Starting phenix.real_space_refine on Tue Nov 18 00:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uar_8461/11_2025/5uar_8461.map" } resolution = 3.73 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= 0.013 sd= 0.196 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 6177 2.51 5 N 1585 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9489 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9469 Classifications: {'peptide': 1184} Link IDs: {'PTRANS': 39, 'TRANS': 1144} Chain breaks: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'D10': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9489 At special positions: 0 Unit cell: (105, 122.64, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1672 8.00 N 1585 7.00 C 6177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.94 Conformation dependent library (CDL) restraints added in 355.1 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 69.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.636A pdb=" N GLU A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 9 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.541A pdb=" N GLY A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 28 " --> pdb=" O MET A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 63 removed outlier: 3.623A pdb=" N ARG A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.501A pdb=" N ARG A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 95 removed outlier: 3.584A pdb=" N PHE A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.701A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 166 removed outlier: 3.532A pdb=" N GLY A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.732A pdb=" N HIS A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.758A pdb=" N LEU A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 177 through 196 removed outlier: 3.771A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 189 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.628A pdb=" N ILE A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.583A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 269 removed outlier: 3.560A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.735A pdb=" N GLN A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.554A pdb=" N VAL A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 328 removed outlier: 3.630A pdb=" N ILE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Proline residue: A 325 - end of helix removed outlier: 3.730A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.514A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 377 removed outlier: 3.544A pdb=" N MET A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.813A pdb=" N MET A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.825A pdb=" N LYS A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.564A pdb=" N ALA A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.781A pdb=" N ARG A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 3.745A pdb=" N LYS A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 590 " --> pdb=" O PHE A 586 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 628 through 634 removed outlier: 3.567A pdb=" N SER A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 653 through 669 removed outlier: 3.718A pdb=" N HIS A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 853 removed outlier: 3.687A pdb=" N VAL A 848 " --> pdb=" O TRP A 844 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 853 " --> pdb=" O ARG A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 882 removed outlier: 3.710A pdb=" N LEU A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 891 removed outlier: 3.741A pdb=" N LEU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 removed outlier: 3.715A pdb=" N ALA A 929 " --> pdb=" O TYR A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.574A pdb=" N LEU A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 943 Processing helix chain 'A' and resid 943 through 966 removed outlier: 3.578A pdb=" N HIS A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 951 " --> pdb=" O HIS A 947 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 958 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 986 removed outlier: 3.572A pdb=" N ARG A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1020 removed outlier: 4.853A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A1000 " --> pdb=" O PRO A 996 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1069 removed outlier: 3.744A pdb=" N ALA A1026 " --> pdb=" O TYR A1022 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 3.561A pdb=" N VAL A1036 " --> pdb=" O ILE A1032 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A1044 " --> pdb=" O TYR A1040 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A1050 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Proline residue: A1058 - end of helix removed outlier: 3.906A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY A1069 " --> pdb=" O MET A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.920A pdb=" N ARG A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1075 " --> pdb=" O TRP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1128 removed outlier: 3.796A pdb=" N PHE A1082 " --> pdb=" O ARG A1078 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1090 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A1093 " --> pdb=" O THR A1089 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1115 " --> pdb=" O ALA A1111 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1118 " --> pdb=" O LEU A1114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A1128 " --> pdb=" O TRP A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1146 removed outlier: 3.719A pdb=" N CYS A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1146 " --> pdb=" O CYS A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1176 removed outlier: 4.469A pdb=" N THR A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A1153 " --> pdb=" O GLY A1149 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A1162 " --> pdb=" O SER A1158 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A1166 " --> pdb=" O ASP A1162 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A1167 " --> pdb=" O GLY A1163 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A1169 " --> pdb=" O MET A1165 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1260 removed outlier: 3.624A pdb=" N LEU A1254 " --> pdb=" O GLY A1250 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1312 through 1324 Processing helix chain 'A' and resid 1326 through 1331 removed outlier: 4.127A pdb=" N GLN A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1364 removed outlier: 3.663A pdb=" N LEU A1354 " --> pdb=" O GLY A1350 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS A1356 " --> pdb=" O LYS A1352 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1377 Processing helix chain 'A' and resid 1378 through 1393 removed outlier: 3.764A pdb=" N LYS A1383 " --> pdb=" O PRO A1379 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1427 through 1433 removed outlier: 3.862A pdb=" N ASN A1433 " --> pdb=" O GLN A1429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 400 removed outlier: 4.805A pdb=" N VAL A 398 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 568 through 569 removed outlier: 6.545A pdb=" N TYR A 568 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 614 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 618 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS A 619 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1288 removed outlier: 6.649A pdb=" N GLY A1288 " --> pdb=" O LEU A1369 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A1401 " --> pdb=" O LEU A1370 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A1413 " --> pdb=" O ARG A1240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1299 through 1300 455 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2933 1.35 - 1.48: 2373 1.48 - 1.61: 4295 1.61 - 1.73: 0 1.73 - 1.86: 93 Bond restraints: 9694 Sorted by residual: bond pdb=" CA ILE A 337 " pdb=" CB ILE A 337 " ideal model delta sigma weight residual 1.539 1.576 -0.037 1.13e-02 7.83e+03 1.06e+01 bond pdb=" N LEU A 995 " pdb=" CA LEU A 995 " ideal model delta sigma weight residual 1.463 1.482 -0.018 6.90e-03 2.10e+04 7.09e+00 bond pdb=" CA ARG A1020 " pdb=" C ARG A1020 " ideal model delta sigma weight residual 1.523 1.548 -0.026 1.00e-02 1.00e+04 6.53e+00 bond pdb=" N LEU A 189 " pdb=" CA LEU A 189 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.36e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.90e-02 2.77e+03 5.78e+00 ... (remaining 9689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11246 1.69 - 3.39: 1713 3.39 - 5.08: 112 5.08 - 6.77: 20 6.77 - 8.47: 4 Bond angle restraints: 13095 Sorted by residual: angle pdb=" N MET A 975 " pdb=" CA MET A 975 " pdb=" C MET A 975 " ideal model delta sigma weight residual 111.28 116.93 -5.65 1.09e+00 8.42e-01 2.69e+01 angle pdb=" N ASN A 188 " pdb=" CA ASN A 188 " pdb=" C ASN A 188 " ideal model delta sigma weight residual 112.23 118.67 -6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" C ASP A1378 " pdb=" N PRO A1379 " pdb=" CA PRO A1379 " ideal model delta sigma weight residual 119.84 125.15 -5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" N PHE A 110 " pdb=" CA PHE A 110 " pdb=" C PHE A 110 " ideal model delta sigma weight residual 108.52 115.42 -6.90 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" C GLN A 39 " ideal model delta sigma weight residual 110.33 115.69 -5.36 1.29e+00 6.01e-01 1.73e+01 ... (remaining 13090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5328 17.79 - 35.59: 385 35.59 - 53.38: 83 53.38 - 71.17: 12 71.17 - 88.97: 2 Dihedral angle restraints: 5810 sinusoidal: 2357 harmonic: 3453 Sorted by residual: dihedral pdb=" CA CYS A 77 " pdb=" C CYS A 77 " pdb=" N TYR A 78 " pdb=" CA TYR A 78 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 174 " pdb=" C ASP A 174 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG A1284 " pdb=" C ARG A1284 " pdb=" N LYS A1285 " pdb=" CA LYS A1285 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1027 0.054 - 0.107: 352 0.107 - 0.161: 97 0.161 - 0.215: 22 0.215 - 0.268: 5 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CA THR A 977 " pdb=" N THR A 977 " pdb=" C THR A 977 " pdb=" CB THR A 977 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE A 201 " pdb=" N PHE A 201 " pdb=" C PHE A 201 " pdb=" CB PHE A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE A1296 " pdb=" N ILE A1296 " pdb=" C ILE A1296 " pdb=" CB ILE A1296 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1500 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 99 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 100 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1057 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A1058 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 325 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.028 5.00e-02 4.00e+02 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3166 2.89 - 3.40: 9441 3.40 - 3.90: 14257 3.90 - 4.40: 15210 4.40 - 4.90: 26547 Nonbonded interactions: 68621 Sorted by model distance: nonbonded pdb=" O VAL A1384 " pdb=" OG1 THR A1388 " model vdw 2.393 3.040 nonbonded pdb=" O TYR A1220 " pdb=" OG1 THR A1221 " model vdw 2.508 3.040 nonbonded pdb=" O ASN A 10 " pdb=" OG SER A 13 " model vdw 2.539 3.040 nonbonded pdb=" O GLU A 293 " pdb=" OG1 THR A 297 " model vdw 2.558 3.040 nonbonded pdb=" O PHE A 945 " pdb=" OG1 THR A 949 " model vdw 2.564 3.040 ... (remaining 68616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.008 0.054 9694 Z= 0.557 Angle : 1.182 8.467 13095 Z= 0.816 Chirality : 0.061 0.268 1503 Planarity : 0.004 0.053 1611 Dihedral : 13.303 88.968 3576 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.50 % Rotamer: Outliers : 1.06 % Allowed : 5.89 % Favored : 93.04 % 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: -3.58 (0.20), residues: 1174 helix: -2.16 (0.15), residues: 702 sheet: -2.76 (0.65), residues: 33 loop : -2.46 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1020 TYR 0.008 0.001 TYR A 248 PHE 0.015 0.001 PHE A 201 TRP 0.011 0.002 TRP A 19 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00770 ( 9694) covalent geometry : angle 1.18184 (13095) hydrogen bonds : bond 0.24332 ( 455) hydrogen bonds : angle 9.29969 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 350 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8247 (mt-10) REVERT: A 11 CYS cc_start: 0.8537 (p) cc_final: 0.8184 (t) REVERT: A 12 LEU cc_start: 0.8953 (mp) cc_final: 0.8511 (tt) REVERT: A 52 ARG cc_start: 0.9218 (ttt180) cc_final: 0.8945 (mmm-85) REVERT: A 56 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8555 (mp0) REVERT: A 60 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 70 LEU cc_start: 0.8466 (tp) cc_final: 0.8139 (tp) REVERT: A 93 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8931 (tp30) REVERT: A 122 TYR cc_start: 0.7951 (m-80) cc_final: 0.7691 (m-80) REVERT: A 207 LEU cc_start: 0.8795 (tp) cc_final: 0.8579 (tt) REVERT: A 288 ASN cc_start: 0.9142 (t0) cc_final: 0.8790 (m110) REVERT: A 296 LEU cc_start: 0.8215 (mt) cc_final: 0.7815 (tp) REVERT: A 336 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8409 (ttp-110) REVERT: A 463 LYS cc_start: 0.7512 (tttp) cc_final: 0.7018 (pttm) REVERT: A 509 LEU cc_start: 0.8964 (mt) cc_final: 0.8212 (tp) REVERT: A 631 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8107 (mp0) REVERT: A 633 GLN cc_start: 0.8168 (mt0) cc_final: 0.7697 (mm-40) REVERT: A 870 ILE cc_start: 0.8348 (mm) cc_final: 0.8064 (pt) REVERT: A 922 TYR cc_start: 0.8447 (p90) cc_final: 0.8133 (p90) REVERT: A 981 MET cc_start: 0.7524 (mmm) cc_final: 0.7323 (mmp) REVERT: A 1133 LYS cc_start: 0.9336 (pttt) cc_final: 0.9011 (pttt) REVERT: A 1170 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7941 (mtm180) REVERT: A 1173 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8692 (mmtm) REVERT: A 1277 LYS cc_start: 0.8625 (mttt) cc_final: 0.8280 (ttmt) REVERT: A 1287 PHE cc_start: 0.8639 (m-80) cc_final: 0.8127 (m-80) REVERT: A 1313 ASP cc_start: 0.8725 (m-30) cc_final: 0.8062 (p0) REVERT: A 1334 ASP cc_start: 0.8369 (m-30) cc_final: 0.7997 (t0) REVERT: A 1337 ASP cc_start: 0.8910 (t70) cc_final: 0.8489 (m-30) REVERT: A 1366 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7776 (tmt170) REVERT: A 1423 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8177 (pttt) outliers start: 11 outliers final: 1 residues processed: 358 average time/residue: 0.1061 time to fit residues: 51.9722 Evaluate side-chains 230 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 396 GLN A 845 ASN ** A1131 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.122361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099885 restraints weight = 24992.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103180 restraints weight = 12737.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105427 restraints weight = 8024.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106966 restraints weight = 5747.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107687 restraints weight = 4505.905| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9694 Z= 0.162 Angle : 0.677 8.347 13095 Z= 0.348 Chirality : 0.042 0.177 1503 Planarity : 0.005 0.048 1611 Dihedral : 5.090 36.748 1297 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.96 % Allowed : 14.30 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1174 helix: -0.10 (0.18), residues: 711 sheet: -2.08 (0.57), residues: 45 loop : -2.22 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 515 TYR 0.016 0.001 TYR A1263 PHE 0.019 0.001 PHE A 940 TRP 0.015 0.002 TRP A1153 HIS 0.008 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9694) covalent geometry : angle 0.67662 (13095) hydrogen bonds : bond 0.05647 ( 455) hydrogen bonds : angle 5.41272 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8138 (ppp) cc_final: 0.7702 (ppp) REVERT: A 12 LEU cc_start: 0.8959 (mp) cc_final: 0.8503 (tt) REVERT: A 24 MET cc_start: 0.8094 (tpp) cc_final: 0.7664 (mtp) REVERT: A 60 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 93 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9246 (tp30) REVERT: A 135 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7786 (ttm110) REVERT: A 207 LEU cc_start: 0.9169 (tp) cc_final: 0.8897 (tt) REVERT: A 288 ASN cc_start: 0.9190 (t0) cc_final: 0.8867 (m110) REVERT: A 345 MET cc_start: 0.8926 (mmm) cc_final: 0.8609 (mmt) REVERT: A 386 TYR cc_start: 0.6327 (p90) cc_final: 0.5557 (p90) REVERT: A 388 LEU cc_start: 0.8967 (mt) cc_final: 0.8470 (mp) REVERT: A 399 THR cc_start: 0.8258 (m) cc_final: 0.7923 (p) REVERT: A 463 LYS cc_start: 0.7747 (tttp) cc_final: 0.7204 (pttp) REVERT: A 496 ILE cc_start: 0.8471 (mm) cc_final: 0.8145 (tp) REVERT: A 509 LEU cc_start: 0.8625 (mt) cc_final: 0.8040 (tp) REVERT: A 540 MET cc_start: 0.8061 (tpp) cc_final: 0.7765 (tpp) REVERT: A 1133 LYS cc_start: 0.8984 (pttt) cc_final: 0.8728 (pttt) REVERT: A 1220 TYR cc_start: 0.6466 (t80) cc_final: 0.5939 (t80) REVERT: A 1277 LYS cc_start: 0.8576 (mttt) cc_final: 0.8267 (ttmt) REVERT: A 1278 MET cc_start: 0.7147 (mtt) cc_final: 0.6539 (mtt) REVERT: A 1313 ASP cc_start: 0.8566 (m-30) cc_final: 0.7969 (p0) REVERT: A 1334 ASP cc_start: 0.7774 (m-30) cc_final: 0.7509 (t0) REVERT: A 1417 MET cc_start: 0.6960 (tmm) cc_final: 0.6683 (tmm) outliers start: 41 outliers final: 18 residues processed: 271 average time/residue: 0.0881 time to fit residues: 33.9903 Evaluate side-chains 217 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100766 restraints weight = 25173.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104045 restraints weight = 12877.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106275 restraints weight = 8123.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107887 restraints weight = 5850.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108890 restraints weight = 4574.607| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9694 Z= 0.130 Angle : 0.626 8.036 13095 Z= 0.314 Chirality : 0.040 0.164 1503 Planarity : 0.004 0.048 1611 Dihedral : 4.779 37.304 1297 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.83 % Allowed : 17.87 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1174 helix: 0.30 (0.19), residues: 717 sheet: -1.60 (0.59), residues: 50 loop : -2.09 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1366 TYR 0.019 0.001 TYR A 122 PHE 0.014 0.001 PHE A 126 TRP 0.011 0.001 TRP A1153 HIS 0.004 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9694) covalent geometry : angle 0.62566 (13095) hydrogen bonds : bond 0.04843 ( 455) hydrogen bonds : angle 4.98625 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8946 (mp) cc_final: 0.8469 (tt) REVERT: A 24 MET cc_start: 0.8075 (tpp) cc_final: 0.7356 (ttm) REVERT: A 33 ARG cc_start: 0.8695 (mtt180) cc_final: 0.7877 (ptp90) REVERT: A 60 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 93 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9154 (tp30) REVERT: A 122 TYR cc_start: 0.7512 (m-80) cc_final: 0.6696 (m-80) REVERT: A 123 PHE cc_start: 0.7590 (m-10) cc_final: 0.6134 (t80) REVERT: A 135 ARG cc_start: 0.8455 (ttp80) cc_final: 0.7837 (ttm110) REVERT: A 138 LEU cc_start: 0.9100 (tp) cc_final: 0.8847 (tp) REVERT: A 207 LEU cc_start: 0.9143 (tp) cc_final: 0.8847 (tt) REVERT: A 288 ASN cc_start: 0.9194 (t0) cc_final: 0.8848 (m110) REVERT: A 344 CYS cc_start: 0.9076 (m) cc_final: 0.8744 (t) REVERT: A 361 MET cc_start: 0.7300 (tmm) cc_final: 0.6862 (tmm) REVERT: A 463 LYS cc_start: 0.7715 (tttp) cc_final: 0.7202 (pttp) REVERT: A 496 ILE cc_start: 0.8464 (mm) cc_final: 0.8256 (tp) REVERT: A 509 LEU cc_start: 0.8611 (mt) cc_final: 0.7989 (tp) REVERT: A 540 MET cc_start: 0.8080 (tpp) cc_final: 0.7820 (tpp) REVERT: A 593 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5787 (mm) REVERT: A 631 GLU cc_start: 0.8265 (mp0) cc_final: 0.7750 (mp0) REVERT: A 635 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 849 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8373 (mtp180) REVERT: A 1220 TYR cc_start: 0.6402 (t80) cc_final: 0.5766 (t80) REVERT: A 1278 MET cc_start: 0.7068 (mtt) cc_final: 0.6825 (ttm) REVERT: A 1313 ASP cc_start: 0.8579 (m-30) cc_final: 0.8011 (p0) REVERT: A 1416 MET cc_start: 0.5016 (ttm) cc_final: 0.4668 (ttm) outliers start: 50 outliers final: 32 residues processed: 262 average time/residue: 0.0916 time to fit residues: 34.6281 Evaluate side-chains 237 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 HIS A 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099635 restraints weight = 24963.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.102785 restraints weight = 12885.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104939 restraints weight = 8195.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106444 restraints weight = 5925.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107497 restraints weight = 4670.985| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9694 Z= 0.123 Angle : 0.605 7.331 13095 Z= 0.304 Chirality : 0.041 0.164 1503 Planarity : 0.004 0.045 1611 Dihedral : 4.668 37.460 1297 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.93 % Allowed : 19.52 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1174 helix: 0.52 (0.19), residues: 721 sheet: -1.18 (0.63), residues: 50 loop : -2.04 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 336 TYR 0.019 0.001 TYR A 925 PHE 0.014 0.001 PHE A 126 TRP 0.017 0.001 TRP A 203 HIS 0.004 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9694) covalent geometry : angle 0.60466 (13095) hydrogen bonds : bond 0.04409 ( 455) hydrogen bonds : angle 4.73284 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8130 (ppp) cc_final: 0.7926 (ppp) REVERT: A 12 LEU cc_start: 0.8989 (mp) cc_final: 0.8579 (tt) REVERT: A 24 MET cc_start: 0.8206 (tpp) cc_final: 0.7904 (mtt) REVERT: A 33 ARG cc_start: 0.8702 (mtt180) cc_final: 0.7814 (ptp90) REVERT: A 43 GLN cc_start: 0.8538 (tp40) cc_final: 0.7924 (tp-100) REVERT: A 60 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 93 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9058 (tp30) REVERT: A 122 TYR cc_start: 0.7684 (m-80) cc_final: 0.6979 (m-80) REVERT: A 123 PHE cc_start: 0.7587 (m-10) cc_final: 0.6197 (t80) REVERT: A 135 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7715 (ttm110) REVERT: A 207 LEU cc_start: 0.9157 (tp) cc_final: 0.8900 (tt) REVERT: A 279 GLU cc_start: 0.7373 (mp0) cc_final: 0.7142 (mp0) REVERT: A 288 ASN cc_start: 0.9184 (t0) cc_final: 0.8836 (m110) REVERT: A 361 MET cc_start: 0.7406 (tmm) cc_final: 0.6984 (tmm) REVERT: A 509 LEU cc_start: 0.8607 (mt) cc_final: 0.7937 (tp) REVERT: A 631 GLU cc_start: 0.8200 (mp0) cc_final: 0.7846 (pt0) REVERT: A 635 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 655 GLU cc_start: 0.7470 (pt0) cc_final: 0.6765 (tm-30) REVERT: A 849 ARG cc_start: 0.8834 (mtt180) cc_final: 0.8395 (mtp180) REVERT: A 960 MET cc_start: 0.8950 (ttt) cc_final: 0.8313 (tmm) REVERT: A 1004 GLN cc_start: 0.8902 (tp40) cc_final: 0.8517 (tp40) REVERT: A 1133 LYS cc_start: 0.8880 (pttt) cc_final: 0.8480 (ptmt) REVERT: A 1220 TYR cc_start: 0.6307 (t80) cc_final: 0.5558 (t80) REVERT: A 1313 ASP cc_start: 0.8594 (m-30) cc_final: 0.8054 (p0) REVERT: A 1366 ARG cc_start: 0.8111 (mmp-170) cc_final: 0.7671 (mmm160) REVERT: A 1416 MET cc_start: 0.5103 (ttt) cc_final: 0.4758 (ttm) REVERT: A 1417 MET cc_start: 0.6604 (tmm) cc_final: 0.6228 (tmm) outliers start: 51 outliers final: 36 residues processed: 257 average time/residue: 0.0872 time to fit residues: 32.7597 Evaluate side-chains 242 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 104 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.124390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102103 restraints weight = 25144.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105264 restraints weight = 13027.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107357 restraints weight = 8322.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108713 restraints weight = 6065.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.109842 restraints weight = 4861.859| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9694 Z= 0.115 Angle : 0.594 8.169 13095 Z= 0.294 Chirality : 0.039 0.156 1503 Planarity : 0.004 0.046 1611 Dihedral : 4.505 37.272 1297 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.15 % Allowed : 20.29 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1174 helix: 0.58 (0.19), residues: 724 sheet: -1.10 (0.65), residues: 46 loop : -1.84 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.014 0.001 TYR A1342 PHE 0.026 0.001 PHE A 863 TRP 0.017 0.001 TRP A 203 HIS 0.003 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9694) covalent geometry : angle 0.59434 (13095) hydrogen bonds : bond 0.04119 ( 455) hydrogen bonds : angle 4.55647 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8122 (ppp) cc_final: 0.7898 (ppp) REVERT: A 12 LEU cc_start: 0.8987 (mp) cc_final: 0.8556 (tt) REVERT: A 24 MET cc_start: 0.8095 (tpp) cc_final: 0.7842 (mtt) REVERT: A 33 ARG cc_start: 0.8680 (mtt180) cc_final: 0.7775 (ptp90) REVERT: A 60 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8311 (mm-30) REVERT: A 93 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9088 (tp30) REVERT: A 122 TYR cc_start: 0.7771 (m-80) cc_final: 0.7013 (m-80) REVERT: A 123 PHE cc_start: 0.7521 (m-10) cc_final: 0.6158 (t80) REVERT: A 135 ARG cc_start: 0.8508 (ttp80) cc_final: 0.7738 (ttm110) REVERT: A 207 LEU cc_start: 0.9160 (tp) cc_final: 0.8906 (tt) REVERT: A 265 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: A 279 GLU cc_start: 0.7419 (mp0) cc_final: 0.6717 (mp0) REVERT: A 288 ASN cc_start: 0.9146 (t0) cc_final: 0.8825 (m110) REVERT: A 361 MET cc_start: 0.7453 (tmm) cc_final: 0.7016 (tmm) REVERT: A 384 MET cc_start: 0.7951 (tmm) cc_final: 0.7696 (tmm) REVERT: A 452 MET cc_start: 0.8122 (tpp) cc_final: 0.7669 (tpp) REVERT: A 509 LEU cc_start: 0.8637 (mt) cc_final: 0.7926 (tp) REVERT: A 517 LYS cc_start: 0.9473 (pttt) cc_final: 0.9259 (pttp) REVERT: A 655 GLU cc_start: 0.7379 (pt0) cc_final: 0.6668 (tm-30) REVERT: A 932 GLU cc_start: 0.9079 (tp30) cc_final: 0.8374 (tp30) REVERT: A 960 MET cc_start: 0.8901 (ttt) cc_final: 0.8251 (tmm) REVERT: A 1133 LYS cc_start: 0.8812 (pttt) cc_final: 0.8455 (pttm) REVERT: A 1220 TYR cc_start: 0.6314 (t80) cc_final: 0.5530 (t80) REVERT: A 1337 ASP cc_start: 0.7349 (m-30) cc_final: 0.6960 (m-30) REVERT: A 1386 LYS cc_start: 0.8897 (mttm) cc_final: 0.8398 (tppt) REVERT: A 1416 MET cc_start: 0.5057 (ttt) cc_final: 0.4739 (ttm) REVERT: A 1417 MET cc_start: 0.6680 (tmm) cc_final: 0.6464 (tmm) outliers start: 43 outliers final: 30 residues processed: 245 average time/residue: 0.0830 time to fit residues: 29.4305 Evaluate side-chains 234 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.100973 restraints weight = 25225.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104108 restraints weight = 12950.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106220 restraints weight = 8238.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107668 restraints weight = 5939.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108698 restraints weight = 4693.648| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9694 Z= 0.121 Angle : 0.598 7.159 13095 Z= 0.296 Chirality : 0.039 0.153 1503 Planarity : 0.004 0.051 1611 Dihedral : 4.473 37.413 1297 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.15 % Allowed : 20.97 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1174 helix: 0.62 (0.19), residues: 714 sheet: -0.38 (0.71), residues: 38 loop : -1.60 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.012 0.001 TYR A1342 PHE 0.010 0.001 PHE A 940 TRP 0.017 0.001 TRP A 203 HIS 0.006 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9694) covalent geometry : angle 0.59791 (13095) hydrogen bonds : bond 0.04012 ( 455) hydrogen bonds : angle 4.48810 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8110 (ppp) cc_final: 0.7890 (ppp) REVERT: A 12 LEU cc_start: 0.9025 (mp) cc_final: 0.8620 (tt) REVERT: A 33 ARG cc_start: 0.8663 (mtt180) cc_final: 0.7808 (ptp90) REVERT: A 43 GLN cc_start: 0.8494 (tp40) cc_final: 0.7981 (tp-100) REVERT: A 60 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8285 (mm-30) REVERT: A 93 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9112 (tp30) REVERT: A 122 TYR cc_start: 0.7836 (m-80) cc_final: 0.7012 (m-80) REVERT: A 123 PHE cc_start: 0.7428 (m-10) cc_final: 0.6165 (t80) REVERT: A 135 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7810 (ttm110) REVERT: A 207 LEU cc_start: 0.9181 (tp) cc_final: 0.8945 (tt) REVERT: A 265 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: A 288 ASN cc_start: 0.9134 (t0) cc_final: 0.8827 (m110) REVERT: A 361 MET cc_start: 0.7542 (tmm) cc_final: 0.7098 (tmm) REVERT: A 399 THR cc_start: 0.8148 (m) cc_final: 0.7878 (p) REVERT: A 452 MET cc_start: 0.8203 (tpp) cc_final: 0.7874 (tpp) REVERT: A 655 GLU cc_start: 0.7401 (pt0) cc_final: 0.6685 (tm-30) REVERT: A 960 MET cc_start: 0.8930 (ttt) cc_final: 0.8209 (tmm) REVERT: A 994 MET cc_start: 0.7821 (mmm) cc_final: 0.7510 (mtp) REVERT: A 1133 LYS cc_start: 0.8817 (pttt) cc_final: 0.8493 (pttm) REVERT: A 1220 TYR cc_start: 0.6333 (t80) cc_final: 0.5474 (t80) REVERT: A 1337 ASP cc_start: 0.7375 (m-30) cc_final: 0.6976 (m-30) REVERT: A 1386 LYS cc_start: 0.8911 (mttm) cc_final: 0.8396 (tppt) REVERT: A 1416 MET cc_start: 0.5034 (ttt) cc_final: 0.4679 (ttm) outliers start: 43 outliers final: 31 residues processed: 233 average time/residue: 0.0814 time to fit residues: 28.0904 Evaluate side-chains 236 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097927 restraints weight = 25241.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100985 restraints weight = 12944.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103046 restraints weight = 8205.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104478 restraints weight = 5929.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105484 restraints weight = 4679.813| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9694 Z= 0.144 Angle : 0.625 9.165 13095 Z= 0.310 Chirality : 0.041 0.169 1503 Planarity : 0.004 0.048 1611 Dihedral : 4.607 37.258 1297 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.31 % Allowed : 20.58 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1174 helix: 0.66 (0.19), residues: 709 sheet: -0.46 (0.66), residues: 43 loop : -1.62 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.013 0.001 TYR A1342 PHE 0.031 0.002 PHE A 863 TRP 0.017 0.001 TRP A 203 HIS 0.005 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9694) covalent geometry : angle 0.62478 (13095) hydrogen bonds : bond 0.04323 ( 455) hydrogen bonds : angle 4.56443 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8261 (ppp) cc_final: 0.8001 (ppp) REVERT: A 12 LEU cc_start: 0.9067 (mp) cc_final: 0.8627 (tt) REVERT: A 33 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7822 (ptp90) REVERT: A 43 GLN cc_start: 0.8539 (tp40) cc_final: 0.8097 (tp-100) REVERT: A 60 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 93 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9278 (tp30) REVERT: A 122 TYR cc_start: 0.8120 (m-80) cc_final: 0.7130 (m-80) REVERT: A 123 PHE cc_start: 0.7439 (m-10) cc_final: 0.6179 (t80) REVERT: A 207 LEU cc_start: 0.9165 (tp) cc_final: 0.8913 (tt) REVERT: A 265 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8225 (tp30) REVERT: A 288 ASN cc_start: 0.9152 (t0) cc_final: 0.8847 (m110) REVERT: A 361 MET cc_start: 0.7730 (tmm) cc_final: 0.7242 (tmm) REVERT: A 399 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7855 (p) REVERT: A 452 MET cc_start: 0.8350 (tpp) cc_final: 0.8085 (tpp) REVERT: A 631 GLU cc_start: 0.8141 (pt0) cc_final: 0.7664 (mt-10) REVERT: A 655 GLU cc_start: 0.7381 (pt0) cc_final: 0.6615 (tm-30) REVERT: A 960 MET cc_start: 0.8970 (ttt) cc_final: 0.8239 (tmm) REVERT: A 1112 ASP cc_start: 0.8417 (t0) cc_final: 0.7877 (t70) REVERT: A 1133 LYS cc_start: 0.8837 (pttt) cc_final: 0.8489 (pttm) REVERT: A 1220 TYR cc_start: 0.6198 (t80) cc_final: 0.5374 (t80) REVERT: A 1278 MET cc_start: 0.6893 (ttm) cc_final: 0.6593 (ttm) REVERT: A 1281 GLN cc_start: 0.8632 (pm20) cc_final: 0.8259 (pm20) REVERT: A 1282 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8737 (pttt) REVERT: A 1337 ASP cc_start: 0.7433 (m-30) cc_final: 0.6984 (m-30) REVERT: A 1386 LYS cc_start: 0.8930 (mttm) cc_final: 0.8424 (tppt) REVERT: A 1416 MET cc_start: 0.4935 (ttt) cc_final: 0.4649 (ttm) REVERT: A 1417 MET cc_start: 0.6653 (tmm) cc_final: 0.6272 (tpp) outliers start: 55 outliers final: 35 residues processed: 243 average time/residue: 0.0893 time to fit residues: 31.4212 Evaluate side-chains 233 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 MET Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1282 LYS Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 91 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.100447 restraints weight = 25266.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.103536 restraints weight = 13011.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105669 restraints weight = 8293.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107130 restraints weight = 5977.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108185 restraints weight = 4714.448| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9694 Z= 0.113 Angle : 0.610 9.778 13095 Z= 0.297 Chirality : 0.039 0.165 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.513 38.318 1297 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.29 % Allowed : 22.90 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1174 helix: 0.80 (0.20), residues: 701 sheet: -0.27 (0.67), residues: 43 loop : -1.38 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.017 0.001 TYR A 925 PHE 0.033 0.001 PHE A 863 TRP 0.018 0.001 TRP A 203 HIS 0.004 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9694) covalent geometry : angle 0.61030 (13095) hydrogen bonds : bond 0.03918 ( 455) hydrogen bonds : angle 4.38942 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8233 (ppp) cc_final: 0.7996 (ppp) REVERT: A 7 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7578 (pt0) REVERT: A 12 LEU cc_start: 0.8992 (mp) cc_final: 0.8566 (tt) REVERT: A 33 ARG cc_start: 0.8647 (mtt180) cc_final: 0.7817 (ptp90) REVERT: A 43 GLN cc_start: 0.8602 (tp40) cc_final: 0.8151 (tp-100) REVERT: A 60 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 93 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9048 (tp30) REVERT: A 122 TYR cc_start: 0.8086 (m-80) cc_final: 0.7204 (m-80) REVERT: A 123 PHE cc_start: 0.7318 (m-10) cc_final: 0.6154 (t80) REVERT: A 135 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7712 (ttm110) REVERT: A 136 PHE cc_start: 0.7762 (m-80) cc_final: 0.7441 (m-80) REVERT: A 138 LEU cc_start: 0.9152 (tp) cc_final: 0.8672 (tp) REVERT: A 207 LEU cc_start: 0.9177 (tp) cc_final: 0.8942 (tt) REVERT: A 279 GLU cc_start: 0.7528 (mp0) cc_final: 0.7309 (mp0) REVERT: A 288 ASN cc_start: 0.9130 (t0) cc_final: 0.8839 (m110) REVERT: A 361 MET cc_start: 0.7683 (tmm) cc_final: 0.7165 (tmm) REVERT: A 399 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 631 GLU cc_start: 0.8116 (pt0) cc_final: 0.7669 (mt-10) REVERT: A 655 GLU cc_start: 0.7368 (pt0) cc_final: 0.6602 (tm-30) REVERT: A 960 MET cc_start: 0.8937 (ttt) cc_final: 0.8228 (tmm) REVERT: A 994 MET cc_start: 0.7866 (mmm) cc_final: 0.7593 (mtp) REVERT: A 1004 GLN cc_start: 0.8859 (tp40) cc_final: 0.8439 (tp40) REVERT: A 1040 TYR cc_start: 0.8855 (t80) cc_final: 0.8564 (t80) REVERT: A 1133 LYS cc_start: 0.8789 (pttt) cc_final: 0.8461 (pttm) REVERT: A 1278 MET cc_start: 0.6835 (ttm) cc_final: 0.6031 (ttm) REVERT: A 1281 GLN cc_start: 0.8611 (pm20) cc_final: 0.8298 (pm20) REVERT: A 1282 LYS cc_start: 0.9123 (ptmt) cc_final: 0.8802 (pttt) REVERT: A 1337 ASP cc_start: 0.7389 (m-30) cc_final: 0.6998 (m-30) REVERT: A 1386 LYS cc_start: 0.8898 (mttm) cc_final: 0.8462 (tppt) REVERT: A 1416 MET cc_start: 0.4931 (ttt) cc_final: 0.4604 (ttm) outliers start: 34 outliers final: 28 residues processed: 234 average time/residue: 0.0881 time to fit residues: 30.2997 Evaluate side-chains 228 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.101227 restraints weight = 25596.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104306 restraints weight = 13219.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106399 restraints weight = 8419.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107829 restraints weight = 6089.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.108870 restraints weight = 4823.634| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9694 Z= 0.115 Angle : 0.628 10.060 13095 Z= 0.304 Chirality : 0.040 0.163 1503 Planarity : 0.004 0.041 1611 Dihedral : 4.506 37.891 1297 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.00 % Allowed : 24.25 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1174 helix: 0.82 (0.20), residues: 700 sheet: -0.21 (0.68), residues: 43 loop : -1.40 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.018 0.001 TYR A1342 PHE 0.034 0.001 PHE A 863 TRP 0.016 0.001 TRP A 203 HIS 0.004 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9694) covalent geometry : angle 0.62846 (13095) hydrogen bonds : bond 0.03878 ( 455) hydrogen bonds : angle 4.37465 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8219 (ppp) cc_final: 0.7990 (ppp) REVERT: A 7 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7594 (pt0) REVERT: A 12 LEU cc_start: 0.9027 (mp) cc_final: 0.8600 (tt) REVERT: A 24 MET cc_start: 0.7759 (mtt) cc_final: 0.7425 (mtm) REVERT: A 33 ARG cc_start: 0.8652 (mtt180) cc_final: 0.7855 (ptp90) REVERT: A 43 GLN cc_start: 0.8619 (tp40) cc_final: 0.8165 (tp-100) REVERT: A 60 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 93 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9042 (tp30) REVERT: A 122 TYR cc_start: 0.8192 (m-80) cc_final: 0.7411 (m-80) REVERT: A 135 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7740 (ttm110) REVERT: A 138 LEU cc_start: 0.9211 (tp) cc_final: 0.8788 (tp) REVERT: A 207 LEU cc_start: 0.9223 (tp) cc_final: 0.8976 (tt) REVERT: A 361 MET cc_start: 0.7709 (tmm) cc_final: 0.7229 (tmm) REVERT: A 452 MET cc_start: 0.8318 (tpp) cc_final: 0.7761 (tpp) REVERT: A 631 GLU cc_start: 0.8090 (pt0) cc_final: 0.7643 (mt-10) REVERT: A 655 GLU cc_start: 0.7375 (pt0) cc_final: 0.6597 (tm-30) REVERT: A 960 MET cc_start: 0.8934 (ttt) cc_final: 0.8226 (tmm) REVERT: A 1004 GLN cc_start: 0.8912 (tp40) cc_final: 0.8448 (tp40) REVERT: A 1040 TYR cc_start: 0.8835 (t80) cc_final: 0.8628 (t80) REVERT: A 1133 LYS cc_start: 0.8813 (pttt) cc_final: 0.8480 (pttm) REVERT: A 1278 MET cc_start: 0.6764 (ttm) cc_final: 0.5701 (ttt) REVERT: A 1281 GLN cc_start: 0.8562 (pm20) cc_final: 0.8298 (pm20) REVERT: A 1282 LYS cc_start: 0.9118 (ptmt) cc_final: 0.8826 (pttt) REVERT: A 1287 PHE cc_start: 0.8590 (m-80) cc_final: 0.8365 (m-10) REVERT: A 1337 ASP cc_start: 0.7402 (m-30) cc_final: 0.7005 (m-30) REVERT: A 1386 LYS cc_start: 0.8901 (mttm) cc_final: 0.8438 (tppt) REVERT: A 1416 MET cc_start: 0.4952 (ttt) cc_final: 0.4631 (ttm) outliers start: 31 outliers final: 28 residues processed: 227 average time/residue: 0.0883 time to fit residues: 29.2914 Evaluate side-chains 226 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.0050 chunk 81 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101657 restraints weight = 25581.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104778 restraints weight = 13246.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106875 restraints weight = 8453.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108352 restraints weight = 6117.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109186 restraints weight = 4832.183| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9694 Z= 0.112 Angle : 0.638 13.798 13095 Z= 0.306 Chirality : 0.039 0.159 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.410 38.278 1297 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 24.64 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1174 helix: 0.85 (0.19), residues: 703 sheet: -0.17 (0.69), residues: 43 loop : -1.46 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1166 TYR 0.018 0.001 TYR A 38 PHE 0.034 0.001 PHE A 863 TRP 0.016 0.001 TRP A 203 HIS 0.003 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9694) covalent geometry : angle 0.63818 (13095) hydrogen bonds : bond 0.03744 ( 455) hydrogen bonds : angle 4.33006 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7661 (pt0) REVERT: A 12 LEU cc_start: 0.9028 (mp) cc_final: 0.8604 (tt) REVERT: A 24 MET cc_start: 0.7688 (mtt) cc_final: 0.7463 (mtm) REVERT: A 33 ARG cc_start: 0.8629 (mtt180) cc_final: 0.7808 (ptp90) REVERT: A 43 GLN cc_start: 0.8605 (tp40) cc_final: 0.8164 (tp-100) REVERT: A 60 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 93 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9051 (tp30) REVERT: A 138 LEU cc_start: 0.9219 (tp) cc_final: 0.8798 (tp) REVERT: A 207 LEU cc_start: 0.9196 (tp) cc_final: 0.8962 (tt) REVERT: A 361 MET cc_start: 0.7694 (tmm) cc_final: 0.7188 (tmm) REVERT: A 452 MET cc_start: 0.8299 (tpp) cc_final: 0.7891 (tpp) REVERT: A 631 GLU cc_start: 0.8102 (pt0) cc_final: 0.7663 (mt-10) REVERT: A 655 GLU cc_start: 0.7382 (pt0) cc_final: 0.6620 (tm-30) REVERT: A 960 MET cc_start: 0.8882 (ttt) cc_final: 0.8175 (tmm) REVERT: A 1004 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8466 (tp40) REVERT: A 1133 LYS cc_start: 0.8840 (pttt) cc_final: 0.8509 (pttm) REVERT: A 1278 MET cc_start: 0.6652 (ttm) cc_final: 0.5432 (ttt) REVERT: A 1281 GLN cc_start: 0.8576 (pm20) cc_final: 0.8358 (pm20) REVERT: A 1282 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8869 (pptt) REVERT: A 1337 ASP cc_start: 0.7411 (m-30) cc_final: 0.7014 (m-30) REVERT: A 1386 LYS cc_start: 0.8899 (mttm) cc_final: 0.8440 (tppt) REVERT: A 1416 MET cc_start: 0.4961 (ttt) cc_final: 0.4653 (ttm) outliers start: 31 outliers final: 29 residues processed: 225 average time/residue: 0.0897 time to fit residues: 29.1514 Evaluate side-chains 228 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 922 TYR Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1004 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1167 SER Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101716 restraints weight = 25497.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104777 restraints weight = 13220.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106893 restraints weight = 8453.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108388 restraints weight = 6118.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109428 restraints weight = 4833.570| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9694 Z= 0.114 Angle : 0.636 13.697 13095 Z= 0.306 Chirality : 0.040 0.161 1503 Planarity : 0.004 0.041 1611 Dihedral : 4.358 38.112 1297 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.90 % Allowed : 24.73 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1174 helix: 0.86 (0.20), residues: 704 sheet: -0.62 (0.64), residues: 50 loop : -1.53 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1166 TYR 0.022 0.001 TYR A1040 PHE 0.034 0.001 PHE A 863 TRP 0.015 0.001 TRP A 203 HIS 0.003 0.001 HIS A1351 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9694) covalent geometry : angle 0.63599 (13095) hydrogen bonds : bond 0.03716 ( 455) hydrogen bonds : angle 4.30914 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.61 seconds wall clock time: 35 minutes 26.44 seconds (2126.44 seconds total)