Starting phenix.real_space_refine on Fri Sep 11 12:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bss_30165/09_2026/7bss_30165.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 45 5.16 5 C 6043 2.51 5 N 1505 2.21 5 O 1690 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 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9289 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6604 Classifications: {'peptide': 816} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 793} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.82, per 1000 atoms: 0.20 Number of scatterers: 9289 At special positions: 0 Unit cell: (113.71, 83, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 45 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1690 8.00 N 1505 7.00 C 6043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG C 401 " - " NAG C 402 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 292.6 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 45.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.543A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.789A pdb=" N PHE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 119 Proline residue: A 94 - end of helix removed outlier: 3.754A pdb=" N GLN A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.689A pdb=" N ILE A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.792A pdb=" N ASN A 273 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.523A pdb=" N THR A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.646A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.833A 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 356 through 357 No H-bonds generated for 'chain 'A' and resid 356 through 357' Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.526A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 removed outlier: 3.546A pdb=" N GLU A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 689 removed outlier: 4.315A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 753 through 761 removed outlier: 3.574A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.820A pdb=" N ILE A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 803 Processing helix chain 'A' and resid 817 through 820 Processing helix chain 'A' and resid 821 through 827 Processing helix chain 'A' and resid 840 through 845 removed outlier: 3.641A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 845' Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 861 through 895 removed outlier: 3.557A pdb=" N LEU A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 3.571A pdb=" N TYR A 891 " --> pdb=" O PRO A 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 removed outlier: 3.541A pdb=" N LEU A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.056A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.545A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.879A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.531A pdb=" N ILE A 945 " --> pdb=" O TYR A 942 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 946 " --> pdb=" O MET A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 removed outlier: 3.684A pdb=" N LEU A 951 " --> pdb=" O ASN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 948 through 951' Processing helix chain 'A' and resid 952 through 975 removed outlier: 3.543A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1012 removed outlier: 4.006A pdb=" N ILE A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 3.772A pdb=" N ALA A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1078 Processing helix chain 'A' and resid 1078 through 1090 removed outlier: 3.654A pdb=" N LEU A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 60 through 72 removed outlier: 3.518A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 4.249A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.173A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.526A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.678A pdb=" N ASN C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 11.736A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.805A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.518A pdb=" N TYR A 847 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR A 747 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP A 752 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.729A pdb=" N ILE C 311 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 106 removed outlier: 5.046A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2807 1.33 - 1.46: 1992 1.46 - 1.58: 4649 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 9519 Sorted by residual: bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.795 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.794 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.789 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C3 NAG C 401 " pdb=" O3 NAG C 401 " ideal model delta sigma weight residual 1.403 1.438 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 9514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.95: 12913 13.95 - 27.89: 4 27.89 - 41.84: 0 41.84 - 55.79: 0 55.79 - 69.73: 2 Bond angle restraints: 12919 Sorted by residual: angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 178.13 -69.45 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 89.55 20.66 3.00e+00 1.11e-01 4.74e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 89.86 19.83 3.00e+00 1.11e-01 4.37e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.89 19.13 3.00e+00 1.11e-01 4.06e+01 ... (remaining 12914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4840 17.74 - 35.47: 587 35.47 - 53.20: 129 53.20 - 70.94: 20 70.94 - 88.67: 12 Dihedral angle restraints: 5588 sinusoidal: 2242 harmonic: 3346 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual -86.00 -24.59 -61.41 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA TRP A1045 " pdb=" C TRP A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual -180.00 -152.87 -27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PHE A 894 " pdb=" C PHE A 894 " pdb=" N CYS A 895 " pdb=" CA CYS A 895 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 5585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 1462 0.356 - 0.711: 1 0.711 - 1.067: 0 1.067 - 1.422: 0 1.422 - 1.778: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -0.62 -1.78 2.00e-02 2.50e+03 7.90e+03 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 180 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1461 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG C 405 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.506 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.323 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C7 NAG C 404 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.486 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.108 2.00e-02 2.50e+03 9.13e-02 1.04e+02 pdb=" C7 NAG C 402 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.145 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.087 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 71 2.46 - 3.07: 6446 3.07 - 3.68: 13615 3.68 - 4.29: 21479 4.29 - 4.90: 35993 Nonbonded interactions: 77604 Sorted by model distance: nonbonded pdb=" F2 ALF A1101 " pdb="MG MG A1102 " model vdw 1.849 2.120 nonbonded pdb=" O3 NAG C 401 " pdb=" O5 NAG C 402 " model vdw 1.914 3.040 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1102 " model vdw 1.943 2.170 nonbonded pdb=" O THR A 411 " pdb="MG MG A1102 " model vdw 2.082 2.170 nonbonded pdb=" OG SER A 163 " pdb=" O THR A 193 " model vdw 2.111 3.040 ... (remaining 77599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 0.433 9527 Z= 0.498 Angle : 1.268 69.732 12937 Z= 0.544 Chirality : 0.069 1.778 1464 Planarity : 0.011 0.285 1611 Dihedral : 16.301 88.674 3421 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.60 % Allowed : 18.66 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.79 (0.18), residues: 1130 helix: -4.49 (0.10), residues: 486 sheet: -3.01 (0.37), residues: 164 loop : -3.22 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1016 TYR 0.022 0.002 TYR C 297 PHE 0.016 0.002 PHE C 214 TRP 0.019 0.003 TRP A 323 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.01045 / 0.45 ( 9519) covalent geometry : angle 1.23368 / 0.53 (12919) SS BOND : bond 0.00606 / 0.26 ( 3) SS BOND : angle 1.31725 / 0.65 ( 6) hydrogen bonds : bond 0.30334 / 20.10 ( 318) hydrogen bonds : angle 11.16704 / 7.62 ( 912) Misc. bond : bond 0.02119 / 1.12 ( 1) link_BETA1-4 : bond 0.43291 / 22.78 ( 1) link_BETA1-4 : angle 17.12130 / 8.55 ( 3) link_NAG-ASN : bond 0.00759 / 0.31 ( 3) link_NAG-ASN : angle 5.35686 / 3.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7284 (p0) cc_final: 0.6935 (p0) REVERT: A 272 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7369 (tt) REVERT: A 330 LYS cc_start: 0.8577 (tmtt) cc_final: 0.7967 (ttmt) REVERT: A 355 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 385 ILE cc_start: 0.8806 (mt) cc_final: 0.8548 (mt) REVERT: A 1055 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8312 (m-80) outliers start: 57 outliers final: 40 residues processed: 171 average time/residue: 0.0954 time to fit residues: 22.9186 Evaluate side-chains 150 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 929 HIS Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 59 ASN A 63 GLN A 106 GLN A 118 ASN A 243 ASN A 392 ASN A 397 ASN A 862 HIS A 864 HIS A 881 ASN A 888 GLN C 216 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.155462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115357 restraints weight = 11462.503| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.81 r_work: 0.3056 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9527 Z= 0.132 Angle : 0.666 10.483 12937 Z= 0.331 Chirality : 0.044 0.341 1464 Planarity : 0.004 0.035 1611 Dihedral : 8.324 59.576 1304 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.83 % Allowed : 21.41 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.21), residues: 1130 helix: -2.59 (0.18), residues: 500 sheet: -2.56 (0.38), residues: 151 loop : -2.64 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.011 0.001 TYR A 324 PHE 0.015 0.001 PHE A 894 TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9519) covalent geometry : angle 0.64971 / 0.33 (12919) SS BOND : bond 0.00293 / 0.13 ( 3) SS BOND : angle 1.11119 / 0.56 ( 6) hydrogen bonds : bond 0.04613 / 3.04 ( 318) hydrogen bonds : angle 5.56915 / 3.85 ( 912) Misc. bond : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : bond 0.00452 / 0.24 ( 1) link_BETA1-4 : angle 3.08728 / 1.48 ( 3) link_NAG-ASN : bond 0.00959 / 0.38 ( 3) link_NAG-ASN : angle 5.19974 / 3.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.349 Fit side-chains REVERT: A 121 ASN cc_start: 0.7002 (p0) cc_final: 0.6686 (p0) REVERT: A 153 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8042 (mt-10) REVERT: A 272 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7265 (tt) REVERT: A 330 LYS cc_start: 0.8510 (tmtt) cc_final: 0.7935 (ttmt) REVERT: A 714 ARG cc_start: 0.7031 (mmm-85) cc_final: 0.6666 (tpm170) REVERT: A 760 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 819 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8166 (p0) REVERT: C 146 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: C 152 ASN cc_start: 0.8564 (p0) cc_final: 0.8169 (p0) REVERT: C 209 ASP cc_start: 0.8542 (p0) cc_final: 0.8299 (p0) REVERT: C 305 ASP cc_start: 0.8938 (t0) cc_final: 0.8460 (t0) outliers start: 39 outliers final: 16 residues processed: 163 average time/residue: 0.0954 time to fit residues: 21.9780 Evaluate side-chains 130 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 111 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116698 restraints weight = 11483.337| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.83 r_work: 0.3076 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9527 Z= 0.116 Angle : 0.608 10.490 12937 Z= 0.301 Chirality : 0.044 0.362 1464 Planarity : 0.004 0.041 1611 Dihedral : 6.552 58.650 1253 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.54 % Allowed : 21.61 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.23), residues: 1130 helix: -1.51 (0.21), residues: 504 sheet: -2.21 (0.39), residues: 155 loop : -2.29 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.013 0.001 TYR A 324 PHE 0.017 0.001 PHE A1032 TRP 0.018 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9519) covalent geometry : angle 0.59303 / 0.30 (12919) SS BOND : bond 0.00331 / 0.13 ( 3) SS BOND : angle 0.75746 / 0.36 ( 6) hydrogen bonds : bond 0.03962 / 2.64 ( 318) hydrogen bonds : angle 4.95492 / 3.40 ( 912) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : bond 0.00228 / 0.12 ( 1) link_BETA1-4 : angle 3.06915 / 1.46 ( 3) link_NAG-ASN : bond 0.00912 / 0.34 ( 3) link_NAG-ASN : angle 4.73297 / 2.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.350 Fit side-chains REVERT: A 121 ASN cc_start: 0.6785 (p0) cc_final: 0.6422 (p0) REVERT: A 122 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8236 (mmtt) REVERT: A 272 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.6935 (tt) REVERT: A 275 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5987 (mp10) REVERT: A 330 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7764 (ttpt) REVERT: A 355 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 696 GLU cc_start: 0.6810 (mp0) cc_final: 0.6475 (mp0) REVERT: A 794 GLN cc_start: 0.8534 (mt0) cc_final: 0.8327 (mt0) REVERT: A 860 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8977 (mt) REVERT: C 152 ASN cc_start: 0.8567 (p0) cc_final: 0.8182 (p0) REVERT: C 305 ASP cc_start: 0.8981 (t0) cc_final: 0.8507 (t0) outliers start: 36 outliers final: 16 residues processed: 160 average time/residue: 0.1007 time to fit residues: 22.5542 Evaluate side-chains 133 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 279 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114298 restraints weight = 11618.341| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.83 r_work: 0.2951 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9527 Z= 0.168 Angle : 0.620 10.430 12937 Z= 0.307 Chirality : 0.045 0.366 1464 Planarity : 0.004 0.035 1611 Dihedral : 6.338 58.880 1245 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.42 % Allowed : 21.51 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.24), residues: 1130 helix: -1.23 (0.22), residues: 506 sheet: -1.78 (0.41), residues: 150 loop : -2.21 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.014 0.001 TYR A 324 PHE 0.015 0.001 PHE A 971 TRP 0.017 0.001 TRP A 323 HIS 0.011 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9519) covalent geometry : angle 0.60742 / 0.30 (12919) SS BOND : bond 0.00317 / 0.15 ( 3) SS BOND : angle 0.87860 / 0.44 ( 6) hydrogen bonds : bond 0.04029 / 2.67 ( 318) hydrogen bonds : angle 4.83178 / 3.34 ( 912) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.00085 / 0.04 ( 1) link_BETA1-4 : angle 2.23858 / 1.07 ( 3) link_NAG-ASN : bond 0.00931 / 0.37 ( 3) link_NAG-ASN : angle 4.65151 / 2.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.299 Fit side-chains REVERT: A 121 ASN cc_start: 0.6915 (p0) cc_final: 0.6696 (p0) REVERT: A 272 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7292 (tt) REVERT: A 330 LYS cc_start: 0.8396 (tmtt) cc_final: 0.7754 (ttpt) REVERT: A 355 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8877 (mp) REVERT: A 359 MET cc_start: 0.9118 (ttm) cc_final: 0.8740 (ttm) REVERT: A 696 GLU cc_start: 0.6880 (mp0) cc_final: 0.6522 (mp0) REVERT: A 794 GLN cc_start: 0.8547 (mt0) cc_final: 0.8327 (mt0) REVERT: A 860 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8980 (mt) REVERT: C 152 ASN cc_start: 0.8631 (p0) cc_final: 0.8201 (p0) REVERT: C 305 ASP cc_start: 0.9008 (t0) cc_final: 0.8555 (t0) outliers start: 45 outliers final: 29 residues processed: 155 average time/residue: 0.0840 time to fit residues: 18.6841 Evaluate side-chains 145 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 0.0020 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 88 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113631 restraints weight = 11558.855| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.88 r_work: 0.2961 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9527 Z= 0.171 Angle : 0.619 10.538 12937 Z= 0.306 Chirality : 0.045 0.370 1464 Planarity : 0.004 0.034 1611 Dihedral : 6.213 58.789 1245 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.91 % Allowed : 21.91 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.24), residues: 1130 helix: -1.03 (0.22), residues: 506 sheet: -1.74 (0.40), residues: 156 loop : -2.11 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.016 0.001 TYR A 324 PHE 0.015 0.001 PHE A 971 TRP 0.019 0.001 TRP A 323 HIS 0.011 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 9519) covalent geometry : angle 0.60637 / 0.30 (12919) SS BOND : bond 0.00413 / 0.17 ( 3) SS BOND : angle 0.89095 / 0.43 ( 6) hydrogen bonds : bond 0.03999 / 2.65 ( 318) hydrogen bonds : angle 4.72896 / 3.27 ( 912) Misc. bond : bond 0.00096 / 0.05 ( 1) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 1.67729 / 0.83 ( 3) link_NAG-ASN : bond 0.00927 / 0.37 ( 3) link_NAG-ASN : angle 4.63391 / 2.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.363 Fit side-chains REVERT: A 272 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.6876 (tt) REVERT: A 275 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: A 330 LYS cc_start: 0.8397 (tmtt) cc_final: 0.7760 (ttpt) REVERT: A 355 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8901 (mp) REVERT: A 696 GLU cc_start: 0.6933 (mp0) cc_final: 0.6569 (mp0) REVERT: A 794 GLN cc_start: 0.8559 (mt0) cc_final: 0.8359 (mt0) REVERT: A 860 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8970 (mt) REVERT: C 152 ASN cc_start: 0.8611 (p0) cc_final: 0.8170 (p0) REVERT: C 248 ASP cc_start: 0.8538 (t70) cc_final: 0.8038 (t0) REVERT: C 254 ASN cc_start: 0.8583 (t0) cc_final: 0.8233 (m-40) REVERT: C 305 ASP cc_start: 0.8998 (t0) cc_final: 0.8548 (t0) outliers start: 50 outliers final: 35 residues processed: 160 average time/residue: 0.0877 time to fit residues: 20.1949 Evaluate side-chains 149 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 34 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS C 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117914 restraints weight = 11540.294| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.86 r_work: 0.3050 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9527 Z= 0.106 Angle : 0.567 10.608 12937 Z= 0.282 Chirality : 0.044 0.411 1464 Planarity : 0.003 0.032 1611 Dihedral : 5.881 58.034 1245 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.83 % Allowed : 23.28 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.24), residues: 1130 helix: -0.60 (0.23), residues: 509 sheet: -1.37 (0.43), residues: 149 loop : -2.04 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 270 TYR 0.016 0.001 TYR A 879 PHE 0.011 0.001 PHE A 894 TRP 0.019 0.001 TRP A 323 HIS 0.009 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9519) covalent geometry : angle 0.55468 / 0.28 (12919) SS BOND : bond 0.00296 / 0.12 ( 3) SS BOND : angle 0.60304 / 0.31 ( 6) hydrogen bonds : bond 0.03432 / 2.30 ( 318) hydrogen bonds : angle 4.52540 / 3.12 ( 912) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : bond 0.00212 / 0.11 ( 1) link_BETA1-4 : angle 1.73694 / 0.87 ( 3) link_NAG-ASN : bond 0.00859 / 0.33 ( 3) link_NAG-ASN : angle 4.39833 / 2.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.251 Fit side-chains REVERT: A 272 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.6953 (tt) REVERT: A 275 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.6068 (mp10) REVERT: A 355 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 359 MET cc_start: 0.9004 (ttm) cc_final: 0.8636 (ttm) REVERT: A 696 GLU cc_start: 0.6948 (mp0) cc_final: 0.6599 (pm20) REVERT: A 794 GLN cc_start: 0.8521 (mt0) cc_final: 0.8318 (mt0) REVERT: A 860 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (mt) REVERT: A 957 LEU cc_start: 0.8352 (pp) cc_final: 0.8012 (mt) REVERT: C 152 ASN cc_start: 0.8577 (p0) cc_final: 0.8151 (p0) REVERT: C 305 ASP cc_start: 0.8959 (t0) cc_final: 0.8529 (t0) outliers start: 39 outliers final: 25 residues processed: 151 average time/residue: 0.0754 time to fit residues: 16.4150 Evaluate side-chains 141 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116262 restraints weight = 11547.797| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.94 r_work: 0.2970 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9527 Z= 0.144 Angle : 0.595 10.448 12937 Z= 0.294 Chirality : 0.045 0.374 1464 Planarity : 0.003 0.032 1611 Dihedral : 5.874 56.390 1245 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.93 % Allowed : 23.28 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1130 helix: -0.47 (0.23), residues: 504 sheet: -1.41 (0.41), residues: 157 loop : -1.93 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.015 0.001 TYR A 324 PHE 0.015 0.001 PHE A1032 TRP 0.019 0.001 TRP A 323 HIS 0.008 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 9519) covalent geometry : angle 0.58373 / 0.29 (12919) SS BOND : bond 0.00377 / 0.16 ( 3) SS BOND : angle 0.80140 / 0.39 ( 6) hydrogen bonds : bond 0.03629 / 2.41 ( 318) hydrogen bonds : angle 4.44636 / 3.07 ( 912) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.00046 / 0.02 ( 1) link_BETA1-4 : angle 1.18010 / 0.62 ( 3) link_NAG-ASN : bond 0.00933 / 0.36 ( 3) link_NAG-ASN : angle 4.40428 / 2.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.328 Fit side-chains REVERT: A 113 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7784 (mtm180) REVERT: A 272 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6905 (tt) REVERT: A 355 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8901 (mp) REVERT: A 359 MET cc_start: 0.9061 (ttm) cc_final: 0.8696 (ttm) REVERT: A 696 GLU cc_start: 0.6909 (mp0) cc_final: 0.6609 (mp0) REVERT: A 794 GLN cc_start: 0.8569 (mt0) cc_final: 0.8348 (mt0) REVERT: A 860 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 926 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8997 (pp) REVERT: A 957 LEU cc_start: 0.8331 (pp) cc_final: 0.8003 (mt) REVERT: C 152 ASN cc_start: 0.8619 (p0) cc_final: 0.8167 (p0) REVERT: C 305 ASP cc_start: 0.9024 (t0) cc_final: 0.8582 (t0) outliers start: 40 outliers final: 28 residues processed: 148 average time/residue: 0.0891 time to fit residues: 19.0872 Evaluate side-chains 141 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118652 restraints weight = 11408.683| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.86 r_work: 0.3043 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9527 Z= 0.106 Angle : 0.573 10.867 12937 Z= 0.282 Chirality : 0.044 0.364 1464 Planarity : 0.003 0.032 1611 Dihedral : 5.728 56.811 1245 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.44 % Allowed : 23.97 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.25), residues: 1130 helix: -0.19 (0.24), residues: 505 sheet: -1.03 (0.44), residues: 150 loop : -1.89 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.017 0.001 TYR A 879 PHE 0.014 0.001 PHE A1032 TRP 0.019 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9519) covalent geometry : angle 0.56189 / 0.28 (12919) SS BOND : bond 0.00573 / 0.22 ( 3) SS BOND : angle 0.53991 / 0.29 ( 6) hydrogen bonds : bond 0.03319 / 2.24 ( 318) hydrogen bonds : angle 4.35512 / 3.01 ( 912) Misc. bond : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : bond 0.00215 / 0.11 ( 1) link_BETA1-4 : angle 1.23984 / 0.64 ( 3) link_NAG-ASN : bond 0.00893 / 0.34 ( 3) link_NAG-ASN : angle 4.24949 / 2.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.404 Fit side-chains REVERT: A 272 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7290 (tt) REVERT: A 355 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 359 MET cc_start: 0.9015 (ttm) cc_final: 0.8632 (ttm) REVERT: A 696 GLU cc_start: 0.6935 (mp0) cc_final: 0.6548 (pm20) REVERT: A 860 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8924 (mt) REVERT: C 152 ASN cc_start: 0.8588 (p0) cc_final: 0.8146 (p0) REVERT: C 305 ASP cc_start: 0.8993 (t0) cc_final: 0.8569 (t0) outliers start: 35 outliers final: 26 residues processed: 151 average time/residue: 0.0899 time to fit residues: 19.6926 Evaluate side-chains 136 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 110 optimal weight: 0.0370 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118466 restraints weight = 11439.084| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.92 r_work: 0.3098 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9527 Z= 0.106 Angle : 0.583 11.722 12937 Z= 0.283 Chirality : 0.043 0.361 1464 Planarity : 0.003 0.033 1611 Dihedral : 5.457 58.035 1243 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.63 % Allowed : 23.38 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1130 helix: -0.04 (0.24), residues: 502 sheet: -0.86 (0.44), residues: 150 loop : -1.79 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.018 0.001 TYR A 879 PHE 0.011 0.001 PHE A1032 TRP 0.019 0.001 TRP A 323 HIS 0.007 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9519) covalent geometry : angle 0.57273 / 0.28 (12919) SS BOND : bond 0.00385 / 0.15 ( 3) SS BOND : angle 0.60588 / 0.33 ( 6) hydrogen bonds : bond 0.03239 / 2.17 ( 318) hydrogen bonds : angle 4.30231 / 2.97 ( 912) Misc. bond : bond 0.00021 / 0.01 ( 1) link_BETA1-4 : bond 0.00146 / 0.08 ( 1) link_BETA1-4 : angle 1.02049 / 0.54 ( 3) link_NAG-ASN : bond 0.00882 / 0.33 ( 3) link_NAG-ASN : angle 4.16503 / 2.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.367 Fit side-chains REVERT: A 272 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7367 (tt) REVERT: A 355 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 359 MET cc_start: 0.9004 (ttm) cc_final: 0.8607 (ttm) REVERT: A 696 GLU cc_start: 0.6881 (mp0) cc_final: 0.6524 (pm20) REVERT: A 860 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8930 (mt) REVERT: A 1084 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (tt) REVERT: C 152 ASN cc_start: 0.8603 (p0) cc_final: 0.8159 (p0) REVERT: C 305 ASP cc_start: 0.9021 (t0) cc_final: 0.8606 (t0) outliers start: 37 outliers final: 30 residues processed: 150 average time/residue: 0.0867 time to fit residues: 18.9328 Evaluate side-chains 149 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 254 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119501 restraints weight = 11386.787| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.90 r_work: 0.3076 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9527 Z= 0.110 Angle : 0.580 10.925 12937 Z= 0.283 Chirality : 0.043 0.359 1464 Planarity : 0.003 0.034 1611 Dihedral : 5.348 58.539 1242 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.73 % Allowed : 23.58 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1130 helix: 0.02 (0.24), residues: 500 sheet: -0.79 (0.45), residues: 150 loop : -1.76 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.019 0.001 TYR A 879 PHE 0.011 0.001 PHE A 971 TRP 0.019 0.001 TRP A 323 HIS 0.012 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9519) covalent geometry : angle 0.56995 / 0.28 (12919) SS BOND : bond 0.00349 / 0.14 ( 3) SS BOND : angle 0.61371 / 0.32 ( 6) hydrogen bonds : bond 0.03234 / 2.16 ( 318) hydrogen bonds : angle 4.30578 / 2.98 ( 912) Misc. bond : bond 0.00028 / 0.01 ( 1) link_BETA1-4 : bond 0.00240 / 0.13 ( 1) link_BETA1-4 : angle 0.93107 / 0.51 ( 3) link_NAG-ASN : bond 0.00871 / 0.33 ( 3) link_NAG-ASN : angle 4.11733 / 2.43 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.388 Fit side-chains REVERT: A 113 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7843 (mtm180) REVERT: A 272 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7418 (tt) REVERT: A 355 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 359 MET cc_start: 0.9029 (ttm) cc_final: 0.8662 (ttm) REVERT: A 696 GLU cc_start: 0.6846 (mp0) cc_final: 0.6531 (pm20) REVERT: A 860 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (mt) REVERT: A 1084 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8000 (tt) REVERT: C 152 ASN cc_start: 0.8606 (p0) cc_final: 0.8161 (p0) REVERT: C 254 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8595 (m-40) REVERT: C 305 ASP cc_start: 0.9027 (t0) cc_final: 0.8589 (t0) outliers start: 38 outliers final: 31 residues processed: 152 average time/residue: 0.0933 time to fit residues: 20.5154 Evaluate side-chains 152 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 348 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 254 ASN C 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117722 restraints weight = 11362.976| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.00 r_work: 0.3052 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9527 Z= 0.154 Angle : 0.609 10.794 12937 Z= 0.296 Chirality : 0.045 0.359 1464 Planarity : 0.004 0.044 1611 Dihedral : 5.406 57.732 1242 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.83 % Allowed : 23.87 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1130 helix: 0.00 (0.24), residues: 500 sheet: -0.79 (0.44), residues: 150 loop : -1.76 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.018 0.001 TYR A 879 PHE 0.013 0.001 PHE A 971 TRP 0.019 0.001 TRP A 323 HIS 0.012 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 9519) covalent geometry : angle 0.59884 / 0.29 (12919) SS BOND : bond 0.00406 / 0.17 ( 3) SS BOND : angle 0.73304 / 0.38 ( 6) hydrogen bonds : bond 0.03421 / 2.29 ( 318) hydrogen bonds : angle 4.31701 / 2.99 ( 912) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : angle 0.63769 / 0.37 ( 3) link_NAG-ASN : bond 0.00860 / 0.33 ( 3) link_NAG-ASN : angle 4.21564 / 2.48 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.49 seconds wall clock time: 41 minutes 42.31 seconds (2502.31 seconds total)