: 0.6063 time to fit residues: 88.9168 Evaluate side-chains 129 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 GLN C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.185494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141887 restraints weight = 11063.729| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.23 r_work: 0.3065 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10844 Z= 0.183 Angle : 0.623 11.021 14721 Z= 0.317 Chirality : 0.046 0.199 1679 Planarity : 0.005 0.060 1831 Dihedral : 7.735 110.914 1474 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.53 % Allowed : 18.31 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1297 helix: 0.65 (0.22), residues: 574 sheet: 0.29 (0.40), residues: 174 loop : -1.23 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 525 TYR 0.021 0.002 TYR A 745 PHE 0.016 0.002 PHE A 968 TRP 0.024 0.002 TRP A 990 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (10836) covalent geometry : angle 0.61643 / 0.32 (14700) SS BOND : bond 0.00180 / 0.09 ( 3) SS BOND : angle 0.74691 / 0.41 ( 6) hydrogen bonds : bond 0.04589 / 2.92 ( 486) hydrogen bonds : angle 4.86568 / 3.42 ( 1392) link_ALPHA1-4 : bond 0.00227 / 0.12 ( 1) link_ALPHA1-4 : angle 3.86055 / 2.06 ( 3) link_BETA1-4 : bond 0.00308 / 0.16 ( 1) link_BETA1-4 : angle 3.17609 / 1.63 ( 3) link_NAG-ASN : bond 0.00463 / 0.22 ( 3) link_NAG-ASN : angle 2.31957 / 1.14 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5711 (mp) REVERT: A 58 LYS cc_start: 0.8033 (mttt) cc_final: 0.7479 (mtmm) REVERT: A 74 ARG cc_start: 0.7908 (tmm160) cc_final: 0.7434 (ttm-80) REVERT: A 184 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: A 214 ARG cc_start: 0.7602 (mpt-90) cc_final: 0.7329 (mmt-90) REVERT: A 222 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 258 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6704 (mmm160) REVERT: A 541 MET cc_start: 0.6098 (tpp) cc_final: 0.5736 (tmt) REVERT: A 596 VAL cc_start: 0.5060 (OUTLIER) cc_final: 0.4649 (m) REVERT: A 754 LYS cc_start: 0.7047 (mttt) cc_final: 0.5993 (mmtm) REVERT: A 776 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 1023 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7974 (ttm) REVERT: C 45 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8136 (mp) REVERT: C 60 ILE cc_start: 0.8471 (tp) cc_final: 0.8186 (tt) REVERT: C 86 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: C 156 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 337 PHE cc_start: 0.7301 (t80) cc_final: 0.6920 (m-80) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 0.5664 time to fit residues: 79.3959 Evaluate side-chains 130 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148314 restraints weight = 11047.695| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.43 r_work: 0.3088 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10844 Z= 0.134 Angle : 0.594 10.850 14721 Z= 0.302 Chirality : 0.044 0.196 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.545 107.650 1474 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.62 % Allowed : 18.22 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1297 helix: 0.84 (0.22), residues: 568 sheet: 0.40 (0.40), residues: 176 loop : -1.12 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.016 0.001 TYR A1010 PHE 0.014 0.001 PHE A 968 TRP 0.025 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10836) covalent geometry : angle 0.58766 / 0.30 (14700) SS BOND : bond 0.00152 / 0.08 ( 3) SS BOND : angle 0.70835 / 0.40 ( 6) hydrogen bonds : bond 0.04229 / 2.68 ( 486) hydrogen bonds : angle 4.75887 / 3.34 ( 1392) link_ALPHA1-4 : bond 0.00038 / 0.02 ( 1) link_ALPHA1-4 : angle 3.62561 / 1.94 ( 3) link_BETA1-4 : bond 0.00262 / 0.14 ( 1) link_BETA1-4 : angle 3.03607 / 1.56 ( 3) link_NAG-ASN : bond 0.00323 / 0.16 ( 3) link_NAG-ASN : angle 2.14771 / 1.06 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.90 seconds wall clock time: 64 minutes 0.82 seconds (3840.82 seconds total)