Starting phenix.real_space_refine on Sun Dec 29 00:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fzq_29637/12_2024/8fzq_29637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzq_29637/12_2024/8fzq_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_29637/12_2024/8fzq_29637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzq_29637/12_2024/8fzq_29637.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzq_29637/12_2024/8fzq_29637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzq_29637/12_2024/8fzq_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-5532/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: 6.35, per 1000 atoms: 0.69 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 2.85 Time building geometry restraints manager: 2.92 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.880 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 32.300 ------------------------------------------------------------------------------- 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 : 1.079 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: 0.1722 time to fit residues: 52.8085 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 : 1.069 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 525 GLN cc_start: 0.5554 (mp10) cc_final: 0.5100 (pp30) REVERT: A 1160 VAL cc_start: 0.8473 (p) cc_final: 0.8126 (p) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1867 time to fit residues: 41.0839 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 : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 0.1980 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2397 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= 0.179 Angle : 0.544 8.245 12771 Z= 0.279 Chirality : 0.040 0.144 1478 Planarity : 0.004 0.048 1560 Dihedral : 7.330 84.699 1306 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 0.92 (0.25), residues: 1121 helix: 1.50 (0.19), residues: 739 sheet: -0.28 (0.63), residues: 70 loop : -1.30 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 202 HIS 0.005 0.001 HIS A 147 PHE 0.022 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 131 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 525 GLN cc_start: 0.5495 (mt0) cc_final: 0.5080 (pp30) REVERT: A 602 LEU cc_start: 0.8036 (tp) cc_final: 0.7522 (mp) REVERT: A 1160 VAL cc_start: 0.8304 (p) cc_final: 0.7687 (p) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1719 time to fit residues: 35.0648 Evaluate side-chains 90 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9436 Z= 0.303 Angle : 0.673 8.475 12771 Z= 0.346 Chirality : 0.044 0.270 1478 Planarity : 0.004 0.047 1560 Dihedral : 7.184 85.788 1306 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.10 % Allowed : 4.83 % Favored : 95.07 % 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: 0.56 (0.25), residues: 1121 helix: 1.15 (0.19), residues: 741 sheet: -0.65 (0.61), residues: 70 loop : -1.19 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 865 HIS 0.005 0.001 HIS A 147 PHE 0.025 0.002 PHE A 131 TYR 0.030 0.002 TYR A 325 ARG 0.006 0.001 ARG A1283 *********************** 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 114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.157 Fit side-chains REVERT: A 602 LEU cc_start: 0.8545 (tp) cc_final: 0.7870 (mp) REVERT: A 1160 VAL cc_start: 0.8721 (p) cc_final: 0.8328 (p) REVERT: A 1328 ILE cc_start: 0.6691 (mm) cc_final: 0.6477 (mt) REVERT: A 1354 MET cc_start: 0.8047 (tpt) cc_final: 0.7667 (tpp) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.1686 time to fit residues: 30.1261 Evaluate side-chains 65 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4509 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= 0.178 Angle : 0.546 7.062 12771 Z= 0.280 Chirality : 0.039 0.153 1478 Planarity : 0.004 0.047 1560 Dihedral : 6.815 83.207 1306 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 0.91 (0.25), residues: 1121 helix: 1.51 (0.20), residues: 734 sheet: -0.58 (0.59), residues: 74 loop : -1.23 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1274 HIS 0.011 0.001 HIS A1079 PHE 0.013 0.001 PHE A1413 TYR 0.014 0.001 TYR A 849 ARG 0.004 0.000 ARG A 75 *********************** 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 112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.066 Fit side-chains REVERT: A 165 LEU cc_start: 0.8952 (tp) cc_final: 0.8715 (tp) REVERT: A 321 SER cc_start: 0.8847 (m) cc_final: 0.8484 (p) REVERT: A 602 LEU cc_start: 0.8454 (tp) cc_final: 0.7817 (mp) REVERT: A 1145 TRP cc_start: 0.7140 (m-10) cc_final: 0.6916 (m-10) REVERT: A 1328 ILE cc_start: 0.6581 (mm) cc_final: 0.6379 (mt) REVERT: A 1354 MET cc_start: 0.7948 (tpt) cc_final: 0.7552 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1819 time to fit residues: 31.6582 Evaluate side-chains 70 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9436 Z= 0.230 Angle : 0.583 9.297 12771 Z= 0.296 Chirality : 0.041 0.326 1478 Planarity : 0.004 0.048 1560 Dihedral : 6.736 82.385 1306 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.79 (0.25), residues: 1121 helix: 1.40 (0.19), residues: 739 sheet: -0.58 (0.61), residues: 70 loop : -1.27 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1274 HIS 0.007 0.001 HIS A1079 PHE 0.028 0.002 PHE A 131 TYR 0.013 0.001 TYR A1073 ARG 0.003 0.000 ARG A1102 *********************** 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 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 469 MET cc_start: 0.9256 (mmt) cc_final: 0.8634 (mpp) REVERT: A 602 LEU cc_start: 0.8489 (tp) cc_final: 0.7806 (mp) REVERT: A 1354 MET cc_start: 0.8091 (tpt) cc_final: 0.7845 (tpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1625 time to fit residues: 25.1697 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 : 1.087 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9436 Z= 0.185 Angle : 0.552 9.732 12771 Z= 0.280 Chirality : 0.040 0.164 1478 Planarity : 0.004 0.048 1560 Dihedral : 6.624 80.667 1306 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1121 helix: 1.51 (0.20), residues: 735 sheet: -0.81 (0.57), residues: 80 loop : -1.23 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 PHE 0.026 0.001 PHE A 490 TYR 0.013 0.001 TYR A 304 ARG 0.002 0.000 ARG A 75 *********************** 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 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8980 (mt) cc_final: 0.8743 (tt) REVERT: A 265 MET cc_start: 0.6903 (tpp) cc_final: 0.6616 (tpp) REVERT: A 469 MET cc_start: 0.9133 (mmt) cc_final: 0.8459 (mpp) REVERT: A 602 LEU cc_start: 0.8496 (tp) cc_final: 0.7837 (mp) REVERT: A 1160 VAL cc_start: 0.8590 (p) cc_final: 0.8092 (p) REVERT: A 1354 MET cc_start: 0.8087 (tpt) cc_final: 0.7863 (tpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1551 time to fit residues: 25.9615 Evaluate side-chains 71 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9436 Z= 0.158 Angle : 0.563 10.508 12771 Z= 0.281 Chirality : 0.039 0.173 1478 Planarity : 0.004 0.048 1560 Dihedral : 6.495 78.422 1306 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.99 (0.25), residues: 1121 helix: 1.59 (0.19), residues: 735 sheet: -0.62 (0.57), residues: 80 loop : -1.27 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1274 HIS 0.007 0.001 HIS A1079 PHE 0.034 0.001 PHE A 131 TYR 0.013 0.001 TYR A1073 ARG 0.004 0.000 ARG A1102 *********************** 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 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8888 (mt) cc_final: 0.8622 (tt) REVERT: A 321 SER cc_start: 0.8709 (m) cc_final: 0.8410 (p) REVERT: A 602 LEU cc_start: 0.8491 (tp) cc_final: 0.7833 (mp) REVERT: A 1160 VAL cc_start: 0.8655 (p) cc_final: 0.8394 (p) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1581 time to fit residues: 26.2879 Evaluate side-chains 74 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9436 Z= 0.153 Angle : 0.565 10.192 12771 Z= 0.280 Chirality : 0.039 0.178 1478 Planarity : 0.003 0.047 1560 Dihedral : 6.372 75.012 1306 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1.04 (0.25), residues: 1121 helix: 1.65 (0.19), residues: 734 sheet: -0.59 (0.57), residues: 80 loop : -1.31 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 PHE 0.027 0.001 PHE A 131 TYR 0.014 0.001 TYR A1073 ARG 0.003 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 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8898 (mt) cc_final: 0.8619 (tt) REVERT: A 321 SER cc_start: 0.8685 (m) cc_final: 0.8391 (p) REVERT: A 602 LEU cc_start: 0.8480 (tp) cc_final: 0.7838 (mp) REVERT: A 1145 TRP cc_start: 0.7002 (m-10) cc_final: 0.6791 (m-10) REVERT: A 1160 VAL cc_start: 0.8595 (p) cc_final: 0.8281 (p) REVERT: A 1354 MET cc_start: 0.8507 (tpp) cc_final: 0.8304 (tpt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1747 time to fit residues: 29.4663 Evaluate side-chains 73 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 0.0370 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 0.0670 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9436 Z= 0.154 Angle : 0.561 10.555 12771 Z= 0.278 Chirality : 0.040 0.187 1478 Planarity : 0.004 0.047 1560 Dihedral : 6.302 69.427 1306 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % 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: 1.10 (0.26), residues: 1121 helix: 1.70 (0.20), residues: 732 sheet: -0.45 (0.57), residues: 81 loop : -1.32 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 PHE 0.028 0.001 PHE A1257 TYR 0.014 0.001 TYR A1073 ARG 0.007 0.000 ARG A 153 ********************** 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 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.126 Fit side-chains REVERT: A 265 MET cc_start: 0.6677 (tpp) cc_final: 0.6292 (tpp) REVERT: A 321 SER cc_start: 0.8669 (m) cc_final: 0.8405 (p) REVERT: A 472 MET cc_start: 0.7870 (mtm) cc_final: 0.7619 (mtm) REVERT: A 602 LEU cc_start: 0.8492 (tp) cc_final: 0.7861 (mp) REVERT: A 1160 VAL cc_start: 0.8683 (p) cc_final: 0.8297 (p) REVERT: A 1354 MET cc_start: 0.8470 (tpp) cc_final: 0.8186 (tpt) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1629 time to fit residues: 27.7166 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 : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090443 restraints weight = 24295.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090915 restraints weight = 18436.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091376 restraints weight = 14504.990| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9436 Z= 0.148 Angle : 0.560 9.985 12771 Z= 0.278 Chirality : 0.039 0.186 1478 Planarity : 0.004 0.047 1560 Dihedral : 6.194 61.243 1306 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % 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 (0.26), residues: 1121 helix: 1.72 (0.20), residues: 734 sheet: -0.38 (0.57), residues: 81 loop : -1.34 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1274 HIS 0.008 0.001 HIS A1079 PHE 0.030 0.001 PHE A1257 TYR 0.014 0.001 TYR A1073 ARG 0.006 0.000 ARG A 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.07 seconds wall clock time: 35 minutes 42.38 seconds (2142.38 seconds total)