Starting phenix.real_space_refine on Fri Jul 3 00:06:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vsh_32111/07_2026/7vsh_32111.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 58 5.16 5 C 7106 2.51 5 N 1800 2.21 5 O 2022 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 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10992 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8300 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 25, 'TRANS': 298} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, '17F': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'17F:plan-1': 1, '17F:plan-2': 1, '17F:plan-3': 1, '17F:plan-5': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.07, per 1000 atoms: 0.19 Number of scatterers: 10992 At special positions: 0 Unit cell: (110.39, 87.15, 158.53, 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 58 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2022 8.00 N 1800 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG B 2 " - " MAN B 3 " BETA1-3 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 406.5 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 49.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 88 through 122 Proline residue: A 94 - end of helix removed outlier: 3.605A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.683A pdb=" N ASN A 273 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 282 through 314 removed outlier: 3.565A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.020A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.613A pdb=" N GLY A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.527A pdb=" N LEU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.725A pdb=" N THR A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.719A pdb=" N ILE A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 574 through 591 removed outlier: 3.714A pdb=" N ILE A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.531A pdb=" N ARG A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 633 removed outlier: 3.524A pdb=" N PHE A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.621A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 726 removed outlier: 3.696A pdb=" N LYS A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 718 " --> pdb=" O ARG A 714 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.733A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 853 through 861 removed outlier: 4.346A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 895 removed outlier: 3.599A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.160A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 4.803A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 924 removed outlier: 3.621A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.670A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.887A pdb=" N SER A 946 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 removed outlier: 3.665A 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 976 removed outlier: 3.596A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 980 removed outlier: 3.618A pdb=" N THR A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.595A pdb=" N PHE A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.635A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.820A pdb=" N TRP A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1090 removed outlier: 3.543A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 75 Proline residue: C 52 - end of helix removed outlier: 4.319A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix removed outlier: 3.858A pdb=" N ILE C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.024A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.516A pdb=" N LYS C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.566A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.804A pdb=" N CYS C 157 " --> pdb=" O SER C 154 " (cutoff:3.500A) Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.550A pdb=" N LYS C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.785A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.685A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.706A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.613A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 322 through 350 removed outlier: 4.747A pdb=" N GLY C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.515A pdb=" N LEU A 239 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 11.755A pdb=" N THR A 124 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN A 150 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 260 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.620A 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: 6.657A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 788 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 751 " --> pdb=" O CYS A 788 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 422 removed outlier: 5.594A pdb=" N SER A 418 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 651 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 647 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 512 removed outlier: 5.641A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 540 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 546 " --> pdb=" O PHE A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 7.150A pdb=" N VAL A 598 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.558A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 104 through 109 removed outlier: 4.520A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3451 1.34 - 1.46: 2146 1.46 - 1.58: 5555 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11243 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.801 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.797 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.443 -0.040 2.00e-02 2.50e+03 3.90e+00 ... (remaining 11238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.19: 15226 14.19 - 28.38: 4 28.38 - 42.57: 0 42.57 - 56.76: 0 56.76 - 70.94: 2 Bond angle restraints: 15232 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.62 -70.94 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.50 -69.87 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.06 20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.58 20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.68 19.34 3.00e+00 1.11e-01 4.15e+01 ... (remaining 15227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5994 17.14 - 34.28: 536 34.28 - 51.43: 102 51.43 - 68.57: 17 68.57 - 85.71: 9 Dihedral angle restraints: 6658 sinusoidal: 2689 harmonic: 3969 Sorted by residual: dihedral pdb=" CA THR A 51 " pdb=" C THR A 51 " pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 941 " pdb=" C LEU A 941 " pdb=" N TYR A 942 " pdb=" CA TYR A 942 " ideal model delta harmonic sigma weight residual 180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+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 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1561 0.072 - 0.145: 155 0.145 - 0.217: 5 0.217 - 0.289: 1 0.289 - 0.362: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.27e+02 chirality pdb=" C1 MAN B 3 " pdb=" O3 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1720 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.320 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG C 401 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.317 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG C 402 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.194 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.218 2.00e-02 2.50e+03 1.85e-01 4.30e+02 pdb=" C7 NAG B 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.303 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.169 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 52 2.55 - 3.14: 8655 3.14 - 3.73: 16581 3.73 - 4.31: 24092 4.31 - 4.90: 39963 Nonbonded interactions: 89343 Sorted by model distance: nonbonded pdb="MG MG A1100 " pdb=" F1 ALF A1101 " model vdw 1.964 2.120 nonbonded pdb=" OH TYR A 311 " pdb=" OD2 ASP A 343 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN C 176 " pdb=" OD1 ASN C 235 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR A 484 " pdb=" O ALA A 487 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 2.281 3.040 ... (remaining 89338 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: 1.280 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.005 0.117 11251 Z= 0.212 Angle : 1.088 70.944 15253 Z= 0.454 Chirality : 0.044 0.362 1723 Planarity : 0.011 0.274 1917 Dihedral : 13.449 85.712 4087 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1342 helix: -0.57 (0.21), residues: 565 sheet: -0.13 (0.37), residues: 192 loop : -1.70 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 723 TYR 0.016 0.002 TYR A1054 PHE 0.029 0.002 PHE A 978 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (11243) covalent geometry : angle 1.07467 / 0.45 (15232) SS BOND : bond 0.00614 / 0.24 ( 3) SS BOND : angle 0.87965 / 0.46 ( 6) hydrogen bonds : bond 0.26629 / 16.57 ( 476) hydrogen bonds : angle 8.57156 / 6.07 ( 1353) link_ALPHA1-3 : bond 0.01926 / 1.01 ( 1) link_ALPHA1-3 : angle 2.98823 / 1.37 ( 3) link_BETA1-3 : bond 0.04376 / 2.30 ( 1) link_BETA1-3 : angle 10.37699 / 4.84 ( 3) link_NAG-ASN : bond 0.00294 / 0.13 ( 3) link_NAG-ASN : angle 3.30729 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.333 Fit side-chains REVERT: A 205 LEU cc_start: 0.7316 (tp) cc_final: 0.7008 (tp) REVERT: A 629 MET cc_start: 0.6772 (mmp) cc_final: 0.5886 (mtp) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.0945 time to fit residues: 20.0808 Evaluate side-chains 113 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 457 ASN A 536 HIS A 584 HIS ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120997 restraints weight = 14286.710| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.15 r_work: 0.3164 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11251 Z= 0.125 Angle : 0.574 6.820 15253 Z= 0.300 Chirality : 0.043 0.291 1723 Planarity : 0.004 0.042 1917 Dihedral : 5.032 50.084 1482 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.00 % Allowed : 5.58 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1342 helix: 0.54 (0.21), residues: 575 sheet: 0.07 (0.37), residues: 190 loop : -1.62 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 723 TYR 0.018 0.001 TYR A 324 PHE 0.018 0.001 PHE C 179 TRP 0.012 0.001 TRP A 323 HIS 0.014 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (11243) covalent geometry : angle 0.56655 / 0.30 (15232) SS BOND : bond 0.00436 / 0.17 ( 3) SS BOND : angle 0.97368 / 0.50 ( 6) hydrogen bonds : bond 0.05412 / 3.38 ( 476) hydrogen bonds : angle 5.41268 / 3.80 ( 1353) link_ALPHA1-3 : bond 0.00306 / 0.16 ( 1) link_ALPHA1-3 : angle 1.79224 / 0.94 ( 3) link_BETA1-3 : bond 0.00314 / 0.17 ( 1) link_BETA1-3 : angle 2.47184 / 1.24 ( 3) link_NAG-ASN : bond 0.00693 / 0.30 ( 3) link_NAG-ASN : angle 3.34485 / 1.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.259 Fit side-chains REVERT: A 716 HIS cc_start: 0.6271 (m90) cc_final: 0.6054 (m90) REVERT: A 942 TYR cc_start: 0.7837 (m-80) cc_final: 0.7623 (m-80) REVERT: C 55 PHE cc_start: 0.7287 (m-80) cc_final: 0.6964 (m-80) REVERT: C 303 TYR cc_start: 0.8560 (m-80) cc_final: 0.7997 (m-80) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.0908 time to fit residues: 17.4461 Evaluate side-chains 115 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.151925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116976 restraints weight = 14472.588| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.41 r_work: 0.3068 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11251 Z= 0.216 Angle : 0.627 8.210 15253 Z= 0.323 Chirality : 0.046 0.301 1723 Planarity : 0.005 0.036 1917 Dihedral : 5.135 52.291 1482 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.25 % Allowed : 9.24 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1342 helix: 0.65 (0.21), residues: 589 sheet: 0.03 (0.36), residues: 194 loop : -1.74 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 723 TYR 0.020 0.002 TYR A 71 PHE 0.023 0.002 PHE A 633 TRP 0.016 0.002 TRP A 323 HIS 0.011 0.002 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (11243) covalent geometry : angle 0.62051 / 0.32 (15232) SS BOND : bond 0.00549 / 0.23 ( 3) SS BOND : angle 1.23475 / 0.60 ( 6) hydrogen bonds : bond 0.05339 / 3.35 ( 476) hydrogen bonds : angle 5.04277 / 3.57 ( 1353) link_ALPHA1-3 : bond 0.00239 / 0.13 ( 1) link_ALPHA1-3 : angle 2.56284 / 1.34 ( 3) link_BETA1-3 : bond 0.00107 / 0.06 ( 1) link_BETA1-3 : angle 3.18234 / 1.71 ( 3) link_NAG-ASN : bond 0.00517 / 0.24 ( 3) link_NAG-ASN : angle 2.77217 / 1.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.424 Fit side-chains REVERT: A 258 TYR cc_start: 0.8248 (m-10) cc_final: 0.7963 (m-10) REVERT: A 399 GLU cc_start: 0.8884 (tp30) cc_final: 0.8646 (mm-30) REVERT: A 678 MET cc_start: 0.8371 (tmm) cc_final: 0.8044 (tmm) REVERT: A 716 HIS cc_start: 0.6514 (m90) cc_final: 0.6303 (m90) REVERT: A 942 TYR cc_start: 0.7921 (m-80) cc_final: 0.7528 (m-80) REVERT: C 55 PHE cc_start: 0.7161 (m-80) cc_final: 0.6878 (m-80) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.0938 time to fit residues: 18.1597 Evaluate side-chains 119 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 524 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118094 restraints weight = 14548.845| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.37 r_work: 0.3081 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11251 Z= 0.191 Angle : 0.586 7.754 15253 Z= 0.304 Chirality : 0.045 0.270 1723 Planarity : 0.004 0.036 1917 Dihedral : 5.064 51.593 1482 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.58 % Allowed : 11.49 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1342 helix: 0.73 (0.21), residues: 587 sheet: 0.03 (0.36), residues: 194 loop : -1.74 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 723 TYR 0.016 0.002 TYR A 71 PHE 0.018 0.002 PHE A 633 TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (11243) covalent geometry : angle 0.57973 / 0.30 (15232) SS BOND : bond 0.00556 / 0.23 ( 3) SS BOND : angle 1.16859 / 0.55 ( 6) hydrogen bonds : bond 0.04730 / 2.98 ( 476) hydrogen bonds : angle 4.83492 / 3.43 ( 1353) link_ALPHA1-3 : bond 0.00006 / 0.00 ( 1) link_ALPHA1-3 : angle 2.29612 / 1.21 ( 3) link_BETA1-3 : bond 0.00110 / 0.06 ( 1) link_BETA1-3 : angle 3.26752 / 1.75 ( 3) link_NAG-ASN : bond 0.00467 / 0.21 ( 3) link_NAG-ASN : angle 2.68993 / 1.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.430 Fit side-chains REVERT: A 258 TYR cc_start: 0.8055 (m-10) cc_final: 0.7832 (m-10) REVERT: A 629 MET cc_start: 0.6486 (mmt) cc_final: 0.6232 (mmt) REVERT: A 678 MET cc_start: 0.8312 (tmm) cc_final: 0.7981 (tmm) REVERT: A 942 TYR cc_start: 0.7723 (m-80) cc_final: 0.7385 (m-80) REVERT: C 55 PHE cc_start: 0.7122 (m-80) cc_final: 0.6881 (m-80) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.0925 time to fit residues: 17.6147 Evaluate side-chains 122 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 844 ASN ** A 864 HIS ** 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 = 0.3851 r_free = 0.3851 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120605 restraints weight = 14250.832| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.07 r_work: 0.3155 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11251 Z= 0.112 Angle : 0.516 6.776 15253 Z= 0.267 Chirality : 0.042 0.284 1723 Planarity : 0.004 0.035 1917 Dihedral : 4.702 50.251 1482 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.08 % Allowed : 13.16 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1342 helix: 1.12 (0.21), residues: 576 sheet: 0.15 (0.36), residues: 197 loop : -1.71 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 723 TYR 0.016 0.001 TYR A 324 PHE 0.021 0.001 PHE A 421 TRP 0.012 0.001 TRP A 323 HIS 0.011 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11243) covalent geometry : angle 0.51088 / 0.27 (15232) SS BOND : bond 0.00372 / 0.16 ( 3) SS BOND : angle 0.81929 / 0.40 ( 6) hydrogen bonds : bond 0.03933 / 2.48 ( 476) hydrogen bonds : angle 4.55465 / 3.22 ( 1353) link_ALPHA1-3 : bond 0.00448 / 0.24 ( 1) link_ALPHA1-3 : angle 1.92410 / 1.04 ( 3) link_BETA1-3 : bond 0.00373 / 0.20 ( 1) link_BETA1-3 : angle 2.94543 / 1.49 ( 3) link_NAG-ASN : bond 0.00435 / 0.19 ( 3) link_NAG-ASN : angle 2.38130 / 1.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.361 Fit side-chains REVERT: A 252 LYS cc_start: 0.8062 (tppt) cc_final: 0.7098 (tmtt) REVERT: A 258 TYR cc_start: 0.8186 (m-10) cc_final: 0.7858 (m-10) REVERT: A 629 MET cc_start: 0.6822 (mmt) cc_final: 0.6558 (mmt) REVERT: A 631 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6702 (mtmt) REVERT: A 678 MET cc_start: 0.8356 (tmm) cc_final: 0.8044 (tmm) REVERT: A 942 TYR cc_start: 0.7833 (m-80) cc_final: 0.7568 (m-80) REVERT: A 943 MET cc_start: 0.8208 (tpt) cc_final: 0.6121 (tpt) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.0966 time to fit residues: 18.2959 Evaluate side-chains 120 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 HIS ** 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 = 0.3821 r_free = 0.3821 target = 0.152939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118335 restraints weight = 14458.387| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.31 r_work: 0.3100 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11251 Z= 0.168 Angle : 0.560 7.523 15253 Z= 0.289 Chirality : 0.044 0.271 1723 Planarity : 0.004 0.036 1917 Dihedral : 4.825 51.983 1482 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.83 % Allowed : 13.49 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.23), residues: 1342 helix: 1.06 (0.21), residues: 576 sheet: 0.25 (0.36), residues: 193 loop : -1.69 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 723 TYR 0.015 0.001 TYR A 71 PHE 0.018 0.002 PHE A 633 TRP 0.014 0.001 TRP A 323 HIS 0.011 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (11243) covalent geometry : angle 0.55368 / 0.29 (15232) SS BOND : bond 0.00472 / 0.20 ( 3) SS BOND : angle 1.10164 / 0.52 ( 6) hydrogen bonds : bond 0.04342 / 2.74 ( 476) hydrogen bonds : angle 4.58110 / 3.24 ( 1353) link_ALPHA1-3 : bond 0.00081 / 0.04 ( 1) link_ALPHA1-3 : angle 2.19630 / 1.16 ( 3) link_BETA1-3 : bond 0.00193 / 0.10 ( 1) link_BETA1-3 : angle 3.17605 / 1.70 ( 3) link_NAG-ASN : bond 0.00492 / 0.22 ( 3) link_NAG-ASN : angle 2.48102 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.319 Fit side-chains REVERT: A 145 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 252 LYS cc_start: 0.7954 (tppt) cc_final: 0.7457 (ttmt) REVERT: A 258 TYR cc_start: 0.8071 (m-10) cc_final: 0.7730 (m-10) REVERT: A 629 MET cc_start: 0.6769 (mmt) cc_final: 0.6513 (mmt) REVERT: A 631 LYS cc_start: 0.7404 (ttpt) cc_final: 0.6653 (mtmt) REVERT: A 678 MET cc_start: 0.8263 (tmm) cc_final: 0.7931 (tmm) REVERT: A 942 TYR cc_start: 0.7665 (m-80) cc_final: 0.7356 (m-80) REVERT: A 1060 MET cc_start: 0.8799 (ttm) cc_final: 0.8572 (ttp) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.0977 time to fit residues: 18.7470 Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.153816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119078 restraints weight = 14396.124| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.32 r_work: 0.3114 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11251 Z= 0.142 Angle : 0.541 7.102 15253 Z= 0.281 Chirality : 0.043 0.270 1723 Planarity : 0.004 0.037 1917 Dihedral : 4.752 51.667 1482 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 1.67 % Allowed : 14.07 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1342 helix: 1.13 (0.21), residues: 579 sheet: 0.31 (0.36), residues: 193 loop : -1.69 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.014 0.001 TYR A 324 PHE 0.017 0.001 PHE A 633 TRP 0.014 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11243) covalent geometry : angle 0.53489 / 0.28 (15232) SS BOND : bond 0.00667 / 0.26 ( 3) SS BOND : angle 1.63823 / 0.77 ( 6) hydrogen bonds : bond 0.04101 / 2.59 ( 476) hydrogen bonds : angle 4.52091 / 3.20 ( 1353) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-3 : angle 2.03959 / 1.09 ( 3) link_BETA1-3 : bond 0.00302 / 0.16 ( 1) link_BETA1-3 : angle 3.11257 / 1.63 ( 3) link_NAG-ASN : bond 0.00451 / 0.19 ( 3) link_NAG-ASN : angle 2.39384 / 1.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.413 Fit side-chains REVERT: A 145 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8151 (p0) REVERT: A 252 LYS cc_start: 0.7954 (tppt) cc_final: 0.7045 (tmtt) REVERT: A 258 TYR cc_start: 0.8045 (m-10) cc_final: 0.7649 (m-10) REVERT: A 629 MET cc_start: 0.6727 (mmt) cc_final: 0.6460 (mmt) REVERT: A 631 LYS cc_start: 0.7424 (ttpt) cc_final: 0.6678 (mtmt) REVERT: A 634 ASP cc_start: 0.7477 (t0) cc_final: 0.7254 (t0) REVERT: A 678 MET cc_start: 0.8266 (tmm) cc_final: 0.7950 (tmm) REVERT: A 942 TYR cc_start: 0.7638 (m-80) cc_final: 0.7324 (m-80) REVERT: A 943 MET cc_start: 0.8218 (tpt) cc_final: 0.5968 (tpt) REVERT: A 1060 MET cc_start: 0.8775 (ttm) cc_final: 0.8553 (ttp) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.0973 time to fit residues: 18.8770 Evaluate side-chains 128 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 HIS ** 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 = 0.3852 r_free = 0.3852 target = 0.155535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120798 restraints weight = 14226.032| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.08 r_work: 0.3166 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11251 Z= 0.111 Angle : 0.516 6.647 15253 Z= 0.266 Chirality : 0.042 0.273 1723 Planarity : 0.004 0.035 1917 Dihedral : 4.530 50.771 1480 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.67 % Allowed : 13.74 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1342 helix: 1.44 (0.22), residues: 565 sheet: 0.31 (0.36), residues: 194 loop : -1.68 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 723 TYR 0.015 0.001 TYR A 324 PHE 0.015 0.001 PHE A 633 TRP 0.012 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11243) covalent geometry : angle 0.51092 / 0.26 (15232) SS BOND : bond 0.00921 / 0.35 ( 3) SS BOND : angle 1.21879 / 0.61 ( 6) hydrogen bonds : bond 0.03738 / 2.37 ( 476) hydrogen bonds : angle 4.37709 / 3.09 ( 1353) link_ALPHA1-3 : bond 0.00457 / 0.24 ( 1) link_ALPHA1-3 : angle 1.87706 / 1.02 ( 3) link_BETA1-3 : bond 0.00456 / 0.24 ( 1) link_BETA1-3 : angle 3.02132 / 1.55 ( 3) link_NAG-ASN : bond 0.00458 / 0.19 ( 3) link_NAG-ASN : angle 2.21755 / 1.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.458 Fit side-chains REVERT: A 145 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8236 (p0) REVERT: A 193 THR cc_start: 0.8325 (p) cc_final: 0.7898 (p) REVERT: A 252 LYS cc_start: 0.8075 (tppt) cc_final: 0.7181 (tmtt) REVERT: A 258 TYR cc_start: 0.8183 (m-10) cc_final: 0.7917 (m-10) REVERT: A 629 MET cc_start: 0.6729 (mmt) cc_final: 0.6478 (mmt) REVERT: A 631 LYS cc_start: 0.7405 (ttpt) cc_final: 0.6667 (mtmt) REVERT: A 678 MET cc_start: 0.8307 (tmm) cc_final: 0.7997 (tmm) REVERT: A 942 TYR cc_start: 0.7797 (m-80) cc_final: 0.7477 (m-80) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.0872 time to fit residues: 17.3520 Evaluate side-chains 136 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 864 HIS ** 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 = 0.3796 r_free = 0.3796 target = 0.150639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116031 restraints weight = 14473.037| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.41 r_work: 0.3050 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11251 Z= 0.244 Angle : 0.634 8.182 15253 Z= 0.327 Chirality : 0.047 0.261 1723 Planarity : 0.005 0.054 1917 Dihedral : 4.967 52.500 1480 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.00 % Allowed : 14.07 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1342 helix: 0.88 (0.21), residues: 582 sheet: 0.22 (0.36), residues: 196 loop : -1.72 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 723 TYR 0.039 0.002 TYR A 722 PHE 0.022 0.002 PHE A 633 TRP 0.017 0.002 TRP A 323 HIS 0.008 0.002 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (11243) covalent geometry : angle 0.62749 / 0.33 (15232) SS BOND : bond 0.01112 / 0.43 ( 3) SS BOND : angle 1.50838 / 0.77 ( 6) hydrogen bonds : bond 0.04798 / 3.03 ( 476) hydrogen bonds : angle 4.65800 / 3.29 ( 1353) link_ALPHA1-3 : bond 0.00057 / 0.03 ( 1) link_ALPHA1-3 : angle 2.49252 / 1.31 ( 3) link_BETA1-3 : bond 0.00021 / 0.01 ( 1) link_BETA1-3 : angle 3.50425 / 1.92 ( 3) link_NAG-ASN : bond 0.00612 / 0.28 ( 3) link_NAG-ASN : angle 2.53052 / 1.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.276 Fit side-chains REVERT: A 145 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (p0) REVERT: A 193 THR cc_start: 0.8322 (p) cc_final: 0.7927 (p) REVERT: A 258 TYR cc_start: 0.8097 (m-10) cc_final: 0.7823 (m-10) REVERT: A 629 MET cc_start: 0.6649 (mmt) cc_final: 0.6391 (mmt) REVERT: A 631 LYS cc_start: 0.7402 (ttpt) cc_final: 0.6573 (mtmt) REVERT: A 678 MET cc_start: 0.8311 (tmm) cc_final: 0.7953 (tmm) REVERT: A 942 TYR cc_start: 0.7747 (m-80) cc_final: 0.7423 (m-80) REVERT: C 44 ILE cc_start: 0.7779 (tp) cc_final: 0.7391 (tp) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.0833 time to fit residues: 16.4510 Evaluate side-chains 131 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 102 optimal weight: 0.0770 chunk 127 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119112 restraints weight = 14330.062| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.11 r_work: 0.3129 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11251 Z= 0.149 Angle : 0.557 7.135 15253 Z= 0.288 Chirality : 0.044 0.259 1723 Planarity : 0.004 0.053 1917 Dihedral : 4.731 48.691 1480 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.42 % Allowed : 14.49 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1342 helix: 1.19 (0.21), residues: 565 sheet: 0.21 (0.36), residues: 197 loop : -1.71 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 723 TYR 0.038 0.002 TYR A 722 PHE 0.018 0.001 PHE A 633 TRP 0.013 0.001 TRP A 323 HIS 0.009 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11243) covalent geometry : angle 0.55178 / 0.29 (15232) SS BOND : bond 0.00849 / 0.33 ( 3) SS BOND : angle 1.08665 / 0.55 ( 6) hydrogen bonds : bond 0.04184 / 2.65 ( 476) hydrogen bonds : angle 4.53052 / 3.20 ( 1353) link_ALPHA1-3 : bond 0.00227 / 0.12 ( 1) link_ALPHA1-3 : angle 2.05333 / 1.09 ( 3) link_BETA1-3 : bond 0.00477 / 0.25 ( 1) link_BETA1-3 : angle 3.22265 / 1.69 ( 3) link_NAG-ASN : bond 0.00459 / 0.20 ( 3) link_NAG-ASN : angle 2.40251 / 1.36 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.459 Fit side-chains REVERT: A 145 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8272 (p0) REVERT: A 193 THR cc_start: 0.8343 (p) cc_final: 0.7932 (p) REVERT: A 252 LYS cc_start: 0.8073 (tppt) cc_final: 0.7351 (tmtt) REVERT: A 258 TYR cc_start: 0.8217 (m-10) cc_final: 0.7973 (m-10) REVERT: A 631 LYS cc_start: 0.7424 (ttpt) cc_final: 0.6638 (mtmt) REVERT: A 678 MET cc_start: 0.8328 (tmm) cc_final: 0.7982 (tmm) REVERT: A 942 TYR cc_start: 0.7849 (m-80) cc_final: 0.7535 (m-80) outliers start: 17 outliers final: 15 residues processed: 127 average time/residue: 0.0953 time to fit residues: 17.7593 Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 8 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 864 HIS ** 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 = 0.3847 r_free = 0.3847 target = 0.155123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120949 restraints weight = 14232.549| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.09 r_work: 0.3150 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11251 Z= 0.118 Angle : 0.534 6.739 15253 Z= 0.274 Chirality : 0.043 0.267 1723 Planarity : 0.004 0.048 1917 Dihedral : 4.537 46.454 1480 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.58 % Allowed : 14.65 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1342 helix: 1.35 (0.22), residues: 564 sheet: 0.36 (0.36), residues: 195 loop : -1.66 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 723 TYR 0.015 0.001 TYR A 324 PHE 0.013 0.001 PHE A 633 TRP 0.012 0.001 TRP A 323 HIS 0.010 0.001 HIS A 716 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11243) covalent geometry : angle 0.52861 / 0.27 (15232) SS BOND : bond 0.00701 / 0.27 ( 3) SS BOND : angle 0.91732 / 0.45 ( 6) hydrogen bonds : bond 0.03865 / 2.45 ( 476) hydrogen bonds : angle 4.40578 / 3.10 ( 1353) link_ALPHA1-3 : bond 0.00331 / 0.17 ( 1) link_ALPHA1-3 : angle 1.88367 / 1.01 ( 3) link_BETA1-3 : bond 0.00496 / 0.26 ( 1) link_BETA1-3 : angle 3.11737 / 1.61 ( 3) link_NAG-ASN : bond 0.00445 / 0.19 ( 3) link_NAG-ASN : angle 2.24745 / 1.27 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.34 seconds wall clock time: 41 minutes 0.41 seconds (2460.41 seconds total)