Starting phenix.real_space_refine on Fri Mar 14 07:14:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uar_8461/03_2025/5uar_8461.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uar_8461/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5uar_8461/03_2025/5uar_8461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uar_8461/03_2025/5uar_8461.map" model { file = "/net/cci-nas-00/data/ceres_data/5uar_8461/03_2025/5uar_8461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uar_8461/03_2025/5uar_8461.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.31, per 1000 atoms: 0.66 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.10 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: 3.52 Time building geometry restraints manager: 3.11 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: 3.190 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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= 0.504 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (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 TRP 0.011 0.002 TRP A 19 HIS 0.005 0.001 HIS A 114 PHE 0.015 0.001 PHE A 201 TYR 0.008 0.001 TYR A 248 ARG 0.007 0.001 ARG A1020 *********************** 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 : 1.079 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: 0.8197 (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: 0.8930 (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: 0.8791 (m110) REVERT: A 296 LEU cc_start: 0.8215 (mt) cc_final: 0.7816 (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: 0.7017 (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: 0.7940 (mtm180) REVERT: A 1173 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8693 (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: 0.8485 (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: 0.2513 time to fit residues: 125.0916 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 : 1.054 ------------------------------------------------------------------------------- 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 99 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 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 396 GLN ** A1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.124504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101994 restraints weight = 24623.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105367 restraints weight = 12514.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107627 restraints weight = 7862.318| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9694 Z= 0.204 Angle : 0.659 7.956 13095 Z= 0.338 Chirality : 0.041 0.182 1503 Planarity : 0.004 0.048 1611 Dihedral : 4.996 37.035 1297 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.86 % Allowed : 13.72 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1174 helix: -0.10 (0.18), residues: 711 sheet: -2.04 (0.58), residues: 45 loop : -2.18 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1106 HIS 0.007 0.001 HIS A1311 PHE 0.018 0.001 PHE A 940 TYR 0.016 0.001 TYR A1263 ARG 0.004 0.001 ARG A 599 *********************** 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 297 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 CYS cc_start: 0.8566 (p) cc_final: 0.8359 (t) REVERT: A 12 LEU cc_start: 0.8920 (mp) cc_final: 0.8467 (tt) REVERT: A 24 MET cc_start: 0.8119 (tpp) cc_final: 0.7674 (mtp) REVERT: A 60 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 93 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9157 (tp30) REVERT: A 122 TYR cc_start: 0.7487 (m-80) cc_final: 0.7039 (m-80) REVERT: A 135 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7757 (ttm110) REVERT: A 185 MET cc_start: 0.7776 (ttp) cc_final: 0.7548 (ttp) REVERT: A 207 LEU cc_start: 0.9220 (tp) cc_final: 0.8970 (tt) REVERT: A 288 ASN cc_start: 0.9183 (t0) cc_final: 0.8855 (m110) REVERT: A 336 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8424 (ttp-110) REVERT: A 386 TYR cc_start: 0.6387 (p90) cc_final: 0.5714 (p90) REVERT: A 388 LEU cc_start: 0.8988 (mt) cc_final: 0.8498 (mp) REVERT: A 399 THR cc_start: 0.8265 (m) cc_final: 0.7931 (p) REVERT: A 463 LYS cc_start: 0.7670 (tttp) cc_final: 0.7152 (pttp) REVERT: A 496 ILE cc_start: 0.8402 (mm) cc_final: 0.8094 (tp) REVERT: A 509 LEU cc_start: 0.8614 (mt) cc_final: 0.8061 (tp) REVERT: A 540 MET cc_start: 0.7999 (tpp) cc_final: 0.7703 (tpp) REVERT: A 631 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7980 (mp0) REVERT: A 635 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 1170 ARG cc_start: 0.8304 (mmt90) cc_final: 0.8104 (mtm180) REVERT: A 1220 TYR cc_start: 0.6478 (t80) cc_final: 0.5948 (t80) REVERT: A 1277 LYS cc_start: 0.8547 (mttt) cc_final: 0.8246 (ttmt) REVERT: A 1278 MET cc_start: 0.7106 (mtt) cc_final: 0.6526 (mtt) REVERT: A 1287 PHE cc_start: 0.8716 (m-80) cc_final: 0.7538 (m-80) REVERT: A 1313 ASP cc_start: 0.8534 (m-30) cc_final: 0.7916 (p0) REVERT: A 1334 ASP cc_start: 0.7865 (m-30) cc_final: 0.7570 (t0) REVERT: A 1417 MET cc_start: 0.7023 (tmm) cc_final: 0.6724 (tmm) outliers start: 40 outliers final: 18 residues processed: 280 average time/residue: 0.2040 time to fit residues: 80.8065 Evaluate side-chains 226 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 1013 ILE Chi-restraints excluded: chain A residue 1016 VAL 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 103 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100258 restraints weight = 24920.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103528 restraints weight = 12565.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105719 restraints weight = 7892.227| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4004 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= 0.197 Angle : 0.608 7.034 13095 Z= 0.311 Chirality : 0.041 0.159 1503 Planarity : 0.004 0.052 1611 Dihedral : 4.772 36.890 1297 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.31 % Allowed : 16.71 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1174 helix: 0.33 (0.19), residues: 716 sheet: -1.43 (0.62), residues: 45 loop : -2.09 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1153 HIS 0.005 0.001 HIS A1311 PHE 0.015 0.001 PHE A 126 TYR 0.012 0.001 TYR A 38 ARG 0.003 0.000 ARG A1038 *********************** 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: 55 poor density : 228 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8204 (ppp) cc_final: 0.7989 (ppp) REVERT: A 7 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7636 (pt0) REVERT: A 12 LEU cc_start: 0.8999 (mp) cc_final: 0.8502 (tt) REVERT: A 24 MET cc_start: 0.8088 (tpp) cc_final: 0.7379 (ttm) REVERT: A 43 GLN cc_start: 0.8549 (tp40) cc_final: 0.7933 (tp-100) REVERT: A 60 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8356 (mm-30) REVERT: A 122 TYR cc_start: 0.7562 (m-80) cc_final: 0.7247 (m-80) REVERT: A 123 PHE cc_start: 0.7618 (m-10) cc_final: 0.6141 (t80) REVERT: A 135 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7882 (ttm110) REVERT: A 207 LEU cc_start: 0.9169 (tp) cc_final: 0.8926 (tt) REVERT: A 288 ASN cc_start: 0.9180 (t0) cc_final: 0.8843 (m110) REVERT: A 361 MET cc_start: 0.7333 (tmm) cc_final: 0.6956 (tmm) REVERT: A 388 LEU cc_start: 0.8961 (mt) cc_final: 0.8489 (mp) REVERT: A 463 LYS cc_start: 0.7743 (tttp) cc_final: 0.7242 (pttp) REVERT: A 509 LEU cc_start: 0.8610 (mt) cc_final: 0.7985 (tp) REVERT: A 540 MET cc_start: 0.8060 (tpp) cc_final: 0.7848 (tpp) REVERT: A 571 ASP cc_start: 0.8881 (t70) cc_final: 0.8634 (t70) REVERT: A 593 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5890 (mm) REVERT: A 631 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7761 (mp0) REVERT: A 635 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 1004 GLN cc_start: 0.8908 (tp40) cc_final: 0.8322 (tp40) REVERT: A 1112 ASP cc_start: 0.8267 (t0) cc_final: 0.7992 (t0) REVERT: A 1133 LYS cc_start: 0.8899 (pttt) cc_final: 0.8363 (ptmt) REVERT: A 1170 ARG cc_start: 0.8336 (mmt90) cc_final: 0.8114 (mtm180) REVERT: A 1220 TYR cc_start: 0.6352 (t80) cc_final: 0.5717 (t80) REVERT: A 1313 ASP cc_start: 0.8616 (m-30) cc_final: 0.8043 (p0) REVERT: A 1416 MET cc_start: 0.5395 (ttt) cc_final: 0.4933 (ttm) REVERT: A 1417 MET cc_start: 0.6757 (tmm) cc_final: 0.6416 (tmm) outliers start: 55 outliers final: 31 residues processed: 256 average time/residue: 0.1929 time to fit residues: 72.2637 Evaluate side-chains 233 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 232 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 314 SER 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 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 1014 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 1168 VAL Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1290 VAL 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 96 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 104 optimal weight: 0.0070 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.124677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101681 restraints weight = 24634.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104977 restraints weight = 12513.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107158 restraints weight = 7913.556| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9694 Z= 0.154 Angle : 0.596 8.587 13095 Z= 0.299 Chirality : 0.039 0.166 1503 Planarity : 0.004 0.049 1611 Dihedral : 4.592 36.811 1297 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.86 % Allowed : 20.39 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1174 helix: 0.51 (0.19), residues: 729 sheet: -1.17 (0.65), residues: 47 loop : -2.01 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1153 HIS 0.004 0.001 HIS A1311 PHE 0.024 0.001 PHE A 863 TYR 0.017 0.001 TYR A1040 ARG 0.007 0.000 ARG A 599 *********************** 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: 40 poor density : 238 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8150 (ppp) cc_final: 0.7897 (ppp) REVERT: A 12 LEU cc_start: 0.8982 (mp) cc_final: 0.8581 (tt) REVERT: A 24 MET cc_start: 0.8191 (tpp) cc_final: 0.7870 (mtt) REVERT: A 33 ARG cc_start: 0.8673 (mtt180) cc_final: 0.7746 (ptp90) REVERT: A 43 GLN cc_start: 0.8541 (tp40) cc_final: 0.7966 (tp-100) REVERT: A 60 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8380 (mm-30) REVERT: A 93 GLU cc_start: 0.9352 (tp30) cc_final: 0.8967 (tp30) REVERT: A 122 TYR cc_start: 0.7531 (m-80) cc_final: 0.7100 (m-80) REVERT: A 123 PHE cc_start: 0.7575 (m-10) cc_final: 0.6142 (t80) REVERT: A 135 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7678 (ttm110) REVERT: A 207 LEU cc_start: 0.9185 (tp) cc_final: 0.8960 (tt) REVERT: A 288 ASN cc_start: 0.9186 (t0) cc_final: 0.8836 (m110) REVERT: A 361 MET cc_start: 0.7266 (tmm) cc_final: 0.6819 (tmm) REVERT: A 388 LEU cc_start: 0.8906 (mt) cc_final: 0.8411 (mp) REVERT: A 452 MET cc_start: 0.8197 (tpp) cc_final: 0.7724 (tpp) REVERT: A 509 LEU cc_start: 0.8541 (mt) cc_final: 0.7888 (tp) REVERT: A 567 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (mm) REVERT: A 594 MET cc_start: 0.7509 (ptp) cc_final: 0.7173 (pmm) REVERT: A 631 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7669 (mp0) REVERT: A 635 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 655 GLU cc_start: 0.7469 (pt0) cc_final: 0.6782 (tm-30) REVERT: A 960 MET cc_start: 0.8871 (ttt) cc_final: 0.8354 (tmm) REVERT: A 1133 LYS cc_start: 0.8805 (pttt) cc_final: 0.8353 (ptmt) REVERT: A 1170 ARG cc_start: 0.8359 (mmt90) cc_final: 0.8115 (mtm180) REVERT: A 1220 TYR cc_start: 0.6227 (t80) cc_final: 0.5484 (t80) REVERT: A 1313 ASP cc_start: 0.8556 (m-30) cc_final: 0.8017 (p0) REVERT: A 1342 TYR cc_start: 0.7370 (m-10) cc_final: 0.7167 (m-80) REVERT: A 1366 ARG cc_start: 0.8116 (mmp-170) cc_final: 0.7747 (mmm160) REVERT: A 1416 MET cc_start: 0.5190 (ttt) cc_final: 0.4792 (ttm) outliers start: 40 outliers final: 27 residues processed: 260 average time/residue: 0.1958 time to fit residues: 73.0059 Evaluate side-chains 238 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 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 567 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 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 1116 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A1256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100938 restraints weight = 25204.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104068 restraints weight = 13101.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106160 restraints weight = 8378.122| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4813 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= 0.173 Angle : 0.592 8.042 13095 Z= 0.295 Chirality : 0.039 0.170 1503 Planarity : 0.004 0.048 1611 Dihedral : 4.543 36.907 1297 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.25 % Allowed : 20.29 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1174 helix: 0.69 (0.19), residues: 718 sheet: -0.79 (0.69), residues: 40 loop : -1.70 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1153 HIS 0.005 0.001 HIS A1311 PHE 0.019 0.001 PHE A 317 TYR 0.012 0.001 TYR A 922 ARG 0.006 0.000 ARG A 171 *********************** 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 262 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8147 (ppp) cc_final: 0.7893 (ppp) REVERT: A 12 LEU cc_start: 0.9033 (mp) cc_final: 0.8628 (tt) REVERT: A 24 MET cc_start: 0.8067 (tpp) cc_final: 0.7855 (mtt) REVERT: A 33 ARG cc_start: 0.8698 (mtt180) cc_final: 0.7823 (ptp90) REVERT: A 60 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 93 GLU cc_start: 0.9370 (tp30) cc_final: 0.9003 (tp30) REVERT: A 122 TYR cc_start: 0.7582 (m-80) cc_final: 0.7345 (m-80) REVERT: A 123 PHE cc_start: 0.7503 (m-10) cc_final: 0.6172 (t80) REVERT: A 135 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7937 (ttm110) REVERT: A 207 LEU cc_start: 0.9204 (tp) cc_final: 0.8980 (tt) REVERT: A 265 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: A 288 ASN cc_start: 0.9113 (t0) cc_final: 0.8794 (m110) REVERT: A 361 MET cc_start: 0.7349 (tmm) cc_final: 0.6899 (tmm) REVERT: A 388 LEU cc_start: 0.8853 (mt) cc_final: 0.8363 (mp) REVERT: A 452 MET cc_start: 0.8093 (tpp) cc_final: 0.7849 (tpp) REVERT: A 509 LEU cc_start: 0.8591 (mt) cc_final: 0.7905 (tp) REVERT: A 631 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7835 (mp0) REVERT: A 655 GLU cc_start: 0.7384 (pt0) cc_final: 0.6687 (tm-30) REVERT: A 960 MET cc_start: 0.8935 (ttt) cc_final: 0.8334 (tmm) REVERT: A 1133 LYS cc_start: 0.8791 (pttt) cc_final: 0.8368 (ptmt) REVERT: A 1170 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8146 (mtm180) REVERT: A 1220 TYR cc_start: 0.6285 (t80) cc_final: 0.5494 (t80) REVERT: A 1305 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8900 (tt) REVERT: A 1366 ARG cc_start: 0.8150 (mmp-170) cc_final: 0.7895 (mmp-170) REVERT: A 1386 LYS cc_start: 0.8881 (mttm) cc_final: 0.8403 (tppt) REVERT: A 1416 MET cc_start: 0.5158 (ttt) cc_final: 0.4822 (ttm) outliers start: 44 outliers final: 35 residues processed: 241 average time/residue: 0.1863 time to fit residues: 65.1411 Evaluate side-chains 244 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 209 CYS 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 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 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 1168 VAL Chi-restraints excluded: chain A residue 1176 ASP 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 1305 LEU Chi-restraints excluded: chain A residue 1370 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 34 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 63 optimal weight: 0.0050 chunk 92 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.124152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101796 restraints weight = 24913.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104940 restraints weight = 12965.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106988 restraints weight = 8287.719| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5036 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= 0.163 Angle : 0.606 8.129 13095 Z= 0.296 Chirality : 0.039 0.158 1503 Planarity : 0.004 0.043 1611 Dihedral : 4.500 37.317 1297 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.86 % Allowed : 21.45 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1174 helix: 0.69 (0.19), residues: 711 sheet: -0.50 (0.68), residues: 40 loop : -1.64 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1283 HIS 0.004 0.001 HIS A1311 PHE 0.026 0.001 PHE A 863 TYR 0.015 0.001 TYR A1342 ARG 0.004 0.000 ARG A 336 *********************** 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 253 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8227 (ppp) cc_final: 0.7963 (ppp) REVERT: A 7 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7647 (pt0) REVERT: A 12 LEU cc_start: 0.9008 (mp) cc_final: 0.8602 (tt) REVERT: A 24 MET cc_start: 0.8191 (tpp) cc_final: 0.7971 (mtt) REVERT: A 33 ARG cc_start: 0.8681 (mtt180) cc_final: 0.7776 (ptp90) REVERT: A 60 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 93 GLU cc_start: 0.9367 (tp30) cc_final: 0.8991 (tp30) REVERT: A 122 TYR cc_start: 0.7596 (m-80) cc_final: 0.7344 (m-80) REVERT: A 123 PHE cc_start: 0.7485 (m-10) cc_final: 0.6184 (t80) REVERT: A 207 LEU cc_start: 0.9154 (tp) cc_final: 0.8926 (tt) REVERT: A 265 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: A 288 ASN cc_start: 0.9121 (t0) cc_final: 0.8779 (m110) REVERT: A 361 MET cc_start: 0.7572 (tmm) cc_final: 0.6950 (tmm) REVERT: A 388 LEU cc_start: 0.8900 (mt) cc_final: 0.8440 (mp) REVERT: A 452 MET cc_start: 0.8338 (tpp) cc_final: 0.7835 (tpp) REVERT: A 497 MET cc_start: 0.8202 (ttt) cc_final: 0.7978 (ttm) REVERT: A 631 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7871 (mp0) REVERT: A 655 GLU cc_start: 0.7375 (pt0) cc_final: 0.6679 (tm-30) REVERT: A 960 MET cc_start: 0.8879 (ttt) cc_final: 0.8277 (tmm) REVERT: A 1133 LYS cc_start: 0.8801 (pttt) cc_final: 0.8383 (ptmt) REVERT: A 1170 ARG cc_start: 0.8417 (mmt90) cc_final: 0.8059 (mtm180) REVERT: A 1220 TYR cc_start: 0.6277 (t80) cc_final: 0.5438 (t80) REVERT: A 1270 ILE cc_start: 0.8209 (mt) cc_final: 0.8004 (mm) REVERT: A 1278 MET cc_start: 0.6431 (ttm) cc_final: 0.5708 (tpp) REVERT: A 1281 GLN cc_start: 0.8648 (pm20) cc_final: 0.8415 (pm20) REVERT: A 1282 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.7979 (pptt) REVERT: A 1305 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 1386 LYS cc_start: 0.8938 (mttm) cc_final: 0.8455 (tppt) REVERT: A 1416 MET cc_start: 0.5105 (ttt) cc_final: 0.4754 (ttm) REVERT: A 1417 MET cc_start: 0.6540 (tmm) cc_final: 0.6223 (tpp) outliers start: 40 outliers final: 32 residues processed: 235 average time/residue: 0.1813 time to fit residues: 62.3078 Evaluate side-chains 244 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 265 GLU 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 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 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 1168 VAL Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1263 TYR 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 Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1370 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 4 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.101861 restraints weight = 24969.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105045 restraints weight = 12870.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.107174 restraints weight = 8171.625| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9694 Z= 0.151 Angle : 0.593 8.656 13095 Z= 0.290 Chirality : 0.039 0.157 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.405 37.835 1297 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.35 % Allowed : 21.64 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1174 helix: 0.80 (0.19), residues: 702 sheet: 0.03 (0.72), residues: 38 loop : -1.60 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 887 HIS 0.004 0.001 HIS A1311 PHE 0.019 0.001 PHE A 317 TYR 0.018 0.001 TYR A1342 ARG 0.004 0.000 ARG A 599 *********************** 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 262 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8126 (ppp) cc_final: 0.7857 (ppp) REVERT: A 7 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7637 (pt0) REVERT: A 12 LEU cc_start: 0.9024 (mp) cc_final: 0.8617 (tt) REVERT: A 33 ARG cc_start: 0.8649 (mtt180) cc_final: 0.7780 (ptp90) REVERT: A 43 GLN cc_start: 0.8518 (tp40) cc_final: 0.7974 (tp-100) REVERT: A 60 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8285 (mm-30) REVERT: A 93 GLU cc_start: 0.9338 (tp30) cc_final: 0.8998 (tp30) REVERT: A 122 TYR cc_start: 0.7608 (m-80) cc_final: 0.7288 (m-80) REVERT: A 123 PHE cc_start: 0.7313 (m-10) cc_final: 0.6063 (t80) REVERT: A 135 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7653 (ttm110) REVERT: A 207 LEU cc_start: 0.9186 (tp) cc_final: 0.8963 (tt) REVERT: A 265 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: A 288 ASN cc_start: 0.9104 (t0) cc_final: 0.8785 (m110) REVERT: A 361 MET cc_start: 0.7635 (tmm) cc_final: 0.6967 (tmm) REVERT: A 388 LEU cc_start: 0.8865 (mt) cc_final: 0.8403 (mp) REVERT: A 399 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 497 MET cc_start: 0.8140 (ttt) cc_final: 0.7886 (ttm) REVERT: A 631 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7834 (pt0) REVERT: A 655 GLU cc_start: 0.7359 (pt0) cc_final: 0.6655 (tm-30) REVERT: A 960 MET cc_start: 0.8881 (ttt) cc_final: 0.8293 (tmm) REVERT: A 1133 LYS cc_start: 0.8789 (pttt) cc_final: 0.8400 (ptmt) REVERT: A 1170 ARG cc_start: 0.8418 (mmt90) cc_final: 0.8105 (mtm180) REVERT: A 1220 TYR cc_start: 0.6186 (t80) cc_final: 0.5287 (t80) REVERT: A 1282 LYS cc_start: 0.8888 (pttt) cc_final: 0.8212 (tmtt) REVERT: A 1305 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8887 (tt) REVERT: A 1386 LYS cc_start: 0.8894 (mttm) cc_final: 0.8435 (tppt) REVERT: A 1417 MET cc_start: 0.6464 (tmm) cc_final: 0.6206 (tpp) outliers start: 45 outliers final: 30 residues processed: 245 average time/residue: 0.1882 time to fit residues: 67.1881 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 : 1.135 ------------------------------------------------------------------------------- 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 83 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 209 CYS 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 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 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 1168 VAL Chi-restraints excluded: chain A residue 1176 ASP Chi-restraints excluded: chain A residue 1258 LEU 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 1305 LEU Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103033 restraints weight = 25254.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.106295 restraints weight = 12915.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108484 restraints weight = 8149.666| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9694 Z= 0.148 Angle : 0.613 10.925 13095 Z= 0.293 Chirality : 0.039 0.172 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.363 37.571 1297 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.77 % Allowed : 22.51 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1174 helix: 0.87 (0.19), residues: 700 sheet: 0.18 (0.72), residues: 38 loop : -1.50 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1106 HIS 0.004 0.001 HIS A 666 PHE 0.026 0.001 PHE A 136 TYR 0.017 0.001 TYR A 925 ARG 0.007 0.000 ARG A 486 *********************** 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 254 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8184 (ppp) cc_final: 0.7899 (ppp) REVERT: A 7 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7645 (pt0) REVERT: A 12 LEU cc_start: 0.9022 (mp) cc_final: 0.8624 (tt) REVERT: A 33 ARG cc_start: 0.8649 (mtt180) cc_final: 0.7770 (ptp90) REVERT: A 43 GLN cc_start: 0.8550 (tp40) cc_final: 0.8014 (tp-100) REVERT: A 60 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8311 (mm-30) REVERT: A 93 GLU cc_start: 0.9362 (tp30) cc_final: 0.9038 (tp30) REVERT: A 122 TYR cc_start: 0.7774 (m-80) cc_final: 0.7413 (m-80) REVERT: A 135 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7554 (ttm110) REVERT: A 207 LEU cc_start: 0.9166 (tp) cc_final: 0.8955 (tt) REVERT: A 288 ASN cc_start: 0.9099 (t0) cc_final: 0.8767 (m110) REVERT: A 361 MET cc_start: 0.7702 (tmm) cc_final: 0.7064 (tmm) REVERT: A 388 LEU cc_start: 0.8898 (mt) cc_final: 0.8448 (mp) REVERT: A 399 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 631 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7803 (pt0) REVERT: A 655 GLU cc_start: 0.7355 (pt0) cc_final: 0.6640 (tm-30) REVERT: A 960 MET cc_start: 0.8912 (ttt) cc_final: 0.8304 (tmm) REVERT: A 1040 TYR cc_start: 0.8781 (t80) cc_final: 0.8517 (t80) REVERT: A 1133 LYS cc_start: 0.8811 (pttt) cc_final: 0.8409 (pttm) REVERT: A 1170 ARG cc_start: 0.8420 (mmt90) cc_final: 0.8087 (mtm180) REVERT: A 1220 TYR cc_start: 0.6054 (t80) cc_final: 0.5228 (t80) REVERT: A 1282 LYS cc_start: 0.8808 (pttt) cc_final: 0.7986 (tmtt) REVERT: A 1305 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 1386 LYS cc_start: 0.8900 (mttm) cc_final: 0.8490 (tppt) REVERT: A 1417 MET cc_start: 0.6617 (tmm) cc_final: 0.6325 (tpp) outliers start: 39 outliers final: 30 residues processed: 239 average time/residue: 0.1984 time to fit residues: 68.4931 Evaluate side-chains 246 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 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 209 CYS 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 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 1168 VAL Chi-restraints excluded: chain A residue 1176 ASP 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 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 58 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103629 restraints weight = 25472.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106771 restraints weight = 13205.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108930 restraints weight = 8422.031| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5550 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= 0.154 Angle : 0.624 14.036 13095 Z= 0.299 Chirality : 0.039 0.158 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.371 37.660 1297 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.38 % Allowed : 22.90 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1174 helix: 0.91 (0.19), residues: 701 sheet: 0.07 (0.68), residues: 43 loop : -1.47 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1106 HIS 0.004 0.001 HIS A1311 PHE 0.032 0.001 PHE A 863 TYR 0.016 0.001 TYR A1342 ARG 0.004 0.000 ARG A 599 *********************** 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 253 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8190 (ppp) cc_final: 0.7856 (ppp) REVERT: A 7 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7626 (pt0) REVERT: A 12 LEU cc_start: 0.9008 (mp) cc_final: 0.8603 (tt) REVERT: A 33 ARG cc_start: 0.8655 (mtt180) cc_final: 0.7782 (ptp90) REVERT: A 43 GLN cc_start: 0.8583 (tp40) cc_final: 0.8110 (tp-100) REVERT: A 60 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 93 GLU cc_start: 0.9372 (tp30) cc_final: 0.9043 (tp30) REVERT: A 122 TYR cc_start: 0.7848 (m-80) cc_final: 0.7435 (m-80) REVERT: A 136 PHE cc_start: 0.7567 (m-80) cc_final: 0.7258 (m-80) REVERT: A 207 LEU cc_start: 0.9179 (tp) cc_final: 0.8962 (tt) REVERT: A 288 ASN cc_start: 0.9087 (t0) cc_final: 0.8762 (m110) REVERT: A 361 MET cc_start: 0.7730 (tmm) cc_final: 0.7115 (tmm) REVERT: A 388 LEU cc_start: 0.8857 (mt) cc_final: 0.8402 (mp) REVERT: A 399 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (p) REVERT: A 554 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8393 (mmt90) REVERT: A 615 ILE cc_start: 0.9169 (pt) cc_final: 0.8563 (mm) REVERT: A 631 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7764 (pt0) REVERT: A 655 GLU cc_start: 0.7360 (pt0) cc_final: 0.6610 (tm-30) REVERT: A 960 MET cc_start: 0.8909 (ttt) cc_final: 0.8245 (tmm) REVERT: A 1170 ARG cc_start: 0.8437 (mmt90) cc_final: 0.8105 (mtm180) REVERT: A 1220 TYR cc_start: 0.6127 (t80) cc_final: 0.5303 (t80) REVERT: A 1278 MET cc_start: 0.6367 (ttm) cc_final: 0.5871 (ttt) REVERT: A 1305 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8873 (tt) REVERT: A 1386 LYS cc_start: 0.8881 (mttm) cc_final: 0.8479 (tppt) outliers start: 35 outliers final: 29 residues processed: 238 average time/residue: 0.1937 time to fit residues: 66.3652 Evaluate side-chains 244 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 209 CYS 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 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 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 1168 VAL Chi-restraints excluded: chain A residue 1176 ASP 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 1305 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 42 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.125906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103853 restraints weight = 25521.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107037 restraints weight = 13238.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109218 restraints weight = 8408.769| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- 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 = 0.79 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 = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9694 Z= 0.156 Angle : 0.642 14.242 13095 Z= 0.304 Chirality : 0.039 0.162 1503 Planarity : 0.004 0.042 1611 Dihedral : 4.395 37.469 1297 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.09 % Allowed : 23.09 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1174 helix: 0.97 (0.19), residues: 701 sheet: 0.13 (0.70), residues: 43 loop : -1.46 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1106 HIS 0.004 0.001 HIS A1311 PHE 0.033 0.001 PHE A 863 TYR 0.019 0.001 TYR A 925 ARG 0.004 0.000 ARG A 599 ********************** 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 244 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8214 (ppp) cc_final: 0.7908 (ppp) REVERT: A 7 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7641 (pt0) REVERT: A 12 LEU cc_start: 0.9037 (mp) cc_final: 0.8626 (tt) REVERT: A 33 ARG cc_start: 0.8654 (mtt180) cc_final: 0.7779 (ptp90) REVERT: A 43 GLN cc_start: 0.8609 (tp40) cc_final: 0.8121 (tp-100) REVERT: A 60 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8268 (mm-30) REVERT: A 93 GLU cc_start: 0.9368 (tp30) cc_final: 0.9066 (tp30) REVERT: A 122 TYR cc_start: 0.7938 (m-80) cc_final: 0.7456 (m-80) REVERT: A 136 PHE cc_start: 0.7593 (m-80) cc_final: 0.7292 (m-80) REVERT: A 207 LEU cc_start: 0.9198 (tp) cc_final: 0.8975 (tt) REVERT: A 288 ASN cc_start: 0.9102 (t0) cc_final: 0.8787 (m110) REVERT: A 361 MET cc_start: 0.7760 (tmm) cc_final: 0.7139 (tmm) REVERT: A 388 LEU cc_start: 0.8861 (mt) cc_final: 0.8373 (mp) REVERT: A 399 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (p) REVERT: A 631 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7799 (pt0) REVERT: A 655 GLU cc_start: 0.7359 (pt0) cc_final: 0.6519 (tm-30) REVERT: A 960 MET cc_start: 0.8893 (ttt) cc_final: 0.8282 (tmm) REVERT: A 1133 LYS cc_start: 0.8985 (pttt) cc_final: 0.8399 (ptmt) REVERT: A 1170 ARG cc_start: 0.8469 (mmt90) cc_final: 0.8141 (mtm180) REVERT: A 1305 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8893 (tt) REVERT: A 1386 LYS cc_start: 0.8886 (mttm) cc_final: 0.8476 (tppt) outliers start: 32 outliers final: 29 residues processed: 233 average time/residue: 0.1933 time to fit residues: 65.1448 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 : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 209 CYS 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 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 965 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 1168 VAL Chi-restraints excluded: chain A residue 1176 ASP 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 1305 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 56 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099565 restraints weight = 25629.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102663 restraints weight = 13217.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104746 restraints weight = 8340.085| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5759 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= 0.165 Angle : 0.642 14.794 13095 Z= 0.308 Chirality : 0.040 0.214 1503 Planarity : 0.004 0.050 1611 Dihedral : 4.435 39.788 1297 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.19 % Allowed : 23.09 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1174 helix: 1.02 (0.19), residues: 703 sheet: 0.06 (0.70), residues: 43 loop : -1.42 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1106 HIS 0.004 0.001 HIS A1311 PHE 0.034 0.001 PHE A 863 TYR 0.021 0.001 TYR A1040 ARG 0.003 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3637.92 seconds wall clock time: 63 minutes 38.21 seconds (3818.21 seconds total)