Starting phenix.real_space_refine on Thu Jul 2 17:15:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fzq_29637/07_2026/8fzq_29637.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 6017 2.51 5 N 1530 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4844 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 4336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4336 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 535} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.90, per 1000 atoms: 0.21 Number of scatterers: 9244 At special positions: 0 Unit cell: (108.15, 117.42, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1643 8.00 N 1530 7.00 C 6017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 313.7 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 71.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.654A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 removed outlier: 4.088A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 116 through 166 removed outlier: 4.045A pdb=" N ALA A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.859A pdb=" N ASP A 173 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 198 removed outlier: 4.046A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 4.130A pdb=" N ILE A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 223 through 267 removed outlier: 4.181A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 327 removed outlier: 3.834A pdb=" N LYS A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.624A pdb=" N LEU A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.920A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 352 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.748A pdb=" N PHE A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 755 through 765 removed outlier: 4.666A pdb=" N UNK A 761 " --> pdb=" O UNK A 757 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N UNK A 762 " --> pdb=" O UNK A 758 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N UNK A 765 " --> pdb=" O UNK A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 854 removed outlier: 3.852A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 883 removed outlier: 3.502A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 removed outlier: 4.305A pdb=" N VAL A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 934 through 957 Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.747A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.635A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.145A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1047 removed outlier: 3.837A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.771A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.999A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.523A pdb=" N LEU A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1169 removed outlier: 4.191A pdb=" N GLY A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A1162 " --> pdb=" O ARG A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1278 through 1286 removed outlier: 3.728A pdb=" N PHE A1286 " --> pdb=" O TRP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1324 through 1331 removed outlier: 3.965A pdb=" N PHE A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1392 Processing helix chain 'A' and resid 1404 through 1410 removed outlier: 3.759A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1409 " --> pdb=" O ALA A1406 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A1410 " --> pdb=" O MET A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1434 removed outlier: 3.793A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 394 removed outlier: 3.665A pdb=" N VAL A 392 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 removed outlier: 5.691A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 6.097A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A1230 " --> pdb=" O LEU A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 6.097A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A1230 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A1266 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A1217 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN A1262 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1367 through 1368 removed outlier: 7.677A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG A1239 " --> pdb=" O GLN A1412 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A1414 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY A1241 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A1416 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A1243 " --> pdb=" O ILE A1416 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2877 1.34 - 1.46: 2110 1.46 - 1.58: 4362 1.58 - 1.69: 10 1.69 - 1.81: 77 Bond restraints: 9436 Sorted by residual: bond pdb=" C ALA A1081 " pdb=" O ALA A1081 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.19e-02 7.06e+03 7.62e-01 bond pdb=" CA ILE A 328 " pdb=" C ILE A 328 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.22e-01 bond pdb=" CB MET A 265 " pdb=" CG MET A 265 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.68e-01 bond pdb=" CA HIS A 139 " pdb=" C HIS A 139 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.04e-01 bond pdb=" N GLN A 493 " pdb=" CA GLN A 493 " ideal model delta sigma weight residual 1.459 1.450 0.009 1.19e-02 7.06e+03 5.94e-01 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12628 1.96 - 3.91: 116 3.91 - 5.87: 23 5.87 - 7.82: 3 7.82 - 9.78: 1 Bond angle restraints: 12771 Sorted by residual: angle pdb=" N GLN A 493 " pdb=" CA GLN A 493 " pdb=" C GLN A 493 " ideal model delta sigma weight residual 111.07 105.15 5.92 1.07e+00 8.73e-01 3.06e+01 angle pdb=" C ARG A1048 " pdb=" N SER A1049 " pdb=" CA SER A1049 " ideal model delta sigma weight residual 120.06 123.71 -3.65 1.19e+00 7.06e-01 9.38e+00 angle pdb=" C THR A 388 " pdb=" N THR A 389 " pdb=" CA THR A 389 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.21e+00 angle pdb=" CA LEU A 327 " pdb=" CB LEU A 327 " pdb=" CG LEU A 327 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.81e+00 angle pdb=" N LEU A1335 " pdb=" CA LEU A1335 " pdb=" CB LEU A1335 " ideal model delta sigma weight residual 113.65 109.82 3.83 1.47e+00 4.63e-01 6.79e+00 ... (remaining 12766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4940 17.67 - 35.35: 521 35.35 - 53.02: 91 53.02 - 70.69: 14 70.69 - 88.37: 5 Dihedral angle restraints: 5571 sinusoidal: 2225 harmonic: 3346 Sorted by residual: dihedral pdb=" CA LEU A 387 " pdb=" C LEU A 387 " pdb=" N THR A 388 " pdb=" CA THR A 388 " ideal model delta harmonic sigma weight residual 180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" N VAL A 591 " pdb=" CA VAL A 591 " ideal model delta harmonic sigma weight residual 180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA CYS A 76 " pdb=" C CYS A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 5568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 974 0.032 - 0.063: 356 0.063 - 0.095: 99 0.095 - 0.127: 44 0.127 - 0.159: 5 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA GLN A 493 " pdb=" N GLN A 493 " pdb=" C GLN A 493 " pdb=" CB GLN A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA LEU A 323 " pdb=" N LEU A 323 " pdb=" C LEU A 323 " pdb=" CB LEU A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1475 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1274 " 0.017 2.00e-02 2.50e+03 1.33e-02 4.44e+00 pdb=" CG TRP A1274 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1274 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A1274 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1274 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1274 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1274 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1274 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1274 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1274 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1049 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A1050 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 98 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 99 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.023 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 66 2.58 - 3.16: 7702 3.16 - 3.74: 14700 3.74 - 4.32: 18177 4.32 - 4.90: 30625 Nonbonded interactions: 71270 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.999 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.003 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.043 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3B ATP A1503 " model vdw 2.062 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.137 2.170 ... (remaining 71265 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=1.00 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.002 0.026 9436 Z= 0.111 Angle : 0.529 9.779 12771 Z= 0.275 Chirality : 0.039 0.159 1478 Planarity : 0.003 0.044 1560 Dihedral : 14.561 88.368 3407 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1121 helix: 1.60 (0.20), residues: 743 sheet: -0.26 (0.66), residues: 65 loop : -1.42 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 975 TYR 0.011 0.001 TYR A 304 PHE 0.024 0.001 PHE A 587 TRP 0.035 0.001 TRP A1274 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9436) covalent geometry : angle 0.52913 / 0.27 (12771) hydrogen bonds : bond 0.11123 / 7.91 ( 553) hydrogen bonds : angle 4.66953 / 3.44 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1354 MET cc_start: 0.8421 (tpp) cc_final: 0.8190 (tpt) outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.0628 time to fit residues: 19.6123 Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN A 525 GLN A 620 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087891 restraints weight = 23953.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088557 restraints weight = 18228.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088971 restraints weight = 14235.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089111 restraints weight = 11668.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090223 restraints weight = 11015.145| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9436 Z= 0.155 Angle : 0.584 6.478 12771 Z= 0.301 Chirality : 0.041 0.154 1478 Planarity : 0.004 0.046 1560 Dihedral : 4.426 37.768 1244 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.30 % Allowed : 5.64 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1121 helix: 1.44 (0.19), residues: 736 sheet: -0.47 (0.62), residues: 70 loop : -1.35 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1158 TYR 0.013 0.001 TYR A1032 PHE 0.019 0.002 PHE A 131 TRP 0.021 0.001 TRP A1274 HIS 0.002 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 9436) covalent geometry : angle 0.58392 / 0.30 (12771) hydrogen bonds : bond 0.04512 / 2.96 ( 553) hydrogen bonds : angle 4.11946 / 3.02 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5479 (tp) REVERT: A 452 GLN cc_start: 0.8175 (mt0) cc_final: 0.7948 (mt0) REVERT: A 602 LEU cc_start: 0.8272 (tp) cc_final: 0.7710 (mp) REVERT: A 1105 MET cc_start: 0.7944 (mtt) cc_final: 0.7726 (mtt) REVERT: A 1160 VAL cc_start: 0.8727 (p) cc_final: 0.8220 (p) REVERT: A 1257 PHE cc_start: 0.8449 (m-10) cc_final: 0.8122 (m-80) REVERT: A 1354 MET cc_start: 0.8542 (tpp) cc_final: 0.8210 (tpp) outliers start: 3 outliers final: 0 residues processed: 141 average time/residue: 0.0665 time to fit residues: 13.9849 Evaluate side-chains 89 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 81 optimal weight: 0.5980 chunk 91 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089574 restraints weight = 23604.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090189 restraints weight = 17582.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090604 restraints weight = 13308.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091144 restraints weight = 11203.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091198 restraints weight = 10478.935| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9436 Z= 0.122 Angle : 0.539 8.940 12771 Z= 0.276 Chirality : 0.039 0.158 1478 Planarity : 0.004 0.055 1560 Dihedral : 4.291 35.083 1244 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.20 % Allowed : 4.23 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1121 helix: 1.54 (0.19), residues: 739 sheet: -0.35 (0.63), residues: 70 loop : -1.29 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 170 TYR 0.013 0.001 TYR A 325 PHE 0.025 0.001 PHE A 131 TRP 0.030 0.002 TRP A 202 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9436) covalent geometry : angle 0.53872 / 0.28 (12771) hydrogen bonds : bond 0.04249 / 2.82 ( 553) hydrogen bonds : angle 3.93993 / 2.87 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 602 LEU cc_start: 0.8310 (tp) cc_final: 0.7737 (mp) REVERT: A 1105 MET cc_start: 0.7994 (mtt) cc_final: 0.7710 (mtp) REVERT: A 1257 PHE cc_start: 0.8395 (m-10) cc_final: 0.8159 (m-80) REVERT: A 1354 MET cc_start: 0.8479 (tpp) cc_final: 0.8175 (tpp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.0680 time to fit residues: 13.8955 Evaluate side-chains 84 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085057 restraints weight = 24907.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085647 restraints weight = 18591.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085950 restraints weight = 14180.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086475 restraints weight = 11999.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086590 restraints weight = 11258.021| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9436 Z= 0.223 Angle : 0.712 8.833 12771 Z= 0.365 Chirality : 0.045 0.203 1478 Planarity : 0.005 0.062 1560 Dihedral : 4.833 35.100 1244 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1121 helix: 1.07 (0.19), residues: 740 sheet: -0.92 (0.59), residues: 70 loop : -1.34 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1259 TYR 0.021 0.002 TYR A1032 PHE 0.027 0.002 PHE A 131 TRP 0.014 0.002 TRP A 202 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 ( 9436) covalent geometry : angle 0.71214 / 0.36 (12771) hydrogen bonds : bond 0.05123 / 3.35 ( 553) hydrogen bonds : angle 4.38806 / 3.21 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.401 Fit side-chains REVERT: A 394 MET cc_start: 0.4617 (ptm) cc_final: 0.4261 (ptm) REVERT: A 469 MET cc_start: 0.9308 (mmt) cc_final: 0.8715 (mpp) REVERT: A 602 LEU cc_start: 0.8644 (tp) cc_final: 0.7952 (mp) REVERT: A 1354 MET cc_start: 0.8741 (tpp) cc_final: 0.8473 (tpt) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0663 time to fit residues: 11.6816 Evaluate side-chains 63 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3496 r_free = 0.3496 target = 0.100502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086857 restraints weight = 24311.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087863 restraints weight = 17550.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088386 restraints weight = 12273.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088479 restraints weight = 10563.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089618 restraints weight = 9797.273| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.150 Angle : 0.573 7.526 12771 Z= 0.295 Chirality : 0.040 0.179 1478 Planarity : 0.004 0.048 1560 Dihedral : 4.622 32.920 1244 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1121 helix: 1.35 (0.19), residues: 741 sheet: -0.89 (0.60), residues: 70 loop : -1.29 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 153 TYR 0.017 0.001 TYR A 325 PHE 0.028 0.002 PHE A1257 TRP 0.025 0.001 TRP A1274 HIS 0.013 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9436) covalent geometry : angle 0.57337 / 0.29 (12771) hydrogen bonds : bond 0.04612 / 3.00 ( 553) hydrogen bonds : angle 4.12587 / 3.02 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.220 Fit side-chains REVERT: A 304 TYR cc_start: 0.8073 (t80) cc_final: 0.7850 (t80) REVERT: A 602 LEU cc_start: 0.8553 (tp) cc_final: 0.7889 (mp) REVERT: A 1354 MET cc_start: 0.8587 (tpp) cc_final: 0.8280 (tpp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0608 time to fit residues: 9.8509 Evaluate side-chains 67 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3507 r_free = 0.3507 target = 0.100880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088185 restraints weight = 25090.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089242 restraints weight = 18435.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089660 restraints weight = 12880.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090101 restraints weight = 11033.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090160 restraints weight = 10109.594| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9436 Z= 0.120 Angle : 0.537 6.938 12771 Z= 0.274 Chirality : 0.039 0.158 1478 Planarity : 0.004 0.049 1560 Dihedral : 4.470 30.067 1244 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1121 helix: 1.55 (0.20), residues: 732 sheet: -0.82 (0.60), residues: 69 loop : -1.29 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1325 TYR 0.010 0.001 TYR A 304 PHE 0.024 0.001 PHE A1257 TRP 0.027 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9436) covalent geometry : angle 0.53691 / 0.27 (12771) hydrogen bonds : bond 0.04286 / 2.79 ( 553) hydrogen bonds : angle 3.98239 / 2.91 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.353 Fit side-chains REVERT: A 136 LEU cc_start: 0.8980 (mt) cc_final: 0.8775 (tt) REVERT: A 602 LEU cc_start: 0.8609 (tp) cc_final: 0.7904 (mp) REVERT: A 1354 MET cc_start: 0.8403 (tpp) cc_final: 0.8140 (tpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0718 time to fit residues: 11.9268 Evaluate side-chains 65 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3481 r_free = 0.3481 target = 0.098848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085544 restraints weight = 23958.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086360 restraints weight = 18311.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086737 restraints weight = 13537.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087030 restraints weight = 11497.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087203 restraints weight = 10572.730| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9436 Z= 0.150 Angle : 0.568 9.643 12771 Z= 0.293 Chirality : 0.040 0.155 1478 Planarity : 0.004 0.049 1560 Dihedral : 4.469 30.748 1244 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1121 helix: 1.50 (0.19), residues: 738 sheet: -0.86 (0.59), residues: 69 loop : -1.31 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1070 TYR 0.013 0.001 TYR A1032 PHE 0.028 0.001 PHE A 131 TRP 0.020 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9436) covalent geometry : angle 0.56761 / 0.29 (12771) hydrogen bonds : bond 0.04430 / 2.89 ( 553) hydrogen bonds : angle 4.07019 / 2.97 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.248 Fit side-chains REVERT: A 602 LEU cc_start: 0.8622 (tp) cc_final: 0.7926 (mp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0658 time to fit residues: 10.5142 Evaluate side-chains 65 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3479 r_free = 0.3479 target = 0.098880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085910 restraints weight = 23914.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086713 restraints weight = 19974.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087102 restraints weight = 15689.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087199 restraints weight = 13104.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088245 restraints weight = 12356.070| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9436 Z= 0.135 Angle : 0.551 9.181 12771 Z= 0.283 Chirality : 0.040 0.166 1478 Planarity : 0.004 0.049 1560 Dihedral : 4.466 30.065 1244 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1121 helix: 1.49 (0.20), residues: 743 sheet: -1.05 (0.55), residues: 79 loop : -1.32 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.012 0.001 TYR A 304 PHE 0.029 0.001 PHE A 131 TRP 0.022 0.001 TRP A1274 HIS 0.006 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9436) covalent geometry : angle 0.55061 / 0.28 (12771) hydrogen bonds : bond 0.04339 / 2.82 ( 553) hydrogen bonds : angle 4.01307 / 2.92 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.257 Fit side-chains REVERT: A 265 MET cc_start: 0.7217 (tpp) cc_final: 0.6866 (tpp) REVERT: A 602 LEU cc_start: 0.8632 (tp) cc_final: 0.7935 (mp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0658 time to fit residues: 10.0055 Evaluate side-chains 67 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3470 r_free = 0.3470 target = 0.098400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085980 restraints weight = 23960.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086807 restraints weight = 18925.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087163 restraints weight = 14615.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087452 restraints weight = 12180.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087612 restraints weight = 11066.528| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9436 Z= 0.123 Angle : 0.552 9.035 12771 Z= 0.282 Chirality : 0.040 0.177 1478 Planarity : 0.004 0.049 1560 Dihedral : 4.440 29.264 1244 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1121 helix: 1.56 (0.20), residues: 734 sheet: -0.93 (0.56), residues: 74 loop : -1.39 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.013 0.001 TYR A 304 PHE 0.030 0.001 PHE A 131 TRP 0.020 0.001 TRP A1274 HIS 0.007 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9436) covalent geometry : angle 0.55238 / 0.28 (12771) hydrogen bonds : bond 0.04221 / 2.76 ( 553) hydrogen bonds : angle 4.02109 / 2.95 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.315 Fit side-chains REVERT: A 321 SER cc_start: 0.8760 (m) cc_final: 0.8450 (p) REVERT: A 602 LEU cc_start: 0.8588 (tp) cc_final: 0.7871 (mp) REVERT: A 1257 PHE cc_start: 0.8047 (m-80) cc_final: 0.7730 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0586 time to fit residues: 9.3920 Evaluate side-chains 66 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3436 r_free = 0.3436 target = 0.096411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084005 restraints weight = 24537.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084275 restraints weight = 19422.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084670 restraints weight = 16158.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085382 restraints weight = 13086.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085463 restraints weight = 12167.781| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9436 Z= 0.161 Angle : 0.597 9.230 12771 Z= 0.305 Chirality : 0.041 0.174 1478 Planarity : 0.004 0.048 1560 Dihedral : 4.547 30.315 1244 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1121 helix: 1.40 (0.19), residues: 740 sheet: -0.75 (0.59), residues: 70 loop : -1.37 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 600 TYR 0.015 0.001 TYR A1032 PHE 0.036 0.002 PHE A 131 TRP 0.035 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 9436) covalent geometry : angle 0.59703 / 0.30 (12771) hydrogen bonds : bond 0.04485 / 2.94 ( 553) hydrogen bonds : angle 4.14362 / 3.04 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.362 Fit side-chains REVERT: A 321 SER cc_start: 0.8790 (m) cc_final: 0.8445 (p) REVERT: A 602 LEU cc_start: 0.8644 (tp) cc_final: 0.7948 (mp) REVERT: A 1257 PHE cc_start: 0.8145 (m-80) cc_final: 0.7865 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0582 time to fit residues: 9.1213 Evaluate side-chains 66 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 199 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 = 0.3483 r_free = 0.3483 target = 0.099142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086826 restraints weight = 23844.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087915 restraints weight = 16290.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088698 restraints weight = 12193.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089109 restraints weight = 9906.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089137 restraints weight = 8704.252| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9436 Z= 0.115 Angle : 0.552 8.733 12771 Z= 0.280 Chirality : 0.040 0.207 1478 Planarity : 0.004 0.048 1560 Dihedral : 4.420 29.166 1244 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1121 helix: 1.56 (0.20), residues: 733 sheet: -0.88 (0.55), residues: 79 loop : -1.41 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1102 TYR 0.025 0.001 TYR A 304 PHE 0.025 0.001 PHE A 490 TRP 0.036 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 9436) covalent geometry : angle 0.55170 / 0.28 (12771) hydrogen bonds : bond 0.04159 / 2.71 ( 553) hydrogen bonds : angle 3.97564 / 2.92 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.37 seconds wall clock time: 20 minutes 30.33 seconds (1230.33 seconds total)