Starting phenix.real_space_refine on Thu Feb 13 22:02:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fzq_29637/02_2025/8fzq_29637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzq_29637/02_2025/8fzq_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_29637/02_2025/8fzq_29637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzq_29637/02_2025/8fzq_29637.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzq_29637/02_2025/8fzq_29637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzq_29637/02_2025/8fzq_29637.cif" } resolution = 4.3 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.51, per 1000 atoms: 0.60 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: 2.31 Conformation dependent library (CDL) restraints added in 898.8 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: 0.96 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: 2.77 Time building geometry restraints manager: 2.62 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: 4957 17.67 - 35.35: 529 35.35 - 53.02: 111 53.02 - 70.69: 29 70.69 - 88.37: 7 Dihedral angle restraints: 5633 sinusoidal: 2287 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 5630 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: 2.680 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.560 Find NCS groups from input model: 0.100 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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= 0.144 Angle : 0.529 9.779 12771 Z= 0.275 Chirality : 0.039 0.159 1478 Planarity : 0.003 0.044 1560 Dihedral : 15.435 88.368 3469 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 (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: 1.00 (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 TRP 0.035 0.001 TRP A1274 HIS 0.002 0.001 HIS A 609 PHE 0.024 0.001 PHE A 587 TYR 0.011 0.001 TYR A 304 ARG 0.002 0.000 ARG A 975 *********************** 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 : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 GLN cc_start: 0.5535 (mp10) cc_final: 0.5065 (pp30) 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: 0.1740 time to fit residues: 52.9246 Evaluate side-chains 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.0040 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 620 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090126 restraints weight = 23453.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090618 restraints weight = 20926.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091109 restraints weight = 15772.798| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1533 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= 0.171 Angle : 0.537 7.028 12771 Z= 0.276 Chirality : 0.040 0.178 1478 Planarity : 0.004 0.045 1560 Dihedral : 8.072 84.186 1306 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: 1.07 (0.25), residues: 1121 helix: 1.64 (0.20), residues: 738 sheet: -0.13 (0.66), residues: 65 loop : -1.32 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1274 HIS 0.002 0.001 HIS A 139 PHE 0.016 0.001 PHE A 131 TYR 0.010 0.001 TYR A 304 ARG 0.003 0.000 ARG A 352 *********************** 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 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 525 GLN cc_start: 0.5539 (mp10) cc_final: 0.5089 (pp30) REVERT: A 1160 VAL cc_start: 0.8491 (p) cc_final: 0.8152 (p) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2037 time to fit residues: 45.5787 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 : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 50 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091242 restraints weight = 23710.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091874 restraints weight = 17629.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092276 restraints weight = 13600.974| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9436 Z= 0.161 Angle : 0.532 8.338 12771 Z= 0.272 Chirality : 0.039 0.138 1478 Planarity : 0.004 0.059 1560 Dihedral : 7.345 84.385 1306 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 0.98 (0.25), residues: 1121 helix: 1.56 (0.19), residues: 739 sheet: -0.10 (0.66), residues: 65 loop : -1.33 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 202 HIS 0.009 0.001 HIS A 147 PHE 0.024 0.001 PHE A 131 TYR 0.012 0.001 TYR A 325 ARG 0.010 0.000 ARG A 75 *********************** 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 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 525 GLN cc_start: 0.5468 (mt0) cc_final: 0.5079 (pp30) REVERT: A 602 LEU cc_start: 0.7994 (tp) cc_final: 0.7503 (mp) REVERT: A 1160 VAL cc_start: 0.8260 (p) cc_final: 0.7675 (p) REVERT: A 1354 MET cc_start: 0.7545 (tpt) cc_final: 0.7279 (tpt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1600 time to fit residues: 33.9505 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 : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 104 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090021 restraints weight = 23805.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091179 restraints weight = 15733.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091941 restraints weight = 11795.752| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9436 Z= 0.220 Angle : 0.565 7.609 12771 Z= 0.289 Chirality : 0.040 0.152 1478 Planarity : 0.004 0.046 1560 Dihedral : 6.916 85.544 1306 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.25), residues: 1121 helix: 1.53 (0.19), residues: 737 sheet: -0.39 (0.61), residues: 70 loop : -1.11 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1274 HIS 0.003 0.001 HIS A 147 PHE 0.021 0.001 PHE A 131 TYR 0.011 0.001 TYR A 304 ARG 0.005 0.000 ARG A 75 *********************** 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 131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 SER cc_start: 0.8780 (m) cc_final: 0.8402 (p) REVERT: A 602 LEU cc_start: 0.8296 (tp) cc_final: 0.7762 (mp) REVERT: A 1160 VAL cc_start: 0.8523 (p) cc_final: 0.7414 (p) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1720 time to fit residues: 34.1716 Evaluate side-chains 87 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089839 restraints weight = 23915.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091101 restraints weight = 19182.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091916 restraints weight = 12280.224| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9436 Z= 0.199 Angle : 0.553 6.800 12771 Z= 0.282 Chirality : 0.041 0.295 1478 Planarity : 0.004 0.048 1560 Dihedral : 6.735 85.477 1306 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.25), residues: 1121 helix: 1.64 (0.20), residues: 733 sheet: -0.40 (0.61), residues: 70 loop : -1.35 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1274 HIS 0.005 0.001 HIS A 139 PHE 0.024 0.001 PHE A1413 TYR 0.017 0.001 TYR A 304 ARG 0.006 0.000 ARG A1158 *********************** 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 120 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 SER cc_start: 0.8876 (m) cc_final: 0.8543 (p) REVERT: A 525 GLN cc_start: 0.5459 (mp10) cc_final: 0.5249 (pp30) REVERT: A 602 LEU cc_start: 0.8397 (tp) cc_final: 0.7770 (mp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1806 time to fit residues: 33.4141 Evaluate side-chains 82 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089847 restraints weight = 24145.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090665 restraints weight = 19332.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091207 restraints weight = 14487.118| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9436 Z= 0.194 Angle : 0.550 7.218 12771 Z= 0.280 Chirality : 0.039 0.152 1478 Planarity : 0.003 0.046 1560 Dihedral : 6.586 85.795 1306 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 1.00 (0.25), residues: 1121 helix: 1.59 (0.20), residues: 739 sheet: -0.63 (0.57), residues: 80 loop : -1.25 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1274 HIS 0.005 0.001 HIS A 199 PHE 0.018 0.001 PHE A 131 TYR 0.014 0.001 TYR A 325 ARG 0.004 0.000 ARG A 134 *********************** 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 118 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8907 (tp) cc_final: 0.8323 (tp) REVERT: A 321 SER cc_start: 0.8903 (m) cc_final: 0.8587 (p) REVERT: A 602 LEU cc_start: 0.8460 (tp) cc_final: 0.7836 (mp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1703 time to fit residues: 30.4537 Evaluate side-chains 79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088553 restraints weight = 24393.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089304 restraints weight = 17131.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089715 restraints weight = 13029.201| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9436 Z= 0.215 Angle : 0.581 10.018 12771 Z= 0.299 Chirality : 0.040 0.170 1478 Planarity : 0.004 0.046 1560 Dihedral : 6.596 85.896 1306 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.10 % Allowed : 1.11 % 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 (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: 0.96 (0.25), residues: 1121 helix: 1.58 (0.20), residues: 728 sheet: -0.64 (0.57), residues: 74 loop : -1.24 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1274 HIS 0.002 0.001 HIS A1085 PHE 0.031 0.002 PHE A 77 TYR 0.014 0.001 TYR A 325 ARG 0.004 0.000 ARG A 153 *********************** 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 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.071 Fit side-chains REVERT: A 321 SER cc_start: 0.8795 (m) cc_final: 0.8470 (p) REVERT: A 602 LEU cc_start: 0.8505 (tp) cc_final: 0.7840 (mp) REVERT: A 1167 ILE cc_start: 0.8109 (mm) cc_final: 0.7817 (mt) REVERT: A 1354 MET cc_start: 0.7906 (tpt) cc_final: 0.7355 (tpp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1824 time to fit residues: 29.7801 Evaluate side-chains 68 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089162 restraints weight = 24726.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090006 restraints weight = 17848.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090512 restraints weight = 13576.636| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9436 Z= 0.162 Angle : 0.570 10.746 12771 Z= 0.286 Chirality : 0.039 0.183 1478 Planarity : 0.004 0.046 1560 Dihedral : 6.482 85.297 1306 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 1.31 % Favored : 98.59 % 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: 1.07 (0.25), residues: 1121 helix: 1.69 (0.20), residues: 728 sheet: -0.72 (0.56), residues: 80 loop : -1.21 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1274 HIS 0.005 0.001 HIS A 199 PHE 0.018 0.001 PHE A 131 TYR 0.018 0.001 TYR A1073 ARG 0.004 0.000 ARG A 75 *********************** 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 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 265 MET cc_start: 0.6815 (tpp) cc_final: 0.6370 (tpp) REVERT: A 321 SER cc_start: 0.8752 (m) cc_final: 0.8422 (p) REVERT: A 602 LEU cc_start: 0.8461 (tp) cc_final: 0.7808 (mp) REVERT: A 1167 ILE cc_start: 0.8028 (mm) cc_final: 0.7824 (mt) REVERT: A 1354 MET cc_start: 0.7645 (tpt) cc_final: 0.7071 (tpp) outliers start: 1 outliers final: 1 residues processed: 108 average time/residue: 0.1667 time to fit residues: 28.1288 Evaluate side-chains 73 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 10.0000 chunk 70 optimal weight: 0.0030 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089143 restraints weight = 24312.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090763 restraints weight = 14414.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091850 restraints weight = 9879.130| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9436 Z= 0.169 Angle : 0.566 11.118 12771 Z= 0.281 Chirality : 0.040 0.184 1478 Planarity : 0.003 0.046 1560 Dihedral : 6.451 85.557 1306 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.13 (0.25), residues: 1121 helix: 1.68 (0.19), residues: 735 sheet: -0.57 (0.57), residues: 74 loop : -1.13 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1274 HIS 0.005 0.001 HIS A 199 PHE 0.035 0.001 PHE A 131 TYR 0.015 0.001 TYR A1073 ARG 0.002 0.000 ARG A 75 *********************** 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 112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.134 Fit side-chains REVERT: A 165 LEU cc_start: 0.8952 (tp) cc_final: 0.8512 (tp) REVERT: A 319 PHE cc_start: 0.8433 (t80) cc_final: 0.7846 (t80) REVERT: A 321 SER cc_start: 0.8715 (m) cc_final: 0.8441 (p) REVERT: A 469 MET cc_start: 0.9123 (mmt) cc_final: 0.8509 (mpp) REVERT: A 602 LEU cc_start: 0.8466 (tp) cc_final: 0.7812 (mp) REVERT: A 1354 MET cc_start: 0.7793 (tpt) cc_final: 0.7514 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1762 time to fit residues: 30.5049 Evaluate side-chains 76 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088610 restraints weight = 24829.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089743 restraints weight = 16901.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090319 restraints weight = 11909.528| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5242 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= 0.182 Angle : 0.580 10.616 12771 Z= 0.286 Chirality : 0.040 0.181 1478 Planarity : 0.003 0.046 1560 Dihedral : 6.443 85.959 1306 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.02 (0.25), residues: 1121 helix: 1.63 (0.20), residues: 736 sheet: -0.64 (0.57), residues: 75 loop : -1.28 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1274 HIS 0.003 0.001 HIS A1054 PHE 0.030 0.001 PHE A 131 TYR 0.013 0.001 TYR A1073 ARG 0.003 0.000 ARG A1158 ********************** 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 111 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.023 Fit side-chains REVERT: A 165 LEU cc_start: 0.8926 (tp) cc_final: 0.8687 (tp) REVERT: A 319 PHE cc_start: 0.8484 (t80) cc_final: 0.7900 (t80) REVERT: A 321 SER cc_start: 0.8727 (m) cc_final: 0.8451 (p) REVERT: A 469 MET cc_start: 0.9191 (mmt) cc_final: 0.8575 (mpp) REVERT: A 602 LEU cc_start: 0.8507 (tp) cc_final: 0.7842 (mp) REVERT: A 1354 MET cc_start: 0.7974 (tpt) cc_final: 0.7626 (tpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1628 time to fit residues: 28.1477 Evaluate side-chains 78 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090207 restraints weight = 24363.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091390 restraints weight = 17427.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091702 restraints weight = 13419.154| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9436 Z= 0.159 Angle : 0.562 10.060 12771 Z= 0.278 Chirality : 0.039 0.185 1478 Planarity : 0.003 0.046 1560 Dihedral : 6.413 86.237 1306 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % 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 (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: 1.11 (0.25), residues: 1121 helix: 1.69 (0.20), residues: 737 sheet: -0.48 (0.57), residues: 76 loop : -1.29 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1274 HIS 0.004 0.001 HIS A 199 PHE 0.035 0.001 PHE A 131 TYR 0.014 0.001 TYR A1073 ARG 0.005 0.000 ARG A 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.91 seconds wall clock time: 44 minutes 19.32 seconds (2659.32 seconds total)