Starting phenix.real_space_refine on Sun Jun 8 07:33:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bss_30165/06_2025/7bss_30165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bss_30165/06_2025/7bss_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_30165/06_2025/7bss_30165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bss_30165/06_2025/7bss_30165.map" model { file = "/net/cci-nas-00/data/ceres_data/7bss_30165/06_2025/7bss_30165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bss_30165/06_2025/7bss_30165.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.52, per 1000 atoms: 0.59 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: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.00 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: 2.87 Time building geometry restraints manager: 2.83 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 - 22.34: 5134 22.34 - 44.69: 465 44.69 - 67.03: 61 67.03 - 89.37: 22 89.37 - 111.72: 5 Dihedral angle restraints: 5687 sinusoidal: 2341 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 5684 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.590 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 17.071 111.717 3520 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.003 TRP A 323 HIS 0.005 0.001 HIS A 929 PHE 0.016 0.002 PHE C 214 TYR 0.022 0.002 TYR C 297 ARG 0.003 0.000 ARG A1016 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 3) link_NAG-ASN : angle 5.35686 ( 9) link_BETA1-4 : bond 0.43291 ( 1) link_BETA1-4 : angle 17.12130 ( 3) hydrogen bonds : bond 0.30334 ( 318) hydrogen bonds : angle 11.16704 ( 912) SS BOND : bond 0.00606 ( 3) SS BOND : angle 1.31725 ( 6) covalent geometry : bond 0.01045 ( 9519) covalent geometry : angle 1.23368 (12919) Misc. bond : bond 0.02119 ( 1) *********************** 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 : 1.045 Fit side-chains revert: symmetry clash 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: 0.8313 (m-80) outliers start: 57 outliers final: 40 residues processed: 171 average time/residue: 0.2464 time to fit residues: 57.7552 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 : 0.991 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3717 r_free = 0.3717 target = 0.154186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113918 restraints weight = 11428.570| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.81 r_work: 0.3041 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1537 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= 0.139 Angle : 0.667 10.582 12937 Z= 0.332 Chirality : 0.045 0.356 1464 Planarity : 0.004 0.034 1611 Dihedral : 10.637 77.533 1403 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.83 % Allowed : 21.12 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.21), residues: 1130 helix: -2.66 (0.18), residues: 500 sheet: -2.50 (0.38), residues: 157 loop : -2.72 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.004 0.001 HIS A 929 PHE 0.015 0.001 PHE A 894 TYR 0.012 0.001 TYR A 324 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00934 ( 3) link_NAG-ASN : angle 5.11824 ( 9) link_BETA1-4 : bond 0.01158 ( 1) link_BETA1-4 : angle 3.88601 ( 3) hydrogen bonds : bond 0.05025 ( 318) hydrogen bonds : angle 5.64665 ( 912) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.17678 ( 6) covalent geometry : bond 0.00311 ( 9519) covalent geometry : angle 0.65022 (12919) Misc. bond : bond 0.00080 ( 1) *********************** 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 164 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.990 Fit side-chains REVERT: A 121 ASN cc_start: 0.7413 (p0) cc_final: 0.7182 (p0) REVERT: A 139 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 153 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 272 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7260 (tt) REVERT: A 330 LYS cc_start: 0.8511 (tmtt) cc_final: 0.7899 (ttmt) REVERT: A 760 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 819 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8180 (p0) REVERT: C 146 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: C 152 ASN cc_start: 0.8576 (p0) cc_final: 0.8176 (p0) REVERT: C 209 ASP cc_start: 0.8556 (p0) cc_final: 0.8308 (p0) REVERT: C 305 ASP cc_start: 0.8946 (t0) cc_final: 0.8469 (t0) outliers start: 39 outliers final: 16 residues processed: 160 average time/residue: 0.2236 time to fit residues: 50.3635 Evaluate side-chains 131 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 77 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 87 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 overall best weight: 0.9896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114889 restraints weight = 11578.461| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3051 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1908 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= 0.133 Angle : 0.631 10.599 12937 Z= 0.311 Chirality : 0.045 0.369 1464 Planarity : 0.004 0.037 1611 Dihedral : 7.839 59.537 1352 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.23), residues: 1130 helix: -1.68 (0.21), residues: 500 sheet: -2.08 (0.40), residues: 144 loop : -2.36 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.008 0.001 HIS C 302 PHE 0.018 0.001 PHE A1032 TYR 0.012 0.001 TYR A 324 ARG 0.006 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00951 ( 3) link_NAG-ASN : angle 4.68297 ( 9) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 3.33463 ( 3) hydrogen bonds : bond 0.04184 ( 318) hydrogen bonds : angle 5.08414 ( 912) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.81847 ( 6) covalent geometry : bond 0.00301 ( 9519) covalent geometry : angle 0.61713 (12919) Misc. bond : bond 0.00052 ( 1) *********************** 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 158 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.098 Fit side-chains REVERT: A 121 ASN cc_start: 0.7428 (p0) cc_final: 0.6719 (p0) REVERT: A 122 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8075 (mmtt) REVERT: A 153 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 272 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.6913 (tt) REVERT: A 330 LYS cc_start: 0.8446 (tmtt) cc_final: 0.7812 (ttpt) REVERT: A 355 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8893 (mp) REVERT: A 860 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (mt) REVERT: C 146 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: C 152 ASN cc_start: 0.8582 (p0) cc_final: 0.8179 (p0) REVERT: C 305 ASP cc_start: 0.8986 (t0) cc_final: 0.8504 (t0) outliers start: 36 outliers final: 17 residues processed: 152 average time/residue: 0.2120 time to fit residues: 45.5056 Evaluate side-chains 133 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 222 VAL 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 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 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 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 110 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 46 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3762 r_free = 0.3762 target = 0.158417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118223 restraints weight = 11401.547| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.82 r_work: 0.3086 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9527 Z= 0.110 Angle : 0.589 10.450 12937 Z= 0.291 Chirality : 0.044 0.372 1464 Planarity : 0.004 0.035 1611 Dihedral : 6.465 59.737 1345 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.93 % Allowed : 21.71 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1130 helix: -1.11 (0.22), residues: 508 sheet: -1.67 (0.42), residues: 142 loop : -2.17 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.012 0.001 PHE A 995 TYR 0.017 0.001 TYR A 879 ARG 0.006 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.01013 ( 3) link_NAG-ASN : angle 4.31241 ( 9) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 2.96916 ( 3) hydrogen bonds : bond 0.03630 ( 318) hydrogen bonds : angle 4.75017 ( 912) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.61356 ( 6) covalent geometry : bond 0.00247 ( 9519) covalent geometry : angle 0.57651 (12919) Misc. bond : bond 0.00020 ( 1) *********************** 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 165 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.028 Fit side-chains REVERT: A 121 ASN cc_start: 0.7375 (p0) cc_final: 0.7038 (p0) REVERT: A 153 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 272 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7310 (tt) REVERT: A 355 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8863 (mp) REVERT: A 696 GLU cc_start: 0.6781 (mp0) cc_final: 0.6468 (mp0) REVERT: A 794 GLN cc_start: 0.8518 (mt0) cc_final: 0.8316 (mt0) REVERT: A 860 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 79 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: C 152 ASN cc_start: 0.8551 (p0) cc_final: 0.8156 (p0) REVERT: C 305 ASP cc_start: 0.8983 (t0) cc_final: 0.8555 (t0) outliers start: 40 outliers final: 24 residues processed: 160 average time/residue: 0.2224 time to fit residues: 50.0736 Evaluate side-chains 147 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 127 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 296 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 879 TYR 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 62 ILE Chi-restraints excluded: chain C residue 79 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3695 r_free = 0.3695 target = 0.152294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111876 restraints weight = 11589.630| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.95 r_work: 0.2988 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9527 Z= 0.251 Angle : 0.678 11.304 12937 Z= 0.336 Chirality : 0.048 0.379 1464 Planarity : 0.004 0.038 1611 Dihedral : 6.615 59.149 1344 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.91 % Allowed : 21.61 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.24), residues: 1130 helix: -1.17 (0.22), residues: 506 sheet: -1.99 (0.39), residues: 163 loop : -2.07 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.017 0.002 PHE A 995 TYR 0.019 0.002 TYR A 324 ARG 0.007 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.01200 ( 3) link_NAG-ASN : angle 4.78440 ( 9) link_BETA1-4 : bond 0.00083 ( 1) link_BETA1-4 : angle 1.31809 ( 3) hydrogen bonds : bond 0.04453 ( 318) hydrogen bonds : angle 4.82866 ( 912) SS BOND : bond 0.00718 ( 3) SS BOND : angle 1.11195 ( 6) covalent geometry : bond 0.00601 ( 9519) covalent geometry : angle 0.66583 (12919) Misc. bond : bond 0.00148 ( 1) *********************** 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 164 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 1.005 Fit side-chains REVERT: A 121 ASN cc_start: 0.7631 (p0) cc_final: 0.7402 (p0) REVERT: A 266 MET cc_start: 0.7903 (mmt) cc_final: 0.7670 (mmp) REVERT: A 272 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7248 (tt) REVERT: A 330 LYS cc_start: 0.8462 (tmtt) cc_final: 0.7817 (ttpt) REVERT: A 355 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 359 MET cc_start: 0.9126 (ttm) cc_final: 0.8710 (ttm) REVERT: A 696 GLU cc_start: 0.6921 (mp0) cc_final: 0.6522 (mp0) REVERT: A 714 ARG cc_start: 0.5977 (mmm160) cc_final: 0.5642 (mmm160) REVERT: A 860 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8999 (mt) REVERT: C 152 ASN cc_start: 0.8613 (p0) cc_final: 0.8169 (p0) REVERT: C 248 ASP cc_start: 0.8535 (t70) cc_final: 0.8084 (t0) REVERT: C 305 ASP cc_start: 0.8992 (t0) cc_final: 0.8541 (t0) outliers start: 50 outliers final: 33 residues processed: 158 average time/residue: 0.2091 time to fit residues: 46.8382 Evaluate side-chains 144 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 385 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 786 LEU 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 62 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 192 SER 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 342 VAL 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 54 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 108 optimal weight: 0.0370 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117463 restraints weight = 11348.488| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.82 r_work: 0.3063 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2511 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= 0.109 Angle : 0.577 10.323 12937 Z= 0.286 Chirality : 0.044 0.406 1464 Planarity : 0.003 0.033 1611 Dihedral : 6.068 57.544 1344 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 22.99 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 1130 helix: -0.77 (0.22), residues: 512 sheet: -1.63 (0.41), residues: 155 loop : -1.96 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.004 0.001 HIS C 302 PHE 0.012 0.001 PHE A 894 TYR 0.018 0.001 TYR A 879 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.01338 ( 3) link_NAG-ASN : angle 4.35739 ( 9) link_BETA1-4 : bond 0.00125 ( 1) link_BETA1-4 : angle 1.95210 ( 3) hydrogen bonds : bond 0.03520 ( 318) hydrogen bonds : angle 4.57753 ( 912) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.59595 ( 6) covalent geometry : bond 0.00245 ( 9519) covalent geometry : angle 0.56456 (12919) Misc. bond : bond 0.00035 ( 1) *********************** 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 153 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.070 Fit side-chains REVERT: A 121 ASN cc_start: 0.7486 (p0) cc_final: 0.7097 (p0) REVERT: A 266 MET cc_start: 0.7951 (mmt) cc_final: 0.7751 (mmp) REVERT: A 272 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7303 (tt) REVERT: A 355 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8901 (mp) REVERT: A 359 MET cc_start: 0.9084 (ttm) cc_final: 0.8731 (ttm) REVERT: A 696 GLU cc_start: 0.6862 (mp0) cc_final: 0.6570 (mp0) REVERT: A 794 GLN cc_start: 0.8544 (mt0) cc_final: 0.8342 (mt0) REVERT: A 860 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8937 (mt) REVERT: C 152 ASN cc_start: 0.8584 (p0) cc_final: 0.8159 (p0) REVERT: C 305 ASP cc_start: 0.8950 (t0) cc_final: 0.8520 (t0) outliers start: 33 outliers final: 25 residues processed: 146 average time/residue: 0.2169 time to fit residues: 44.7257 Evaluate side-chains 143 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 786 LEU 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 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 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 52 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.157979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117004 restraints weight = 11501.017| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.90 r_work: 0.2997 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2691 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= 0.114 Angle : 0.573 11.109 12937 Z= 0.284 Chirality : 0.043 0.381 1464 Planarity : 0.003 0.032 1611 Dihedral : 5.826 58.105 1344 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.03 % Allowed : 22.50 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 1130 helix: -0.44 (0.23), residues: 506 sheet: -1.44 (0.42), residues: 155 loop : -1.89 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.004 0.001 HIS C 302 PHE 0.012 0.001 PHE A 971 TYR 0.017 0.001 TYR A 879 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 3) link_NAG-ASN : angle 4.51974 ( 9) link_BETA1-4 : bond 0.00230 ( 1) link_BETA1-4 : angle 1.36360 ( 3) hydrogen bonds : bond 0.03433 ( 318) hydrogen bonds : angle 4.41553 ( 912) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.65127 ( 6) covalent geometry : bond 0.00263 ( 9519) covalent geometry : angle 0.55997 (12919) Misc. bond : bond 0.00020 ( 1) *********************** 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 160 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.082 Fit side-chains REVERT: A 121 ASN cc_start: 0.7459 (p0) cc_final: 0.7207 (p0) REVERT: A 272 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7297 (tt) REVERT: A 355 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 359 MET cc_start: 0.9087 (ttm) cc_final: 0.8723 (ttm) REVERT: A 696 GLU cc_start: 0.6967 (mp0) cc_final: 0.6512 (mp0) REVERT: A 794 GLN cc_start: 0.8550 (mt0) cc_final: 0.8340 (mt0) REVERT: A 860 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8934 (mt) REVERT: A 926 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9032 (pp) REVERT: A 957 LEU cc_start: 0.8265 (pp) cc_final: 0.7990 (mt) REVERT: C 79 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: C 152 ASN cc_start: 0.8591 (p0) cc_final: 0.8155 (p0) REVERT: C 209 ASP cc_start: 0.8461 (p0) cc_final: 0.8130 (p0) REVERT: C 305 ASP cc_start: 0.9019 (t0) cc_final: 0.8593 (t0) outliers start: 41 outliers final: 28 residues processed: 156 average time/residue: 0.2165 time to fit residues: 47.9629 Evaluate side-chains 149 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 127 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 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 786 LEU 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 29 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 192 SER 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 314 THR 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 49 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115868 restraints weight = 11587.912| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.94 r_work: 0.3043 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2644 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= 0.142 Angle : 0.591 11.377 12937 Z= 0.293 Chirality : 0.045 0.374 1464 Planarity : 0.003 0.033 1611 Dihedral : 5.839 57.687 1344 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.73 % Allowed : 23.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1130 helix: -0.37 (0.23), residues: 505 sheet: -1.44 (0.41), residues: 162 loop : -1.83 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.012 0.001 HIS C 302 PHE 0.014 0.001 PHE A 971 TYR 0.016 0.001 TYR A 324 ARG 0.007 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.01071 ( 3) link_NAG-ASN : angle 4.64579 ( 9) link_BETA1-4 : bond 0.00251 ( 1) link_BETA1-4 : angle 0.99726 ( 3) hydrogen bonds : bond 0.03641 ( 318) hydrogen bonds : angle 4.41785 ( 912) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.79171 ( 6) covalent geometry : bond 0.00338 ( 9519) covalent geometry : angle 0.57791 (12919) Misc. bond : bond 0.00070 ( 1) *********************** 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 155 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.068 Fit side-chains REVERT: A 121 ASN cc_start: 0.7475 (p0) cc_final: 0.7200 (p0) REVERT: A 272 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7317 (tt) REVERT: A 355 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 696 GLU cc_start: 0.6938 (mp0) cc_final: 0.6487 (mp0) REVERT: A 794 GLN cc_start: 0.8572 (mt0) cc_final: 0.8362 (mt0) REVERT: A 860 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 957 LEU cc_start: 0.8294 (pp) cc_final: 0.8049 (mt) REVERT: C 79 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: C 152 ASN cc_start: 0.8613 (p0) cc_final: 0.8166 (p0) REVERT: C 305 ASP cc_start: 0.9009 (t0) cc_final: 0.8587 (t0) outliers start: 38 outliers final: 27 residues processed: 151 average time/residue: 0.2139 time to fit residues: 45.7042 Evaluate side-chains 142 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 127 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 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 786 LEU 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 53 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 79 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 0.0030 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119808 restraints weight = 11373.137| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.86 r_work: 0.3107 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2962 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= 0.100 Angle : 0.568 12.096 12937 Z= 0.278 Chirality : 0.043 0.365 1464 Planarity : 0.003 0.032 1611 Dihedral : 5.389 59.746 1342 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.14 % Allowed : 24.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 1130 helix: -0.02 (0.24), residues: 502 sheet: -0.96 (0.44), residues: 150 loop : -1.79 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 323 HIS 0.002 0.001 HIS A 929 PHE 0.010 0.001 PHE A 995 TYR 0.020 0.001 TYR A 879 ARG 0.007 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.01005 ( 3) link_NAG-ASN : angle 4.42077 ( 9) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.01747 ( 3) hydrogen bonds : bond 0.03162 ( 318) hydrogen bonds : angle 4.29467 ( 912) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.54730 ( 6) covalent geometry : bond 0.00224 ( 9519) covalent geometry : angle 0.55575 (12919) Misc. bond : bond 0.00020 ( 1) *********************** 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 155 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.067 Fit side-chains REVERT: A 121 ASN cc_start: 0.7376 (p0) cc_final: 0.7118 (p0) REVERT: A 272 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 355 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 359 MET cc_start: 0.8964 (ttm) cc_final: 0.8530 (ttm) REVERT: A 696 GLU cc_start: 0.6886 (mp0) cc_final: 0.6563 (mp0) REVERT: A 860 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (mt) REVERT: A 1084 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8014 (tt) REVERT: C 152 ASN cc_start: 0.8565 (p0) cc_final: 0.8131 (p0) REVERT: C 209 ASP cc_start: 0.8275 (p0) cc_final: 0.7654 (p0) REVERT: C 305 ASP cc_start: 0.8998 (t0) cc_final: 0.8574 (t0) outliers start: 32 outliers final: 23 residues processed: 153 average time/residue: 0.2337 time to fit residues: 50.3504 Evaluate side-chains 140 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 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 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 77 GLU Chi-restraints excluded: chain C residue 192 SER 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 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114701 restraints weight = 11579.083| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.08 r_work: 0.2918 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9527 Z= 0.210 Angle : 0.655 11.700 12937 Z= 0.321 Chirality : 0.047 0.374 1464 Planarity : 0.004 0.042 1611 Dihedral : 5.672 56.200 1341 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.44 % Allowed : 23.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.25), residues: 1130 helix: -0.27 (0.23), residues: 507 sheet: -1.32 (0.43), residues: 155 loop : -1.71 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.015 0.002 PHE A 971 TYR 0.021 0.002 TYR A 879 ARG 0.007 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.01061 ( 3) link_NAG-ASN : angle 4.82034 ( 9) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 0.89413 ( 3) hydrogen bonds : bond 0.03900 ( 318) hydrogen bonds : angle 4.45000 ( 912) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.05629 ( 6) covalent geometry : bond 0.00508 ( 9519) covalent geometry : angle 0.64211 (12919) Misc. bond : bond 0.00144 ( 1) ********************** 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 151 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.031 Fit side-chains REVERT: A 121 ASN cc_start: 0.7489 (p0) cc_final: 0.7103 (p0) REVERT: A 272 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 330 LYS cc_start: 0.8378 (tmtt) cc_final: 0.7728 (ttpt) REVERT: A 355 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 696 GLU cc_start: 0.6669 (mp0) cc_final: 0.6269 (mp0) REVERT: A 860 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8954 (mt) REVERT: A 957 LEU cc_start: 0.8310 (pp) cc_final: 0.8046 (mt) REVERT: C 79 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: C 152 ASN cc_start: 0.8655 (p0) cc_final: 0.8180 (p0) REVERT: C 305 ASP cc_start: 0.9086 (t0) cc_final: 0.8597 (t0) outliers start: 35 outliers final: 28 residues processed: 147 average time/residue: 0.2060 time to fit residues: 43.2774 Evaluate side-chains 146 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 83 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 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 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 786 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 885 ILE 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 77 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 192 SER 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 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 41 optimal weight: 4.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116930 restraints weight = 11479.741| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.90 r_work: 0.3065 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2839 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= 0.138 Angle : 0.619 11.451 12937 Z= 0.301 Chirality : 0.045 0.374 1464 Planarity : 0.003 0.035 1611 Dihedral : 5.533 56.458 1341 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 24.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1130 helix: -0.09 (0.24), residues: 500 sheet: -1.08 (0.42), residues: 157 loop : -1.75 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.003 0.001 HIS A 929 PHE 0.013 0.001 PHE A 971 TYR 0.019 0.001 TYR A 879 ARG 0.007 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.01017 ( 3) link_NAG-ASN : angle 4.69031 ( 9) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 0.86135 ( 3) hydrogen bonds : bond 0.03490 ( 318) hydrogen bonds : angle 4.40464 ( 912) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.72617 ( 6) covalent geometry : bond 0.00330 ( 9519) covalent geometry : angle 0.60617 (12919) Misc. bond : bond 0.00078 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5102.56 seconds wall clock time: 88 minutes 53.67 seconds (5333.67 seconds total)