Starting phenix.real_space_refine on Mon Jun 9 19:34:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_9941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_9941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_9941.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_9941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7m_9941/06_2025/6k7m_9941.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.95, per 1000 atoms: 0.66 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.47 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: 5.69 Time building geometry restraints manager: 3.27 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: 6346 29.87 - 59.73: 213 59.73 - 89.60: 17 89.60 - 119.47: 1 119.47 - 149.33: 3 Dihedral angle restraints: 6580 sinusoidal: 2766 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 6577 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: 9.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 29.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 15.416 149.334 4111 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (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 TRP 0.017 0.003 TRP A 990 HIS 0.007 0.002 HIS A 456 PHE 0.032 0.004 PHE C 214 TYR 0.030 0.004 TYR A 849 ARG 0.010 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.01030 ( 3) link_NAG-ASN : angle 3.41353 ( 9) link_ALPHA1-4 : bond 0.00852 ( 1) link_ALPHA1-4 : angle 5.78413 ( 3) link_BETA1-4 : bond 0.00223 ( 1) link_BETA1-4 : angle 2.90925 ( 3) hydrogen bonds : bond 0.13687 ( 486) hydrogen bonds : angle 7.31126 ( 1392) SS BOND : bond 0.00328 ( 3) SS BOND : angle 1.20718 ( 6) covalent geometry : bond 0.01143 (10836) covalent geometry : angle 1.42103 (14700) *********************** 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 : 1.278 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: 0.8176 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 1023 MET cc_start: 0.7541 (ttm) cc_final: 0.7312 (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: 1.6929 time to fit residues: 275.6487 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 : 1.168 ------------------------------------------------------------------------------- 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 109 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.186961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142649 restraints weight = 10917.506| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.66 r_work: 0.3089 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10844 Z= 0.153 Angle : 0.655 9.359 14721 Z= 0.340 Chirality : 0.045 0.244 1679 Planarity : 0.006 0.055 1831 Dihedral : 9.546 113.087 1642 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.44 % Allowed : 11.68 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1297 helix: -0.78 (0.20), residues: 577 sheet: 0.06 (0.42), residues: 151 loop : -1.94 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 PHE 0.015 0.002 PHE A 968 TYR 0.014 0.002 TYR C 297 ARG 0.004 0.000 ARG A 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 3) link_NAG-ASN : angle 2.35584 ( 9) link_ALPHA1-4 : bond 0.00183 ( 1) link_ALPHA1-4 : angle 4.19017 ( 3) link_BETA1-4 : bond 0.00666 ( 1) link_BETA1-4 : angle 3.42611 ( 3) hydrogen bonds : bond 0.05002 ( 486) hydrogen bonds : angle 5.64679 ( 1392) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.95632 ( 6) covalent geometry : bond 0.00338 (10836) covalent geometry : angle 0.64816 (14700) *********************** 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 150 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8018 (mttt) cc_final: 0.7454 (mtmm) REVERT: A 74 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7417 (ttm-80) REVERT: A 180 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6924 (ttm) REVERT: A 184 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: A 541 MET cc_start: 0.6371 (tpp) cc_final: 0.5713 (tmm) REVERT: A 744 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6907 (mp-120) REVERT: A 754 LYS cc_start: 0.7155 (mttt) cc_final: 0.6081 (mmtm) REVERT: A 776 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 1023 MET cc_start: 0.8187 (ttm) cc_final: 0.7800 (ttm) REVERT: C 215 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7531 (mmp-170) REVERT: C 337 PHE cc_start: 0.7335 (t80) cc_final: 0.6872 (m-80) outliers start: 28 outliers final: 10 residues processed: 139 average time/residue: 1.2401 time to fit residues: 186.6733 Evaluate side-chains 119 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 180 MET 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 7 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 487 GLN A 674 GLN A 744 GLN C 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137280 restraints weight = 11180.741| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.35 r_work: 0.2982 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 10844 Z= 0.346 Angle : 0.779 9.144 14721 Z= 0.399 Chirality : 0.053 0.287 1679 Planarity : 0.006 0.058 1831 Dihedral : 9.814 122.098 1635 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.49 % Allowed : 13.86 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.22), residues: 1297 helix: -0.55 (0.21), residues: 574 sheet: 0.22 (0.42), residues: 159 loop : -2.01 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 927 HIS 0.006 0.002 HIS A 832 PHE 0.022 0.003 PHE C 304 TYR 0.024 0.003 TYR A 817 ARG 0.006 0.001 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00875 ( 3) link_NAG-ASN : angle 3.11041 ( 9) link_ALPHA1-4 : bond 0.00820 ( 1) link_ALPHA1-4 : angle 5.20276 ( 3) link_BETA1-4 : bond 0.00456 ( 1) link_BETA1-4 : angle 3.74492 ( 3) hydrogen bonds : bond 0.06164 ( 486) hydrogen bonds : angle 5.63131 ( 1392) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.92142 ( 6) covalent geometry : bond 0.00835 (10836) covalent geometry : angle 0.77000 (14700) *********************** 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 152 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8028 (mttt) cc_final: 0.7481 (mtmm) REVERT: A 74 ARG cc_start: 0.8006 (tmm160) cc_final: 0.7518 (ttm-80) REVERT: A 184 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: A 541 MET cc_start: 0.6341 (tpp) cc_final: 0.5796 (tmm) REVERT: A 612 GLN cc_start: 0.4647 (OUTLIER) cc_final: 0.4249 (mt0) REVERT: A 742 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6636 (p) REVERT: A 754 LYS cc_start: 0.7225 (mttt) cc_final: 0.6205 (mmtm) REVERT: A 776 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 1023 MET cc_start: 0.8331 (ttm) cc_final: 0.7849 (ttm) REVERT: C 45 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 86 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: C 337 PHE cc_start: 0.7334 (t80) cc_final: 0.6918 (m-80) outliers start: 40 outliers final: 16 residues processed: 144 average time/residue: 1.1566 time to fit residues: 181.1832 Evaluate side-chains 122 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 180 MET 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 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 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 784 ILE Chi-restraints excluded: chain A residue 907 LYS 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 164 GLU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 353 ASN A 487 GLN A 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.186400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142457 restraints weight = 10919.331| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.12 r_work: 0.3082 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1699 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= 0.145 Angle : 0.623 9.341 14721 Z= 0.320 Chirality : 0.045 0.201 1679 Planarity : 0.005 0.058 1831 Dihedral : 8.819 112.112 1635 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.84 % Allowed : 14.56 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1297 helix: 0.06 (0.22), residues: 575 sheet: 0.35 (0.42), residues: 163 loop : -1.75 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 990 HIS 0.013 0.001 HIS C 348 PHE 0.013 0.001 PHE A 968 TYR 0.013 0.001 TYR C 122 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 3) link_NAG-ASN : angle 2.39688 ( 9) link_ALPHA1-4 : bond 0.00495 ( 1) link_ALPHA1-4 : angle 4.34927 ( 3) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 3.28751 ( 3) hydrogen bonds : bond 0.04695 ( 486) hydrogen bonds : angle 5.23429 ( 1392) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.79308 ( 6) covalent geometry : bond 0.00330 (10836) covalent geometry : angle 0.61601 (14700) *********************** 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 152 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7973 (mttt) cc_final: 0.7403 (mtmm) REVERT: A 74 ARG cc_start: 0.7923 (tmm160) cc_final: 0.7467 (ttm-80) REVERT: A 134 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: A 184 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: A 468 MET cc_start: 0.6821 (mtm) cc_final: 0.6541 (mtt) REVERT: A 541 MET cc_start: 0.6191 (tpp) cc_final: 0.5860 (tmt) REVERT: A 599 ILE cc_start: 0.3139 (OUTLIER) cc_final: 0.2737 (pp) REVERT: A 612 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4355 (mp10) REVERT: A 730 ASP cc_start: 0.7297 (t0) cc_final: 0.7096 (t0) REVERT: A 742 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6650 (p) REVERT: A 744 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7006 (mp-120) REVERT: A 754 LYS cc_start: 0.7076 (mttt) cc_final: 0.6041 (mmtm) REVERT: A 776 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 1023 MET cc_start: 0.8204 (ttm) cc_final: 0.7907 (ttm) REVERT: C 86 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: C 337 PHE cc_start: 0.7284 (t80) cc_final: 0.6851 (m-80) outliers start: 44 outliers final: 15 residues processed: 146 average time/residue: 1.0789 time to fit residues: 171.7392 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 : 1.091 ------------------------------------------------------------------------------- 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 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 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 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 C residue 53 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.186211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141339 restraints weight = 11017.840| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.22 r_work: 0.3077 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1823 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= 0.153 Angle : 0.615 9.065 14721 Z= 0.315 Chirality : 0.045 0.201 1679 Planarity : 0.005 0.061 1831 Dihedral : 8.466 111.099 1635 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.05 % Allowed : 15.61 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1297 helix: 0.28 (0.22), residues: 575 sheet: 0.39 (0.42), residues: 166 loop : -1.62 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 990 HIS 0.004 0.001 HIS A 124 PHE 0.014 0.001 PHE A 968 TYR 0.017 0.001 TYR A1010 ARG 0.005 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 3) link_NAG-ASN : angle 2.37881 ( 9) link_ALPHA1-4 : bond 0.00214 ( 1) link_ALPHA1-4 : angle 4.23247 ( 3) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 3.36171 ( 3) hydrogen bonds : bond 0.04616 ( 486) hydrogen bonds : angle 5.10442 ( 1392) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.75200 ( 6) covalent geometry : bond 0.00353 (10836) covalent geometry : angle 0.60773 (14700) *********************** 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 146 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7939 (mttt) cc_final: 0.7372 (mtmm) REVERT: A 74 ARG cc_start: 0.7966 (tmm160) cc_final: 0.7485 (ttm-80) REVERT: A 134 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: A 184 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: A 541 MET cc_start: 0.6063 (tpp) cc_final: 0.5683 (tmm) REVERT: A 612 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.4326 (mp10) REVERT: A 754 LYS cc_start: 0.7104 (mttt) cc_final: 0.6058 (mmtm) REVERT: A 776 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 1023 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7883 (ttm) REVERT: C 45 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 86 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: C 96 SER cc_start: 0.8172 (m) cc_final: 0.7957 (p) REVERT: C 337 PHE cc_start: 0.7283 (t80) cc_final: 0.6865 (m-80) outliers start: 35 outliers final: 17 residues processed: 140 average time/residue: 1.2652 time to fit residues: 193.0422 Evaluate side-chains 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 342 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 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 ILE 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 53 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.185933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141802 restraints weight = 11070.867| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.89 r_work: 0.3028 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10844 Z= 0.214 Angle : 0.653 8.979 14721 Z= 0.335 Chirality : 0.047 0.226 1679 Planarity : 0.005 0.061 1831 Dihedral : 8.567 115.881 1635 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.40 % Allowed : 16.13 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1297 helix: 0.29 (0.22), residues: 575 sheet: 0.24 (0.41), residues: 166 loop : -1.57 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 990 HIS 0.004 0.001 HIS A 832 PHE 0.017 0.002 PHE A 968 TYR 0.018 0.002 TYR A 99 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 3) link_NAG-ASN : angle 2.58631 ( 9) link_ALPHA1-4 : bond 0.00429 ( 1) link_ALPHA1-4 : angle 4.40526 ( 3) link_BETA1-4 : bond 0.00355 ( 1) link_BETA1-4 : angle 3.49054 ( 3) hydrogen bonds : bond 0.05037 ( 486) hydrogen bonds : angle 5.12648 ( 1392) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.76626 ( 6) covalent geometry : bond 0.00509 (10836) covalent geometry : angle 0.64473 (14700) *********************** 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 149 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8063 (mttt) cc_final: 0.7507 (mtmm) REVERT: A 74 ARG cc_start: 0.7974 (tmm160) cc_final: 0.7486 (ttm-80) REVERT: A 134 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: A 184 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: A 541 MET cc_start: 0.6232 (tpp) cc_final: 0.5776 (tmt) REVERT: A 612 GLN cc_start: 0.4682 (OUTLIER) cc_final: 0.4411 (mp10) REVERT: A 742 VAL cc_start: 0.7026 (OUTLIER) cc_final: 0.6763 (p) REVERT: A 754 LYS cc_start: 0.7107 (mttt) cc_final: 0.6091 (mmtm) REVERT: A 776 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 1023 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7964 (ttm) REVERT: C 45 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8056 (mp) REVERT: C 60 ILE cc_start: 0.8530 (tp) cc_final: 0.8238 (tt) REVERT: C 86 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: C 96 SER cc_start: 0.8217 (m) cc_final: 0.7983 (p) REVERT: C 337 PHE cc_start: 0.7270 (t80) cc_final: 0.6941 (m-80) outliers start: 39 outliers final: 20 residues processed: 143 average time/residue: 1.1324 time to fit residues: 176.2297 Evaluate side-chains 132 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 342 LEU 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 612 GLN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 656 ILE 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 53 ILE 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 347 ASN Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 744 GLN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.188515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144795 restraints weight = 11153.333| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.12 r_work: 0.3090 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10844 Z= 0.146 Angle : 0.597 9.067 14721 Z= 0.307 Chirality : 0.045 0.199 1679 Planarity : 0.005 0.062 1831 Dihedral : 8.111 110.794 1635 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.96 % Allowed : 17.18 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1297 helix: 0.57 (0.22), residues: 568 sheet: 0.30 (0.41), residues: 168 loop : -1.40 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 PHE 0.014 0.001 PHE A 968 TYR 0.017 0.001 TYR A 99 ARG 0.006 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 3) link_NAG-ASN : angle 2.26455 ( 9) link_ALPHA1-4 : bond 0.00205 ( 1) link_ALPHA1-4 : angle 4.16039 ( 3) link_BETA1-4 : bond 0.00447 ( 1) link_BETA1-4 : angle 3.28866 ( 3) hydrogen bonds : bond 0.04454 ( 486) hydrogen bonds : angle 4.92136 ( 1392) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.70525 ( 6) covalent geometry : bond 0.00340 (10836) covalent geometry : angle 0.58958 (14700) *********************** 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 142 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7989 (mttt) cc_final: 0.7430 (mtmm) REVERT: A 74 ARG cc_start: 0.7880 (tmm160) cc_final: 0.7391 (ttm-80) REVERT: A 134 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: A 184 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6451 (tt0) REVERT: A 214 ARG cc_start: 0.7126 (mmt-90) cc_final: 0.6719 (mmt-90) REVERT: A 541 MET cc_start: 0.5987 (tpp) cc_final: 0.5590 (tmt) REVERT: A 693 MET cc_start: 0.8531 (mmm) cc_final: 0.8004 (tpp) REVERT: A 742 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6757 (p) REVERT: A 754 LYS cc_start: 0.7064 (mttt) cc_final: 0.6001 (mmtm) REVERT: A 776 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 1023 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7868 (ttm) REVERT: C 45 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 86 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6308 (pm20) REVERT: C 337 PHE cc_start: 0.7139 (t80) cc_final: 0.6842 (m-80) outliers start: 34 outliers final: 20 residues processed: 137 average time/residue: 1.1591 time to fit residues: 172.6428 Evaluate side-chains 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 642 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 656 ILE 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 786 ASP Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4074 r_free = 0.4074 target = 0.186748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142754 restraints weight = 11037.616| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.87 r_work: 0.3040 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10844 Z= 0.190 Angle : 0.628 9.586 14721 Z= 0.322 Chirality : 0.046 0.213 1679 Planarity : 0.005 0.061 1831 Dihedral : 8.210 113.975 1635 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.49 % Allowed : 17.18 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1297 helix: 0.51 (0.22), residues: 574 sheet: 0.27 (0.41), residues: 166 loop : -1.38 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 990 HIS 0.003 0.001 HIS A 832 PHE 0.016 0.002 PHE A 968 TYR 0.016 0.002 TYR C 122 ARG 0.005 0.000 ARG A 743 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 3) link_NAG-ASN : angle 2.47277 ( 9) link_ALPHA1-4 : bond 0.00409 ( 1) link_ALPHA1-4 : angle 4.26123 ( 3) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 3.40726 ( 3) hydrogen bonds : bond 0.04770 ( 486) hydrogen bonds : angle 4.97174 ( 1392) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.75550 ( 6) covalent geometry : bond 0.00452 (10836) covalent geometry : angle 0.62089 (14700) *********************** 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 149 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8035 (mttt) cc_final: 0.7493 (mtmm) REVERT: A 74 ARG cc_start: 0.7953 (tmm160) cc_final: 0.7466 (ttm-80) REVERT: A 134 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: A 184 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: A 214 ARG cc_start: 0.7256 (mmt-90) cc_final: 0.6821 (mmt-90) REVERT: A 468 MET cc_start: 0.7111 (mtm) cc_final: 0.6675 (mtt) REVERT: A 541 MET cc_start: 0.6195 (tpp) cc_final: 0.5779 (tmt) REVERT: A 693 MET cc_start: 0.8498 (mmm) cc_final: 0.8097 (tpp) REVERT: A 754 LYS cc_start: 0.7074 (mttt) cc_final: 0.6038 (mmtm) REVERT: A 776 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 1023 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8037 (ttm) REVERT: C 45 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 86 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: C 337 PHE cc_start: 0.7245 (t80) cc_final: 0.6924 (m-80) outliers start: 40 outliers final: 20 residues processed: 144 average time/residue: 1.1539 time to fit residues: 180.0163 Evaluate side-chains 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 642 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 656 ILE 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 907 LYS Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 ILE 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 347 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4085 r_free = 0.4085 target = 0.187943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143649 restraints weight = 11135.304| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.90 r_work: 0.3059 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10844 Z= 0.153 Angle : 0.607 10.225 14721 Z= 0.310 Chirality : 0.045 0.198 1679 Planarity : 0.005 0.062 1831 Dihedral : 8.051 112.976 1635 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.79 % Allowed : 17.79 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1297 helix: 0.66 (0.22), residues: 568 sheet: 0.35 (0.41), residues: 166 loop : -1.30 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 PHE 0.014 0.001 PHE A 968 TYR 0.017 0.001 TYR A1010 ARG 0.005 0.000 ARG A 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 3) link_NAG-ASN : angle 2.32316 ( 9) link_ALPHA1-4 : bond 0.00209 ( 1) link_ALPHA1-4 : angle 4.10694 ( 3) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 3.31335 ( 3) hydrogen bonds : bond 0.04519 ( 486) hydrogen bonds : angle 4.89225 ( 1392) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.71090 ( 6) covalent geometry : bond 0.00356 (10836) covalent geometry : angle 0.59933 (14700) *********************** 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 140 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8044 (mttt) cc_final: 0.7495 (mtmm) REVERT: A 74 ARG cc_start: 0.7950 (tmm160) cc_final: 0.7464 (ttm-80) REVERT: A 134 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: A 184 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6493 (tt0) REVERT: A 214 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.6823 (mmt-90) REVERT: A 222 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 468 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6687 (mtt) REVERT: A 541 MET cc_start: 0.6207 (tpp) cc_final: 0.5735 (tmt) REVERT: A 693 MET cc_start: 0.8438 (mmm) cc_final: 0.8053 (tpp) REVERT: A 754 LYS cc_start: 0.7079 (mttt) cc_final: 0.6035 (mmtm) REVERT: A 776 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8092 (tm-30) REVERT: A 1023 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7960 (ttm) REVERT: C 45 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8092 (mp) REVERT: C 86 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: C 156 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 337 PHE cc_start: 0.7219 (t80) cc_final: 0.6920 (m-80) outliers start: 32 outliers final: 20 residues processed: 135 average time/residue: 1.2423 time to fit residues: 180.8542 Evaluate side-chains 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 581 LEU 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 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN A 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150480 restraints weight = 11025.686| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.26 r_work: 0.3091 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2315 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= 0.128 Angle : 0.585 10.124 14721 Z= 0.299 Chirality : 0.044 0.198 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.732 108.177 1635 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.62 % Allowed : 18.40 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1297 helix: 0.86 (0.22), residues: 567 sheet: 0.29 (0.40), residues: 180 loop : -1.14 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 990 HIS 0.003 0.001 HIS A 124 PHE 0.013 0.001 PHE A 968 TYR 0.016 0.001 TYR A1010 ARG 0.010 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 2.17020 ( 9) link_ALPHA1-4 : bond 0.00008 ( 1) link_ALPHA1-4 : angle 3.89552 ( 3) link_BETA1-4 : bond 0.00353 ( 1) link_BETA1-4 : angle 3.19195 ( 3) hydrogen bonds : bond 0.04197 ( 486) hydrogen bonds : angle 4.75250 ( 1392) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.70879 ( 6) covalent geometry : bond 0.00292 (10836) covalent geometry : angle 0.57838 (14700) ********************** 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 139 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8154 (mttt) cc_final: 0.7664 (mtmm) REVERT: A 74 ARG cc_start: 0.8014 (tmm160) cc_final: 0.7578 (ttm-80) REVERT: A 134 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 184 GLU cc_start: 0.6728 (pt0) cc_final: 0.6505 (tt0) REVERT: A 214 ARG cc_start: 0.7397 (mmt-90) cc_final: 0.6954 (mmt-90) REVERT: A 468 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: A 541 MET cc_start: 0.6712 (tpp) cc_final: 0.6298 (tmm) REVERT: A 693 MET cc_start: 0.8349 (mmm) cc_final: 0.7970 (tpp) REVERT: A 754 LYS cc_start: 0.7185 (mttt) cc_final: 0.6113 (mmtm) REVERT: A 775 LYS cc_start: 0.8088 (mttm) cc_final: 0.7567 (tmmt) REVERT: A 776 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 1023 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: C 45 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (mm) REVERT: C 86 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: C 156 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 337 PHE cc_start: 0.7309 (t80) cc_final: 0.7046 (m-80) outliers start: 30 outliers final: 21 residues processed: 135 average time/residue: 1.2332 time to fit residues: 180.9479 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 : 1.199 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 581 LEU 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 759 CYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142729 restraints weight = 11030.799| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.00 r_work: 0.3058 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2265 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= 0.174 Angle : 0.618 9.762 14721 Z= 0.316 Chirality : 0.046 0.204 1679 Planarity : 0.005 0.061 1831 Dihedral : 7.897 111.969 1635 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.62 % Allowed : 18.74 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1297 helix: 0.76 (0.22), residues: 567 sheet: 0.32 (0.40), residues: 176 loop : -1.15 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 990 HIS 0.003 0.001 HIS A 832 PHE 0.016 0.002 PHE A 968 TYR 0.019 0.002 TYR A1010 ARG 0.007 0.000 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 3) link_NAG-ASN : angle 2.38170 ( 9) link_ALPHA1-4 : bond 0.00272 ( 1) link_ALPHA1-4 : angle 4.06457 ( 3) link_BETA1-4 : bond 0.00354 ( 1) link_BETA1-4 : angle 3.38966 ( 3) hydrogen bonds : bond 0.04603 ( 486) hydrogen bonds : angle 4.83676 ( 1392) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.75426 ( 6) covalent geometry : bond 0.00412 (10836) covalent geometry : angle 0.61100 (14700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8641.74 seconds wall clock time: 149 minutes 10.60 seconds (8950.60 seconds total)