Starting phenix.real_space_refine on Wed Mar 4 13:11:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6w_21567/03_2026/6w6w_21567.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6w_21567/03_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_21567/03_2026/6w6w_21567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6w_21567/03_2026/6w6w_21567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6w_21567/03_2026/6w6w_21567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6w_21567/03_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-dev-5986/lib/python3.9/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: 2.60, per 1000 atoms: 0.24 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: 0.78 Conformation dependent library (CDL) restraints added in 470.2 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: 0.50 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: 2.01 Time building geometry restraints manager: 1.04 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=" 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=" C VAL A1113 " pdb=" N PRO A1114 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" C GLU A1136 " pdb=" N PRO A1137 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.55e+00 bond pdb=" CA VAL B 20 " pdb=" CB VAL B 20 " ideal model delta sigma weight residual 1.550 1.532 0.018 1.03e-02 9.43e+03 3.07e+00 bond pdb=" C GLU D 63 " pdb=" N PRO D 64 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+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: 1318 0.058 - 0.115: 328 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.050 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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= 0.372 Angle : 1.068 32.638 15300 Z= 0.536 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 covalent geometry : bond 0.00566 (11246) covalent geometry : angle 0.99315 (15292) SS BOND : bond 0.00963 ( 1) SS BOND : angle 0.59708 ( 2) hydrogen bonds : bond 0.29162 ( 253) hydrogen bonds : angle 9.92510 ( 711) metal coordination : bond 0.41738 ( 4) metal coordination : angle 19.83962 ( 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 : 0.332 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: 0.6497 time to fit residues: 110.1971 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 : 0.349 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 585 GLN A 587 ASN A 638 HIS A 682 GLN A 691 GLN A 971 GLN A1030 HIS A1120 GLN C 117 GLN C 148 HIS C 245 HIS C 282 GLN 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 = 0.3768 r_free = 0.3768 target = 0.143117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101403 restraints weight = 14800.605| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.27 r_work: 0.3105 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1497 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= 0.168 Angle : 0.722 10.220 15300 Z= 0.362 Chirality : 0.046 0.176 1733 Planarity : 0.006 0.059 1942 Dihedral : 8.186 64.807 1539 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.77 % Favored : 88.94 % Rotamer: Outliers : 1.68 % Allowed : 11.76 % Favored : 86.55 % 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: -4.20 (0.20), residues: 1356 helix: -3.91 (0.20), residues: 272 sheet: -1.75 (0.27), residues: 370 loop : -2.92 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.013 0.002 TYR D 115 PHE 0.017 0.001 PHE C 72 TRP 0.017 0.002 TRP A 153 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00395 (11246) covalent geometry : angle 0.71149 (15292) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.18182 ( 2) hydrogen bonds : bond 0.04289 ( 253) hydrogen bonds : angle 5.84523 ( 711) metal coordination : bond 0.01041 ( 4) metal coordination : angle 6.33612 ( 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 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6922 (t60) cc_final: 0.6482 (t60) REVERT: A 262 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 286 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 300 MET cc_start: 0.6582 (ttp) cc_final: 0.6303 (ptm) REVERT: A 405 ASP cc_start: 0.8020 (t0) cc_final: 0.7599 (t0) REVERT: A 973 GLU cc_start: 0.8700 (tp30) cc_final: 0.8476 (tt0) REVERT: A 1051 ARG cc_start: 0.7855 (mpp80) cc_final: 0.7123 (mtp85) REVERT: A 1091 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8418 (p-80) REVERT: A 1155 ILE cc_start: 0.8763 (tp) cc_final: 0.8526 (pt) REVERT: C 41 ARG cc_start: 0.6861 (tmt-80) cc_final: 0.6127 (mtp180) REVERT: C 201 LEU cc_start: 0.8287 (mt) cc_final: 0.7983 (pp) REVERT: C 211 LYS cc_start: 0.8408 (mppt) cc_final: 0.8093 (ttmt) REVERT: C 341 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7340 (tm-30) REVERT: D 37 MET cc_start: 0.7242 (ttm) cc_final: 0.5950 (mpt) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 0.6359 time to fit residues: 89.3460 Evaluate side-chains 115 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain C residue 127 GLU 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: 2.9990 chunk 136 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 12 optimal weight: 0.0020 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103327 restraints weight = 14954.056| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.29 r_work: 0.3110 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11251 Z= 0.127 Angle : 0.663 12.229 15300 Z= 0.327 Chirality : 0.044 0.195 1733 Planarity : 0.005 0.056 1942 Dihedral : 7.784 64.233 1539 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.55 % Favored : 89.31 % Rotamer: Outliers : 1.68 % Allowed : 14.45 % Favored : 83.87 % 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: -3.55 (0.21), residues: 1356 helix: -2.96 (0.27), residues: 266 sheet: -1.42 (0.28), residues: 343 loop : -2.64 (0.21), 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 0.014 0.001 PHE C 72 TRP 0.012 0.001 TRP A 153 HIS 0.006 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00297 (11246) covalent geometry : angle 0.65753 (15292) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.36084 ( 2) hydrogen bonds : bond 0.03529 ( 253) hydrogen bonds : angle 5.20338 ( 711) metal coordination : bond 0.00541 ( 4) metal coordination : angle 4.18101 ( 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 146 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6759 (t60) cc_final: 0.6321 (t60) REVERT: A 405 ASP cc_start: 0.8012 (t0) cc_final: 0.7544 (t0) REVERT: A 973 GLU cc_start: 0.8719 (tp30) cc_final: 0.8497 (tt0) REVERT: A 1091 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.8290 (p-80) REVERT: C 41 ARG cc_start: 0.6771 (tmt-80) cc_final: 0.5876 (mtp180) REVERT: C 146 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: C 201 LEU cc_start: 0.8279 (mt) cc_final: 0.7995 (pp) REVERT: C 341 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7470 (tm-30) REVERT: C 349 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7731 (mt-10) REVERT: D 37 MET cc_start: 0.7112 (ttm) cc_final: 0.5854 (mpt) outliers start: 20 outliers final: 11 residues processed: 137 average time/residue: 0.6007 time to fit residues: 88.2879 Evaluate side-chains 121 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 805 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 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 = 0.3779 r_free = 0.3779 target = 0.143913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102271 restraints weight = 14946.489| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.28 r_work: 0.3101 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11251 Z= 0.141 Angle : 0.664 12.431 15300 Z= 0.328 Chirality : 0.044 0.205 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.671 64.269 1539 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.91 % Favored : 88.94 % Rotamer: Outliers : 2.10 % Allowed : 15.46 % Favored : 82.44 % 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: -3.27 (0.22), residues: 1356 helix: -2.56 (0.29), residues: 266 sheet: -1.30 (0.29), residues: 345 loop : -2.50 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 306 TYR 0.014 0.001 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.009 0.001 TRP C 89 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00337 (11246) covalent geometry : angle 0.66086 (15292) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.54731 ( 2) hydrogen bonds : bond 0.03334 ( 253) hydrogen bonds : angle 5.02673 ( 711) metal coordination : bond 0.00384 ( 4) metal coordination : angle 3.51980 ( 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 138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6771 (t60) cc_final: 0.6356 (t60) REVERT: A 170 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8028 (tpm-80) REVERT: A 300 MET cc_start: 0.6562 (ttp) cc_final: 0.6228 (ptm) REVERT: A 405 ASP cc_start: 0.8033 (t0) cc_final: 0.7588 (t0) REVERT: A 973 GLU cc_start: 0.8724 (tp30) cc_final: 0.8514 (tt0) REVERT: C 41 ARG cc_start: 0.6761 (tmt-80) cc_final: 0.5633 (mtp180) REVERT: C 146 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: C 176 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8426 (mttp) REVERT: C 201 LEU cc_start: 0.8317 (mt) cc_final: 0.7997 (pp) REVERT: C 341 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7494 (tm-30) REVERT: C 349 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7785 (mt-10) REVERT: D 5 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8763 (mttm) REVERT: D 37 MET cc_start: 0.7158 (ttm) cc_final: 0.5896 (mpt) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.6204 time to fit residues: 84.6836 Evaluate side-chains 119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS 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 = 0.3775 r_free = 0.3775 target = 0.143754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101912 restraints weight = 14916.518| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.29 r_work: 0.3113 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11251 Z= 0.145 Angle : 0.657 12.382 15300 Z= 0.325 Chirality : 0.044 0.201 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.613 63.844 1539 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.77 % Favored : 89.09 % Rotamer: Outliers : 2.52 % Allowed : 15.71 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.22), residues: 1356 helix: -2.37 (0.30), residues: 267 sheet: -1.21 (0.29), residues: 345 loop : -2.41 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 775 TYR 0.015 0.001 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.010 0.001 TRP C 89 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00346 (11246) covalent geometry : angle 0.65404 (15292) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.58147 ( 2) hydrogen bonds : bond 0.03267 ( 253) hydrogen bonds : angle 4.91675 ( 711) metal coordination : bond 0.00351 ( 4) metal coordination : angle 3.34260 ( 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 146 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6740 (t60) cc_final: 0.6384 (t60) REVERT: A 170 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8012 (tpm-80) REVERT: A 176 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7869 (mp0) REVERT: A 300 MET cc_start: 0.6659 (ttp) cc_final: 0.6307 (ptm) REVERT: A 405 ASP cc_start: 0.8008 (t0) cc_final: 0.7598 (t0) REVERT: A 775 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8247 (tpp80) REVERT: A 973 GLU cc_start: 0.8716 (tp30) cc_final: 0.8501 (tt0) REVERT: C 41 ARG cc_start: 0.6691 (tmt-80) cc_final: 0.5639 (mtp180) REVERT: C 146 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: C 176 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: C 201 LEU cc_start: 0.8315 (mt) cc_final: 0.7983 (pp) REVERT: C 267 PHE cc_start: 0.7529 (m-80) cc_final: 0.7316 (m-80) REVERT: C 341 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7526 (tm-30) REVERT: C 349 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7820 (mt-10) REVERT: D 5 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8731 (mttm) REVERT: D 37 MET cc_start: 0.7172 (ttm) cc_final: 0.5940 (mpt) outliers start: 30 outliers final: 19 residues processed: 135 average time/residue: 0.5999 time to fit residues: 86.8128 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU 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 445 ARG 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 664 ASP 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 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 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: 2.9990 chunk 105 optimal weight: 0.0870 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 407 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 = 0.3781 r_free = 0.3781 target = 0.144080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102392 restraints weight = 14935.059| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.29 r_work: 0.3120 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11251 Z= 0.136 Angle : 0.665 12.811 15300 Z= 0.326 Chirality : 0.044 0.211 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.542 63.568 1539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.62 % Favored : 89.23 % Rotamer: Outliers : 2.27 % Allowed : 16.81 % Favored : 80.92 % 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: -2.95 (0.22), residues: 1356 helix: -2.19 (0.31), residues: 266 sheet: -1.14 (0.29), residues: 345 loop : -2.30 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 306 TYR 0.014 0.001 TYR A 991 PHE 0.016 0.001 PHE C 72 TRP 0.010 0.001 TRP C 89 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00325 (11246) covalent geometry : angle 0.66255 (15292) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.50245 ( 2) hydrogen bonds : bond 0.03127 ( 253) hydrogen bonds : angle 4.85648 ( 711) metal coordination : bond 0.00320 ( 4) metal coordination : angle 3.05833 ( 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 149 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6711 (t60) cc_final: 0.6348 (t60) REVERT: A 170 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8006 (tpm-80) REVERT: A 176 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7907 (mp0) REVERT: A 300 MET cc_start: 0.6715 (ttp) cc_final: 0.6336 (ptm) REVERT: A 405 ASP cc_start: 0.8026 (t0) cc_final: 0.7613 (t0) REVERT: A 557 GLU cc_start: 0.8619 (pp20) cc_final: 0.8329 (pt0) REVERT: A 775 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8301 (tpp80) REVERT: C 41 ARG cc_start: 0.6675 (tmt-80) cc_final: 0.5626 (mtp180) REVERT: C 146 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: C 176 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8410 (mttp) REVERT: C 201 LEU cc_start: 0.8313 (mt) cc_final: 0.7986 (pp) REVERT: C 267 PHE cc_start: 0.7516 (m-80) cc_final: 0.7300 (m-80) REVERT: C 341 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7523 (tm-30) REVERT: C 349 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7820 (mt-10) REVERT: D 37 MET cc_start: 0.7146 (ttm) cc_final: 0.5921 (mpt) outliers start: 27 outliers final: 19 residues processed: 137 average time/residue: 0.6239 time to fit residues: 91.8046 Evaluate side-chains 132 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU 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 445 ARG 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 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 176 LYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 134 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 132 optimal weight: 0.0050 chunk 53 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS A1017 GLN 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 = 0.3787 r_free = 0.3787 target = 0.144660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102856 restraints weight = 14811.522| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.28 r_work: 0.3127 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11251 Z= 0.133 Angle : 0.665 12.975 15300 Z= 0.326 Chirality : 0.044 0.211 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.480 63.258 1539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.32 % Favored : 89.53 % Rotamer: Outliers : 2.77 % Allowed : 17.39 % Favored : 79.83 % 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: -2.82 (0.22), residues: 1356 helix: -2.02 (0.32), residues: 267 sheet: -1.03 (0.29), residues: 344 loop : -2.26 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 306 TYR 0.014 0.001 TYR A 991 PHE 0.015 0.001 PHE C 72 TRP 0.025 0.001 TRP A 271 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00319 (11246) covalent geometry : angle 0.66259 (15292) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.46944 ( 2) hydrogen bonds : bond 0.03046 ( 253) hydrogen bonds : angle 4.76399 ( 711) metal coordination : bond 0.00283 ( 4) metal coordination : angle 2.82648 ( 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 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6640 (t60) cc_final: 0.6333 (t60) REVERT: A 170 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7997 (tpm-80) REVERT: A 176 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7936 (mp0) REVERT: A 300 MET cc_start: 0.6704 (ttp) cc_final: 0.6383 (ptm) REVERT: A 405 ASP cc_start: 0.7980 (t0) cc_final: 0.7600 (t0) REVERT: A 445 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8413 (ttt180) REVERT: A 557 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: A 775 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8344 (tpp80) REVERT: A 840 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.5764 (mtm180) REVERT: A 1017 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8197 (pp30) REVERT: A 1120 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8919 (tp40) REVERT: A 1179 PHE cc_start: 0.8436 (m-80) cc_final: 0.8210 (m-80) REVERT: C 41 ARG cc_start: 0.6694 (tmt-80) cc_final: 0.5652 (mtp180) REVERT: C 146 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: C 176 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: C 267 PHE cc_start: 0.7505 (m-80) cc_final: 0.7271 (m-80) REVERT: C 341 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7522 (tm-30) REVERT: C 349 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 37 MET cc_start: 0.7141 (ttm) cc_final: 0.5936 (mpt) outliers start: 33 outliers final: 18 residues processed: 138 average time/residue: 0.6325 time to fit residues: 93.4816 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 445 ARG 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 840 ARG Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1120 GLN 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 176 LYS 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 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: 0.0970 chunk 131 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS A1017 GLN C 289 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103678 restraints weight = 14919.445| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.28 r_work: 0.3118 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11251 Z= 0.122 Angle : 0.667 13.365 15300 Z= 0.326 Chirality : 0.044 0.213 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.406 63.048 1539 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.10 % Favored : 89.75 % Rotamer: Outliers : 2.69 % Allowed : 18.24 % Favored : 79.08 % 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: -2.74 (0.22), residues: 1356 helix: -1.87 (0.32), residues: 267 sheet: -0.97 (0.29), residues: 350 loop : -2.27 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 306 TYR 0.013 0.001 TYR A 991 PHE 0.016 0.001 PHE A 160 TRP 0.017 0.001 TRP A 271 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00294 (11246) covalent geometry : angle 0.66462 (15292) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.53417 ( 2) hydrogen bonds : bond 0.02956 ( 253) hydrogen bonds : angle 4.69354 ( 711) metal coordination : bond 0.00277 ( 4) metal coordination : angle 2.65122 ( 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 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6468 (t60) cc_final: 0.6127 (t60) REVERT: A 170 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7976 (tpm-80) REVERT: A 300 MET cc_start: 0.6661 (ttp) cc_final: 0.6360 (ptm) REVERT: A 405 ASP cc_start: 0.7978 (t0) cc_final: 0.7562 (t0) REVERT: A 445 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8384 (ttt180) REVERT: A 557 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: A 775 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8289 (tpp80) REVERT: A 840 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.5709 (mtm180) REVERT: A 1017 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7783 (pp30) REVERT: A 1120 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8942 (tp40) REVERT: A 1179 PHE cc_start: 0.8402 (m-80) cc_final: 0.8186 (m-80) REVERT: C 41 ARG cc_start: 0.6628 (tmt-80) cc_final: 0.5583 (mtp180) REVERT: C 146 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: C 176 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8378 (mttp) REVERT: C 267 PHE cc_start: 0.7435 (m-80) cc_final: 0.7193 (m-80) REVERT: C 341 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7529 (tm-30) REVERT: C 349 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7879 (tm-30) REVERT: D 37 MET cc_start: 0.7114 (ttm) cc_final: 0.5853 (mpt) REVERT: D 45 MET cc_start: 0.8337 (mtt) cc_final: 0.8032 (mtt) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 0.5867 time to fit residues: 87.3222 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 445 ARG 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 840 ARG Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1120 GLN 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 176 LYS 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 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.3771 r_free = 0.3771 target = 0.143325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101234 restraints weight = 14798.466| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.27 r_work: 0.3102 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11251 Z= 0.180 Angle : 0.707 13.514 15300 Z= 0.347 Chirality : 0.046 0.228 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.544 63.600 1539 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.21 % Favored : 88.64 % Rotamer: Outliers : 2.27 % Allowed : 18.40 % Favored : 79.33 % 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: -2.70 (0.23), residues: 1356 helix: -1.82 (0.32), residues: 267 sheet: -1.03 (0.29), residues: 360 loop : -2.21 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 306 TYR 0.040 0.002 TYR A 358 PHE 0.017 0.001 PHE C 72 TRP 0.022 0.001 TRP A 271 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00437 (11246) covalent geometry : angle 0.70426 (15292) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.44866 ( 2) hydrogen bonds : bond 0.03400 ( 253) hydrogen bonds : angle 4.83280 ( 711) metal coordination : bond 0.00400 ( 4) metal coordination : angle 3.35460 ( 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 142 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6767 (t60) cc_final: 0.6444 (t60) REVERT: A 170 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8021 (tpm-80) REVERT: A 300 MET cc_start: 0.6803 (ttp) cc_final: 0.6489 (ptm) REVERT: A 405 ASP cc_start: 0.8027 (t0) cc_final: 0.7634 (t0) REVERT: A 445 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8433 (ttt180) REVERT: A 557 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 775 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8318 (tpp80) REVERT: A 840 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5779 (mtm180) REVERT: A 939 GLU cc_start: 0.8369 (pp20) cc_final: 0.8105 (pp20) REVERT: A 1120 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8919 (tp40) REVERT: C 41 ARG cc_start: 0.6700 (tmt-80) cc_final: 0.5630 (mtp180) REVERT: C 146 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: C 176 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8433 (mttp) REVERT: C 267 PHE cc_start: 0.7552 (m-80) cc_final: 0.7311 (m-80) REVERT: C 341 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7538 (tm-30) REVERT: C 349 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 37 MET cc_start: 0.7157 (ttm) cc_final: 0.5902 (mpt) REVERT: D 45 MET cc_start: 0.8319 (mtt) cc_final: 0.7894 (mtt) outliers start: 27 outliers final: 16 residues processed: 131 average time/residue: 0.6203 time to fit residues: 87.3296 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU 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 445 ARG 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 840 ARG 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 A residue 1120 GLN 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 176 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 62 VAL 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: 0.6980 chunk 116 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.3779 r_free = 0.3779 target = 0.143911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102028 restraints weight = 14828.134| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.26 r_work: 0.3115 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2470 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= 0.151 Angle : 0.697 13.925 15300 Z= 0.343 Chirality : 0.045 0.242 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.515 63.455 1539 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.18 % Favored : 89.68 % Rotamer: Outliers : 2.02 % Allowed : 18.99 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.23), residues: 1356 helix: -1.71 (0.33), residues: 267 sheet: -1.05 (0.28), residues: 359 loop : -2.16 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 306 TYR 0.032 0.002 TYR A 358 PHE 0.018 0.001 PHE A 160 TRP 0.022 0.001 TRP A 271 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00368 (11246) covalent geometry : angle 0.69433 (15292) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.44823 ( 2) hydrogen bonds : bond 0.03221 ( 253) hydrogen bonds : angle 4.78671 ( 711) metal coordination : bond 0.00351 ( 4) metal coordination : angle 3.22959 ( 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 136 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6684 (t60) cc_final: 0.6389 (t60) REVERT: A 170 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7964 (tpm-80) REVERT: A 300 MET cc_start: 0.6831 (ttp) cc_final: 0.6536 (ptm) REVERT: A 405 ASP cc_start: 0.8004 (t0) cc_final: 0.7609 (t0) REVERT: A 445 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8443 (ttt180) REVERT: A 557 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: A 775 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8328 (tpp80) REVERT: A 840 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5779 (mtm180) REVERT: A 939 GLU cc_start: 0.8365 (pp20) cc_final: 0.7909 (pp20) REVERT: A 1120 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8930 (tp40) REVERT: C 41 ARG cc_start: 0.6694 (tmt-80) cc_final: 0.5642 (mtp180) REVERT: C 146 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: C 176 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8409 (mttp) REVERT: C 267 PHE cc_start: 0.7542 (m-80) cc_final: 0.7305 (m-80) REVERT: C 341 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7546 (tm-30) REVERT: C 349 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7851 (tm-30) REVERT: D 37 MET cc_start: 0.7110 (ttm) cc_final: 0.5893 (mpt) REVERT: D 45 MET cc_start: 0.8333 (mtt) cc_final: 0.7910 (mtt) outliers start: 24 outliers final: 14 residues processed: 125 average time/residue: 0.6494 time to fit residues: 87.0474 Evaluate side-chains 130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 445 ARG 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 840 ARG 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 A residue 1120 GLN 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 176 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 62 VAL 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: 4.9990 chunk 14 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 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 = 0.3809 r_free = 0.3809 target = 0.146447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104635 restraints weight = 14902.359| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.28 r_work: 0.3138 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11251 Z= 0.118 Angle : 0.671 14.291 15300 Z= 0.329 Chirality : 0.044 0.232 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.322 62.644 1539 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.96 % Favored : 89.90 % Rotamer: Outliers : 2.02 % Allowed : 19.08 % Favored : 78.91 % 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: -2.45 (0.23), residues: 1356 helix: -1.51 (0.34), residues: 263 sheet: -0.77 (0.29), residues: 348 loop : -2.14 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 306 TYR 0.026 0.001 TYR A 358 PHE 0.018 0.001 PHE A 160 TRP 0.019 0.001 TRP A 271 HIS 0.005 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00284 (11246) covalent geometry : angle 0.66977 (15292) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.48254 ( 2) hydrogen bonds : bond 0.02795 ( 253) hydrogen bonds : angle 4.59543 ( 711) metal coordination : bond 0.00255 ( 4) metal coordination : angle 2.38950 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.79 seconds wall clock time: 72 minutes 28.43 seconds (4348.43 seconds total)