Starting phenix.real_space_refine on Sat Sep 12 04:59:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6w_21567/09_2026/6w6w_21567.map" } resolution = 3.0 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= 0.006 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3445 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4 5.49 5 S 57 5.16 5 C 7012 2.51 5 N 1933 2.21 5 O 1974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10981 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7121 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 75, 'TRANS': 829} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 213 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2631 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 3 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5956 SG CYS A1043 89.942 97.205 108.219 1.00 59.44 S ATOM 5979 SG CYS A1046 89.489 94.293 111.406 1.00 63.81 S ATOM 6045 SG CYS A1055 91.655 98.287 111.217 1.00 73.01 S ATOM 6094 SG CYS A1062 93.761 95.873 109.555 1.00 82.71 S Time building chain proxies: 2.44, per 1000 atoms: 0.22 Number of scatterers: 10981 At special positions: 0 Unit cell: (143.374, 132.594, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 57 16.00 P 4 15.00 O 1974 8.00 N 1933 7.00 C 7012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 322 " 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 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 500.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " Number of angles added : 6 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 21 sheets defined 19.8% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.606A pdb=" N ARG A 273 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.917A pdb=" N VAL A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.606A pdb=" N TRP A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.551A pdb=" N GLU A 527 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.973A pdb=" N SER A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 580 " --> pdb=" O GLU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.647A pdb=" N LEU A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 648 " --> pdb=" O PRO A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 648' Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.649A pdb=" N GLU A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 675 " --> pdb=" O TRP A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 675' Processing helix chain 'A' and resid 803 through 811 removed outlier: 4.021A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP A 807 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 808 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 810 " --> pdb=" O TRP A 807 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 811 " --> pdb=" O PHE A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 803 through 811' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.984A pdb=" N ALA A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.792A pdb=" N LEU A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 3.727A pdb=" N LEU A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1108 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.515A pdb=" N THR A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 removed outlier: 3.634A pdb=" N TRP C 17 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.712A pdb=" N LEU C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 110 through 118 removed outlier: 3.771A pdb=" N LYS C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.716A pdb=" N MET C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.671A pdb=" N GLU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 4.135A pdb=" N GLU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 219' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.553A pdb=" N GLU C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.629A pdb=" N SER C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.854A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 246 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 removed outlier: 4.416A pdb=" N HIS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.693A pdb=" N GLN C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.564A pdb=" N ALA C 331 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.592A pdb=" N ASP C 353 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.814A pdb=" N ALA D 17 " --> pdb=" O TRP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.893A pdb=" N ARG D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.726A pdb=" N GLY A 228 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 281 " --> pdb=" O GLY A 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.731A pdb=" N TRP A 299 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.654A pdb=" N ARG A 354 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 408 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 406 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.654A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.707A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 592 through 597 removed outlier: 13.580A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 597 removed outlier: 13.580A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 621 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS A 650 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 744 removed outlier: 7.170A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 728 through 738 current: chain 'A' and resid 851 through 853 Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 781 removed outlier: 5.920A pdb=" N GLY A 728 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 760 through 769 current: chain 'A' and resid 859 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 992 through 994 removed outlier: 8.051A pdb=" N HIS A 945 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N CYS A 984 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 947 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 930 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 905 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR A 932 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 896 " --> pdb=" O GLN A 971 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 971 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1024 through 1025 removed outlier: 3.591A pdb=" N ALA A1025 " --> pdb=" O PHE A1159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1024 through 1025 removed outlier: 3.591A pdb=" N ALA A1025 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1203 " --> pdb=" O PRO A1154 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A1085 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS A1198 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR A1087 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N SER A1200 " --> pdb=" O THR A1087 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1086 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A1072 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A1037 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG A1074 " --> pdb=" O PHE A1035 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1033 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A1078 " --> pdb=" O ILE A1031 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A1031 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AB7, first strand: chain 'A' and resid 1175 through 1177 Processing sheet with id=AB8, first strand: chain 'A' and resid 1180 through 1181 removed outlier: 3.630A pdb=" N CYS A1181 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.892A pdb=" N LYS C 38 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 57 through 65 removed outlier: 5.952A pdb=" N GLY C 76 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG C 145 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN C 85 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE C 147 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG C 139 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA C 149 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 137 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 131 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.280A pdb=" N ILE D 74 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 94 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 76 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N VAL D 89 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU D 56 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 91 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS D 58 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL D 93 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 43 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 34 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET D 45 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU D 32 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLN D 47 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLY D 30 " --> pdb=" O GLN D 47 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 711 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: 2.11 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3519 1.34 - 1.46: 2384 1.46 - 1.58: 5263 1.58 - 1.70: 7 1.70 - 1.82: 73 Bond restraints: 11246 Sorted by residual: bond pdb=" C1' DT E 1 " pdb=" N1 DT E 1 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.78e+00 bond pdb=" C3' DA E 2 " pdb=" O3' DA E 2 " ideal model delta sigma weight residual 1.435 1.404 0.031 1.30e-02 5.92e+03 5.74e+00 bond pdb=" C VAL A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.55e+00 bond pdb=" O4' DA E 2 " pdb=" C1' DA E 2 " ideal model delta sigma weight residual 1.420 1.395 0.025 1.10e-02 8.26e+03 5.12e+00 bond pdb=" N7 DA E 2 " pdb=" C5 DA E 2 " ideal model delta sigma weight residual 1.388 1.375 0.013 6.00e-03 2.78e+04 4.97e+00 ... (remaining 11241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 15081 3.34 - 6.68: 171 6.68 - 10.02: 34 10.02 - 13.36: 5 13.36 - 16.70: 1 Bond angle restraints: 15292 Sorted by residual: angle pdb=" N PRO B 35 " pdb=" CA PRO B 35 " pdb=" CB PRO B 35 " ideal model delta sigma weight residual 103.25 113.53 -10.28 1.05e+00 9.07e-01 9.58e+01 angle pdb=" C CYS B 34 " pdb=" N PRO B 35 " pdb=" CA PRO B 35 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.04e+01 angle pdb=" C ASN A1090 " pdb=" N HIS A1091 " pdb=" CA HIS A1091 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N CYS A 482 " pdb=" CA CYS A 482 " pdb=" C CYS A 482 " ideal model delta sigma weight residual 109.81 121.07 -11.26 2.21e+00 2.05e-01 2.59e+01 angle pdb=" C GLU A 941 " pdb=" N PHE A 942 " pdb=" CA PHE A 942 " ideal model delta sigma weight residual 121.80 133.83 -12.03 2.44e+00 1.68e-01 2.43e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 5970 16.68 - 33.37: 631 33.37 - 50.05: 152 50.05 - 66.74: 20 66.74 - 83.42: 16 Dihedral angle restraints: 6789 sinusoidal: 2756 harmonic: 4033 Sorted by residual: dihedral pdb=" CA PRO B 35 " pdb=" C PRO B 35 " pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta harmonic sigma weight residual 180.00 132.63 47.37 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA CYS A 535 " pdb=" C CYS A 535 " pdb=" N PRO A 536 " pdb=" CA PRO A 536 " ideal model delta harmonic sigma weight residual 180.00 -142.56 -37.44 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 6786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1317 0.058 - 0.115: 329 0.115 - 0.173: 75 0.173 - 0.231: 7 0.231 - 0.288: 5 Chirality restraints: 1733 Sorted by residual: chirality pdb=" CB ILE A1005 " pdb=" CA ILE A1005 " pdb=" CG1 ILE A1005 " pdb=" CG2 ILE A1005 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE C 244 " pdb=" CA ILE C 244 " pdb=" CG1 ILE C 244 " pdb=" CG2 ILE C 244 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA CYS A 482 " pdb=" N CYS A 482 " pdb=" C CYS A 482 " pdb=" CB CYS A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1730 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 496 " -0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 497 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 482 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO A 483 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 508 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO A 509 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.041 5.00e-02 4.00e+02 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3100 2.82 - 3.34: 8606 3.34 - 3.86: 16764 3.86 - 4.38: 19469 4.38 - 4.90: 34277 Nonbonded interactions: 82216 Sorted by model distance: nonbonded pdb=" OG SER A 970 " pdb=" O THR A 990 " model vdw 2.303 3.040 nonbonded pdb=" O GLY A1080 " pdb=" OH TYR C 178 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A 363 " pdb=" O LEU A 375 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A1148 " pdb=" OG SER A1150 " model vdw 2.355 3.040 nonbonded pdb=" OD1 ASN A 225 " pdb=" OG1 THR A 284 " model vdw 2.361 3.040 ... (remaining 82211 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.060 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.010 0.614 11251 Z= 0.379 Angle : 1.070 32.638 15300 Z= 0.544 Chirality : 0.055 0.288 1733 Planarity : 0.008 0.093 1942 Dihedral : 14.888 83.419 4164 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.09 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.09 (0.18), residues: 1356 helix: -5.07 (0.09), residues: 269 sheet: -2.15 (0.26), residues: 375 loop : -3.42 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1163 TYR 0.029 0.003 TYR C 30 PHE 0.023 0.002 PHE C 72 TRP 0.040 0.002 TRP A 153 HIS 0.014 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (11246) covalent geometry : angle 0.99550 / 0.54 (15292) SS BOND : bond 0.00963 / 0.51 ( 1) SS BOND : angle 0.59708 / 0.35 ( 2) hydrogen bonds : bond 0.29162 / 18.76 ( 253) hydrogen bonds : angle 9.92510 / 6.61 ( 711) metal coordination : bond 0.41738 / 20.86 ( 4) metal coordination : angle 19.83962 / 11.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6385 (t60) cc_final: 0.6048 (t60) REVERT: A 405 ASP cc_start: 0.7243 (t0) cc_final: 0.6845 (t0) REVERT: A 1064 THR cc_start: 0.7317 (m) cc_final: 0.7070 (p) REVERT: A 1155 ILE cc_start: 0.8755 (tp) cc_final: 0.8379 (pt) REVERT: C 41 ARG cc_start: 0.6346 (tmt-80) cc_final: 0.5465 (mtp180) REVERT: C 140 THR cc_start: 0.8949 (t) cc_final: 0.8589 (m) REVERT: C 211 LYS cc_start: 0.8333 (mppt) cc_final: 0.8083 (ttmt) REVERT: D 34 LEU cc_start: 0.8755 (mp) cc_final: 0.8449 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.6486 time to fit residues: 110.4280 Evaluate side-chains 110 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS A 178 HIS A 407 HIS ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 585 GLN A 587 ASN A 682 GLN A 691 GLN A 971 GLN A1030 HIS A1120 GLN C 117 GLN C 148 HIS C 245 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101144 restraints weight = 14787.135| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.27 r_work: 0.3079 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11251 Z= 0.179 Angle : 0.752 10.310 15300 Z= 0.378 Chirality : 0.047 0.249 1733 Planarity : 0.006 0.071 1942 Dihedral : 8.329 63.440 1539 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.47 % Favored : 89.23 % Rotamer: Outliers : 1.43 % Allowed : 11.34 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.20), residues: 1356 helix: -4.04 (0.18), residues: 272 sheet: -1.70 (0.27), residues: 361 loop : -2.97 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.018 0.002 TYR C 153 PHE 0.014 0.001 PHE C 72 TRP 0.018 0.002 TRP A 153 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (11246) covalent geometry : angle 0.74225 / 0.38 (15292) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.12014 / 0.07 ( 2) hydrogen bonds : bond 0.05484 / 3.46 ( 253) hydrogen bonds : angle 6.20375 / 4.24 ( 711) metal coordination : bond 0.02853 / 1.38 ( 4) metal coordination : angle 6.19929 / 3.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.7028 (t60) cc_final: 0.6528 (t60) REVERT: A 262 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 300 MET cc_start: 0.6600 (ttp) cc_final: 0.6039 (pp-130) REVERT: A 405 ASP cc_start: 0.8094 (t0) cc_final: 0.7642 (t0) REVERT: A 1064 THR cc_start: 0.7278 (m) cc_final: 0.6993 (p) REVERT: A 1091 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8388 (p-80) REVERT: A 1155 ILE cc_start: 0.8738 (tp) cc_final: 0.8439 (pt) REVERT: C 41 ARG cc_start: 0.6817 (tmt-80) cc_final: 0.6089 (mtp180) REVERT: C 118 GLU cc_start: 0.8167 (mp0) cc_final: 0.7911 (mm-30) REVERT: C 176 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8579 (mttp) REVERT: C 201 LEU cc_start: 0.8179 (mt) cc_final: 0.7925 (pp) REVERT: C 341 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7351 (tm-30) REVERT: D 37 MET cc_start: 0.7308 (ttm) cc_final: 0.5980 (mpt) outliers start: 17 outliers final: 5 residues processed: 124 average time/residue: 0.6673 time to fit residues: 88.7058 Evaluate side-chains 114 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098027 restraints weight = 14972.354| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.27 r_work: 0.3030 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11251 Z= 0.259 Angle : 0.778 11.540 15300 Z= 0.387 Chirality : 0.049 0.241 1733 Planarity : 0.005 0.060 1942 Dihedral : 8.343 63.503 1539 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.02 % Favored : 87.68 % Rotamer: Outliers : 2.02 % Allowed : 14.03 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -3.82 (0.21), residues: 1356 helix: -3.23 (0.25), residues: 266 sheet: -1.65 (0.27), residues: 364 loop : -2.77 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 306 TYR 0.018 0.002 TYR A 991 PHE 0.019 0.002 PHE C 72 TRP 0.019 0.002 TRP A 153 HIS 0.005 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (11246) covalent geometry : angle 0.77145 / 0.39 (15292) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 0.10173 / 0.05 ( 2) hydrogen bonds : bond 0.04811 / 3.12 ( 253) hydrogen bonds : angle 5.71158 / 3.90 ( 711) metal coordination : bond 0.00709 / 0.36 ( 4) metal coordination : angle 5.22861 / 3.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.7300 (t60) cc_final: 0.6754 (t60) REVERT: A 170 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8041 (tpm-80) REVERT: A 262 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8243 (mm) REVERT: A 287 ARG cc_start: 0.6044 (mpt180) cc_final: 0.5518 (mmp-170) REVERT: A 405 ASP cc_start: 0.8110 (t0) cc_final: 0.7653 (t0) REVERT: A 973 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: A 1091 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8393 (p-80) REVERT: A 1100 CYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8149 (m) REVERT: C 41 ARG cc_start: 0.6677 (tmt-80) cc_final: 0.5973 (mtp180) REVERT: C 118 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: C 176 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8571 (mttp) REVERT: C 201 LEU cc_start: 0.8205 (mt) cc_final: 0.7945 (pp) REVERT: C 341 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7348 (tm-30) REVERT: C 349 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7507 (mt-10) REVERT: D 5 LYS cc_start: 0.9068 (mmtm) cc_final: 0.8816 (mttm) REVERT: D 37 MET cc_start: 0.7382 (ttm) cc_final: 0.6060 (mpt) outliers start: 24 outliers final: 12 residues processed: 131 average time/residue: 0.6140 time to fit residues: 86.7659 Evaluate side-chains 128 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1100 CYS Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 HIS A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098550 restraints weight = 14947.063| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.28 r_work: 0.3042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11251 Z= 0.216 Angle : 0.742 12.057 15300 Z= 0.369 Chirality : 0.048 0.232 1733 Planarity : 0.005 0.058 1942 Dihedral : 8.252 62.720 1539 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.28 % Favored : 88.42 % Rotamer: Outliers : 2.61 % Allowed : 15.13 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.21), residues: 1356 helix: -2.79 (0.28), residues: 260 sheet: -1.56 (0.27), residues: 359 loop : -2.62 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 775 TYR 0.016 0.002 TYR A 991 PHE 0.018 0.002 PHE C 72 TRP 0.012 0.002 TRP A 153 HIS 0.006 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (11246) covalent geometry : angle 0.73711 / 0.37 (15292) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.23968 / 0.13 ( 2) hydrogen bonds : bond 0.04084 / 2.64 ( 253) hydrogen bonds : angle 5.40206 / 3.70 ( 711) metal coordination : bond 0.00481 / 0.25 ( 4) metal coordination : angle 4.57070 / 2.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.7173 (t60) cc_final: 0.6623 (t60) REVERT: A 170 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8061 (tpm-80) REVERT: A 176 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7881 (mp0) REVERT: A 287 ARG cc_start: 0.6015 (mpt180) cc_final: 0.5432 (mmp-170) REVERT: A 300 MET cc_start: 0.6635 (ttp) cc_final: 0.6267 (ptm) REVERT: A 405 ASP cc_start: 0.8084 (t0) cc_final: 0.7625 (t0) REVERT: A 973 GLU cc_start: 0.8806 (tp30) cc_final: 0.8535 (tt0) REVERT: A 1091 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8393 (p-80) REVERT: A 1113 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 1138 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7924 (mmm) REVERT: C 41 ARG cc_start: 0.6841 (tmt-80) cc_final: 0.6118 (mtp180) REVERT: C 118 GLU cc_start: 0.8162 (mp0) cc_final: 0.7881 (mm-30) REVERT: C 146 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: C 176 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8527 (mttp) REVERT: C 201 LEU cc_start: 0.8235 (mt) cc_final: 0.7955 (pp) REVERT: C 211 LYS cc_start: 0.8353 (mppt) cc_final: 0.8120 (tttt) REVERT: C 341 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7371 (tm-30) REVERT: C 349 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7770 (mt-10) REVERT: D 5 LYS cc_start: 0.9065 (mmtm) cc_final: 0.8852 (mttm) REVERT: D 37 MET cc_start: 0.7257 (ttm) cc_final: 0.5939 (mpt) outliers start: 31 outliers final: 11 residues processed: 138 average time/residue: 0.6057 time to fit residues: 90.1619 Evaluate side-chains 123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS C 289 ASN ** C 363 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 = 0.3752 r_free = 0.3752 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100170 restraints weight = 14886.350| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.27 r_work: 0.3085 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11251 Z= 0.156 Angle : 0.699 12.220 15300 Z= 0.346 Chirality : 0.046 0.206 1733 Planarity : 0.005 0.057 1942 Dihedral : 8.065 61.850 1539 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.99 % Favored : 88.72 % Rotamer: Outliers : 2.69 % Allowed : 16.47 % Favored : 80.84 % 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: -3.29 (0.22), residues: 1356 helix: -2.46 (0.30), residues: 265 sheet: -1.41 (0.28), residues: 343 loop : -2.50 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 306 TYR 0.014 0.002 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.010 0.001 TRP A 592 HIS 0.006 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11246) covalent geometry : angle 0.69508 / 0.35 (15292) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 0.59463 / 0.32 ( 2) hydrogen bonds : bond 0.03546 / 2.28 ( 253) hydrogen bonds : angle 5.15908 / 3.54 ( 711) metal coordination : bond 0.00367 / 0.18 ( 4) metal coordination : angle 3.80483 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6923 (t60) cc_final: 0.6487 (t60) REVERT: A 170 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7997 (tpm-80) REVERT: A 300 MET cc_start: 0.6644 (ttp) cc_final: 0.6252 (ptm) REVERT: A 405 ASP cc_start: 0.8031 (t0) cc_final: 0.7599 (t0) REVERT: A 973 GLU cc_start: 0.8755 (tp30) cc_final: 0.8530 (tt0) REVERT: A 1113 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8550 (p) REVERT: C 41 ARG cc_start: 0.6893 (tmt-80) cc_final: 0.5780 (mtp180) REVERT: C 118 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: C 176 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8508 (mttp) REVERT: C 201 LEU cc_start: 0.8230 (mt) cc_final: 0.7959 (pp) REVERT: C 319 GLU cc_start: 0.4882 (OUTLIER) cc_final: 0.3985 (tp30) REVERT: C 341 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7412 (tm-30) REVERT: C 349 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7789 (mt-10) REVERT: D 37 MET cc_start: 0.7198 (ttm) cc_final: 0.5952 (mpt) outliers start: 32 outliers final: 14 residues processed: 140 average time/residue: 0.5946 time to fit residues: 90.1484 Evaluate side-chains 128 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS C 269 ASN C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098306 restraints weight = 14963.905| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.27 r_work: 0.3058 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11251 Z= 0.233 Angle : 0.750 12.462 15300 Z= 0.371 Chirality : 0.048 0.212 1733 Planarity : 0.005 0.057 1942 Dihedral : 8.138 62.547 1539 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.02 % Favored : 87.76 % Rotamer: Outliers : 3.03 % Allowed : 17.06 % Favored : 79.92 % 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: -3.25 (0.22), residues: 1356 helix: -2.36 (0.30), residues: 265 sheet: -1.42 (0.28), residues: 362 loop : -2.50 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 306 TYR 0.018 0.002 TYR A 991 PHE 0.019 0.002 PHE C 72 TRP 0.011 0.002 TRP A 592 HIS 0.007 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (11246) covalent geometry : angle 0.74572 / 0.37 (15292) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 0.27303 / 0.14 ( 2) hydrogen bonds : bond 0.03924 / 2.53 ( 253) hydrogen bonds : angle 5.22656 / 3.58 ( 711) metal coordination : bond 0.00499 / 0.25 ( 4) metal coordination : angle 4.04336 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.7154 (t60) cc_final: 0.6630 (t60) REVERT: A 170 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8001 (tpm-80) REVERT: A 238 LYS cc_start: 0.7053 (mmmm) cc_final: 0.6828 (mppt) REVERT: A 287 ARG cc_start: 0.6166 (mpt180) cc_final: 0.5644 (mmp-170) REVERT: A 300 MET cc_start: 0.6629 (ttp) cc_final: 0.6262 (ptm) REVERT: A 405 ASP cc_start: 0.8072 (t0) cc_final: 0.7654 (t0) REVERT: A 973 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: A 1113 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 1138 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: C 41 ARG cc_start: 0.6616 (tmt-80) cc_final: 0.5491 (mtp180) REVERT: C 118 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: C 146 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: C 176 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8508 (mttp) REVERT: C 201 LEU cc_start: 0.8230 (mt) cc_final: 0.7962 (pp) REVERT: C 341 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7482 (tm-30) REVERT: C 349 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7792 (mt-10) REVERT: D 37 MET cc_start: 0.7254 (ttm) cc_final: 0.5973 (mpt) outliers start: 36 outliers final: 18 residues processed: 137 average time/residue: 0.5988 time to fit residues: 88.6561 Evaluate side-chains 130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 134 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS A 737 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100443 restraints weight = 14752.380| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.25 r_work: 0.3092 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11251 Z= 0.153 Angle : 0.705 12.875 15300 Z= 0.348 Chirality : 0.046 0.204 1733 Planarity : 0.005 0.056 1942 Dihedral : 7.997 61.287 1539 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.69 % Favored : 89.01 % Rotamer: Outliers : 2.52 % Allowed : 18.07 % Favored : 79.41 % 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: -3.10 (0.22), residues: 1356 helix: -2.20 (0.31), residues: 265 sheet: -1.29 (0.29), residues: 345 loop : -2.43 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 306 TYR 0.014 0.001 TYR A 991 PHE 0.017 0.001 PHE C 72 TRP 0.010 0.001 TRP A 592 HIS 0.006 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (11246) covalent geometry : angle 0.70156 / 0.35 (15292) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 0.29618 / 0.16 ( 2) hydrogen bonds : bond 0.03371 / 2.16 ( 253) hydrogen bonds : angle 5.02987 / 3.45 ( 711) metal coordination : bond 0.00332 / 0.17 ( 4) metal coordination : angle 3.48529 / 2.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6811 (t60) cc_final: 0.6382 (t60) REVERT: A 170 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7918 (tpm-80) REVERT: A 176 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8133 (mp0) REVERT: A 287 ARG cc_start: 0.6065 (mpt180) cc_final: 0.5546 (mmp-170) REVERT: A 300 MET cc_start: 0.6711 (ttp) cc_final: 0.6235 (ptm) REVERT: A 405 ASP cc_start: 0.7965 (t0) cc_final: 0.7575 (t0) REVERT: A 557 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: A 775 ARG cc_start: 0.8692 (tpp80) cc_final: 0.8288 (tpp80) REVERT: A 973 GLU cc_start: 0.8777 (tp30) cc_final: 0.8552 (tt0) REVERT: A 1113 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8504 (p) REVERT: C 41 ARG cc_start: 0.6733 (tmt-80) cc_final: 0.5689 (mtp180) REVERT: C 146 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: C 201 LEU cc_start: 0.8235 (mt) cc_final: 0.7954 (pp) REVERT: C 341 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7484 (tm-30) REVERT: C 349 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 37 MET cc_start: 0.7174 (ttm) cc_final: 0.5933 (mpt) outliers start: 30 outliers final: 18 residues processed: 137 average time/residue: 0.5747 time to fit residues: 85.0737 Evaluate side-chains 130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099343 restraints weight = 14922.220| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.26 r_work: 0.3053 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11251 Z= 0.193 Angle : 0.729 13.349 15300 Z= 0.359 Chirality : 0.047 0.209 1733 Planarity : 0.005 0.057 1942 Dihedral : 8.007 61.766 1539 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.87 % Favored : 87.91 % Rotamer: Outliers : 2.61 % Allowed : 18.57 % Favored : 78.82 % 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: -3.05 (0.22), residues: 1356 helix: -2.14 (0.31), residues: 265 sheet: -1.25 (0.29), residues: 346 loop : -2.41 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 775 TYR 0.017 0.002 TYR A 991 PHE 0.018 0.001 PHE C 72 TRP 0.010 0.001 TRP A 592 HIS 0.005 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (11246) covalent geometry : angle 0.72629 / 0.36 (15292) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 0.29787 / 0.16 ( 2) hydrogen bonds : bond 0.03602 / 2.32 ( 253) hydrogen bonds : angle 5.08495 / 3.48 ( 711) metal coordination : bond 0.00415 / 0.21 ( 4) metal coordination : angle 3.51160 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.7029 (t60) cc_final: 0.6546 (t60) REVERT: A 170 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7929 (tpm-80) REVERT: A 287 ARG cc_start: 0.5937 (mpt180) cc_final: 0.5482 (mmp-170) REVERT: A 300 MET cc_start: 0.6641 (ttp) cc_final: 0.6231 (ptm) REVERT: A 405 ASP cc_start: 0.8057 (t0) cc_final: 0.7607 (t0) REVERT: A 445 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.8315 (ttt180) REVERT: A 557 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 973 GLU cc_start: 0.8807 (tp30) cc_final: 0.8530 (tt0) REVERT: A 1113 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 41 ARG cc_start: 0.6683 (tmt-80) cc_final: 0.5605 (mtp180) REVERT: C 146 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: C 201 LEU cc_start: 0.8236 (mt) cc_final: 0.7959 (pp) REVERT: C 341 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7481 (tm-30) REVERT: C 349 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7871 (tm-30) REVERT: D 37 MET cc_start: 0.7216 (ttm) cc_final: 0.5908 (mpt) outliers start: 31 outliers final: 21 residues processed: 134 average time/residue: 0.5924 time to fit residues: 85.7578 Evaluate side-chains 134 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 737 HIS C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100862 restraints weight = 14775.335| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.27 r_work: 0.3100 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11251 Z= 0.143 Angle : 0.715 13.629 15300 Z= 0.350 Chirality : 0.046 0.215 1733 Planarity : 0.004 0.056 1942 Dihedral : 7.910 60.947 1539 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.84 % Favored : 88.86 % Rotamer: Outliers : 2.44 % Allowed : 18.91 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.22), residues: 1356 helix: -2.01 (0.32), residues: 265 sheet: -1.21 (0.29), residues: 348 loop : -2.34 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 306 TYR 0.014 0.001 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.015 0.001 TRP A 271 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11246) covalent geometry : angle 0.71177 / 0.35 (15292) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.33277 / 0.18 ( 2) hydrogen bonds : bond 0.03245 / 2.08 ( 253) hydrogen bonds : angle 4.96712 / 3.41 ( 711) metal coordination : bond 0.00311 / 0.16 ( 4) metal coordination : angle 3.26544 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6801 (t60) cc_final: 0.6390 (t60) REVERT: A 170 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7912 (tpm-80) REVERT: A 238 LYS cc_start: 0.6883 (mmmm) cc_final: 0.6533 (mmtm) REVERT: A 287 ARG cc_start: 0.5931 (mpt180) cc_final: 0.5517 (mmp-170) REVERT: A 300 MET cc_start: 0.6646 (ttp) cc_final: 0.6278 (ptm) REVERT: A 405 ASP cc_start: 0.7966 (t0) cc_final: 0.7559 (t0) REVERT: A 445 ARG cc_start: 0.8524 (ttt-90) cc_final: 0.8317 (ttt180) REVERT: A 557 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: A 775 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8266 (tpp80) REVERT: A 973 GLU cc_start: 0.8758 (tp30) cc_final: 0.8536 (tt0) REVERT: A 1113 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 1138 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: C 41 ARG cc_start: 0.6731 (tmt-80) cc_final: 0.5687 (mtp180) REVERT: C 146 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: C 201 LEU cc_start: 0.8275 (mt) cc_final: 0.7979 (pp) REVERT: C 341 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7482 (tm-30) REVERT: C 349 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 37 MET cc_start: 0.7182 (ttm) cc_final: 0.5924 (mpt) outliers start: 29 outliers final: 18 residues processed: 134 average time/residue: 0.6014 time to fit residues: 87.0729 Evaluate side-chains 134 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 34 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 HIS C 289 ASN ** C 363 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 = 0.3785 r_free = 0.3785 target = 0.144646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102985 restraints weight = 14827.948| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.28 r_work: 0.3109 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11251 Z= 0.122 Angle : 0.705 13.753 15300 Z= 0.343 Chirality : 0.044 0.211 1733 Planarity : 0.004 0.056 1942 Dihedral : 7.737 61.317 1539 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.47 % Favored : 89.31 % Rotamer: Outliers : 2.02 % Allowed : 19.24 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.23), residues: 1356 helix: -1.82 (0.33), residues: 266 sheet: -1.05 (0.29), residues: 344 loop : -2.30 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 306 TYR 0.011 0.001 TYR A 991 PHE 0.015 0.001 PHE C 72 TRP 0.024 0.001 TRP A 271 HIS 0.005 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (11246) covalent geometry : angle 0.70336 / 0.34 (15292) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 0.38776 / 0.22 ( 2) hydrogen bonds : bond 0.02905 / 1.85 ( 253) hydrogen bonds : angle 4.83507 / 3.32 ( 711) metal coordination : bond 0.00284 / 0.14 ( 4) metal coordination : angle 2.62622 / 1.57 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6579 (t60) cc_final: 0.6200 (t60) REVERT: A 170 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7872 (tpm-80) REVERT: A 238 LYS cc_start: 0.7096 (mmmm) cc_final: 0.6737 (mmtm) REVERT: A 287 ARG cc_start: 0.5896 (mpt180) cc_final: 0.5401 (mmp-170) REVERT: A 300 MET cc_start: 0.6606 (ttp) cc_final: 0.6247 (ptm) REVERT: A 395 MET cc_start: 0.9093 (tpp) cc_final: 0.8842 (mmm) REVERT: A 405 ASP cc_start: 0.7978 (t0) cc_final: 0.7576 (t0) REVERT: A 557 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: A 775 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8223 (tpp80) REVERT: A 973 GLU cc_start: 0.8710 (tp30) cc_final: 0.8489 (tt0) REVERT: A 1091 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8319 (p-80) REVERT: C 41 ARG cc_start: 0.6676 (tmt-80) cc_final: 0.5637 (mtp180) REVERT: C 146 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: C 201 LEU cc_start: 0.8248 (mt) cc_final: 0.7966 (pp) REVERT: C 319 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4762 (tp30) REVERT: C 341 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7558 (tm-30) REVERT: C 349 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 37 MET cc_start: 0.7049 (ttm) cc_final: 0.5786 (mpt) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.5996 time to fit residues: 90.1809 Evaluate side-chains 137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 737 HIS C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102247 restraints weight = 14894.689| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.27 r_work: 0.3117 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11251 Z= 0.138 Angle : 0.701 14.007 15300 Z= 0.342 Chirality : 0.045 0.216 1733 Planarity : 0.004 0.057 1942 Dihedral : 7.723 61.110 1539 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.32 % Favored : 89.45 % Rotamer: Outliers : 2.18 % Allowed : 19.58 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.23), residues: 1356 helix: -1.75 (0.33), residues: 266 sheet: -1.08 (0.29), residues: 343 loop : -2.26 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 306 TYR 0.012 0.001 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.023 0.001 TRP A 271 HIS 0.006 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11246) covalent geometry : angle 0.69947 / 0.34 (15292) SS BOND : bond 0.00139 / 0.07 ( 1) SS BOND : angle 0.40701 / 0.23 ( 2) hydrogen bonds : bond 0.03064 / 1.97 ( 253) hydrogen bonds : angle 4.86979 / 3.34 ( 711) metal coordination : bond 0.00229 / 0.11 ( 4) metal coordination : angle 2.51767 / 1.49 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.58 seconds wall clock time: 75 minutes 31.59 seconds (4531.59 seconds total)