Starting phenix.real_space_refine on Sat Sep 12 01:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm3_30400/09_2026/7cm3_30400.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.096 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 96 5.16 5 C 8194 2.51 5 N 1956 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12418 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10442 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1232} Chain breaks: 5 Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 412 Unusual residues: {'NAG': 1, 'PC1': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.18 Number of scatterers: 12418 At special positions: 0 Unit cell: (160.876, 108.7, 111.961, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 10 15.00 O 2162 8.00 N 1956 7.00 C 8194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.02 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.04 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 261 " distance=2.04 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1801 " - " ASN A 216 " " NAG B 501 " - " ASN B 217 " " NAG C 1 " - " ASN A1064 " " NAG D 1 " - " ASN A 210 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 514.0 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 5 sheets defined 71.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.969A pdb=" N LEU A 41 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 65 through 92 removed outlier: 4.171A pdb=" N TYR A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.770A pdb=" N GLY A 140 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.669A pdb=" N LEU A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.603A pdb=" N ALA A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 200 removed outlier: 3.562A pdb=" N GLN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.603A pdb=" N LEU A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 294 through 310 removed outlier: 3.834A pdb=" N SER A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 336 removed outlier: 3.794A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.884A pdb=" N MET A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'A' and resid 419 through 441 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.501A pdb=" N THR A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.957A pdb=" N GLN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 3.577A pdb=" N LYS A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.590A pdb=" N GLU A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 4.228A pdb=" N LEU A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.658A pdb=" N GLY A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 605 through 617 removed outlier: 3.525A pdb=" N SER A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 886 through 904 Processing helix chain 'A' and resid 911 through 914 Processing helix chain 'A' and resid 915 through 941 removed outlier: 4.893A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 972 Processing helix chain 'A' and resid 980 through 989 Processing helix chain 'A' and resid 990 through 993 Proline residue: A 993 - end of helix No H-bonds generated for 'chain 'A' and resid 990 through 993' Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.934A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1012 Processing helix chain 'A' and resid 1013 through 1040 Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.686A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1128 Processing helix chain 'A' and resid 1132 through 1145 removed outlier: 3.980A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1163 removed outlier: 4.083A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.740A pdb=" N ALA A1201 " --> pdb=" O ASP A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.978A pdb=" N ARG A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1228 No H-bonds generated for 'chain 'A' and resid 1226 through 1228' Processing helix chain 'A' and resid 1237 through 1263 removed outlier: 3.579A pdb=" N LEU A1241 " --> pdb=" O VAL A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1269 Processing helix chain 'A' and resid 1271 through 1295 Processing helix chain 'A' and resid 1296 through 1312 Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1318 through 1335 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1374 through 1388 Processing helix chain 'A' and resid 1390 through 1399 Processing helix chain 'A' and resid 1419 through 1436 removed outlier: 3.611A pdb=" N CYS A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 4.189A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1443 " --> pdb=" O LEU A1439 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A1451 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1478 removed outlier: 3.681A pdb=" N VAL A1477 " --> pdb=" O ILE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1494 removed outlier: 4.207A pdb=" N LYS A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1502 removed outlier: 4.396A pdb=" N LEU A1501 " --> pdb=" O ARG A1498 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A1502 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1502' Processing helix chain 'A' and resid 1508 through 1523 removed outlier: 3.532A pdb=" N MET A1519 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS A1523 " --> pdb=" O MET A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1540 Processing helix chain 'A' and resid 1543 through 1548 Processing helix chain 'A' and resid 1549 through 1577 removed outlier: 3.985A pdb=" N LEU A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A1555 " --> pdb=" O GLU A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1602 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 262 through 288 removed outlier: 4.213A pdb=" N GLU B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 Processing helix chain 'B' and resid 331 through 341 removed outlier: 4.000A pdb=" N LEU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 209 removed outlier: 4.023A pdb=" N HIS A 206 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 246 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1045 through 1046 Processing sheet with id=AA3, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id=AA4, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329 720 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1861 1.28 - 1.41: 3408 1.41 - 1.55: 7233 1.55 - 1.69: 67 1.69 - 1.82: 150 Bond restraints: 12719 Sorted by residual: bond pdb=" C LEU A 78 " pdb=" N MET A 79 " ideal model delta sigma weight residual 1.335 1.245 0.090 1.30e-02 5.92e+03 4.83e+01 bond pdb=" C38 PC1 A1808 " pdb=" C39 PC1 A1808 " ideal model delta sigma weight residual 1.523 1.433 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" N GLU B 373 " pdb=" CA GLU B 373 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.68e+01 bond pdb=" N VAL A 458 " pdb=" CA VAL A 458 " ideal model delta sigma weight residual 1.459 1.510 -0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" C ARG A 992 " pdb=" O ARG A 992 " ideal model delta sigma weight residual 1.243 1.204 0.039 9.90e-03 1.02e+04 1.52e+01 ... (remaining 12714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 14775 2.62 - 5.24: 2285 5.24 - 7.85: 105 7.85 - 10.47: 9 10.47 - 13.09: 6 Bond angle restraints: 17180 Sorted by residual: angle pdb=" N GLN A 414 " pdb=" CA GLN A 414 " pdb=" C GLN A 414 " ideal model delta sigma weight residual 112.93 99.84 13.09 1.33e+00 5.65e-01 9.69e+01 angle pdb=" N ASP B 372 " pdb=" CA ASP B 372 " pdb=" C ASP B 372 " ideal model delta sigma weight residual 111.28 103.22 8.06 1.09e+00 8.42e-01 5.47e+01 angle pdb=" N TYR A 419 " pdb=" CA TYR A 419 " pdb=" C TYR A 419 " ideal model delta sigma weight residual 113.55 105.76 7.79 1.26e+00 6.30e-01 3.82e+01 angle pdb=" CA ASP A 247 " pdb=" CB ASP A 247 " pdb=" CG ASP A 247 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" N PRO A 65 " pdb=" CA PRO A 65 " pdb=" C PRO A 65 " ideal model delta sigma weight residual 110.70 117.39 -6.69 1.22e+00 6.72e-01 3.00e+01 ... (remaining 17175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 6796 18.07 - 36.14: 493 36.14 - 54.21: 130 54.21 - 72.28: 41 72.28 - 90.35: 13 Dihedral angle restraints: 7473 sinusoidal: 3179 harmonic: 4294 Sorted by residual: dihedral pdb=" CB CYS A1046 " pdb=" SG CYS A1046 " pdb=" SG CYS A1057 " pdb=" CB CYS A1057 " ideal model delta sinusoidal sigma weight residual -86.00 -155.69 69.69 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CA CYS A 229 " pdb=" C CYS A 229 " pdb=" N SER A 230 " pdb=" CA SER A 230 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS B 324 " pdb=" SG CYS B 324 " pdb=" SG CYS B 377 " pdb=" CB CYS B 377 " ideal model delta sinusoidal sigma weight residual -86.00 -125.75 39.75 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 7470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 1809 0.182 - 0.365: 104 0.365 - 0.547: 0 0.547 - 0.729: 1 0.729 - 0.911: 1 Chirality restraints: 1915 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.30e+01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 217 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1912 not shown) Planarity restraints: 2082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.359 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG D 1 " 0.101 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.216 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.277 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG D 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 217 " -0.081 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" CG ASN B 217 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 217 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 217 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " -0.130 2.00e-02 2.50e+03 ... (remaining 2079 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 334 2.74 - 3.28: 12331 3.28 - 3.82: 18812 3.82 - 4.36: 25064 4.36 - 4.90: 40190 Nonbonded interactions: 96731 Sorted by model distance: nonbonded pdb=" O3 NAG D 1 " pdb=" O7 NAG D 1 " model vdw 2.199 3.040 nonbonded pdb=" CE MET A 545 " pdb=" O22 PC1 A1805 " model vdw 2.224 3.460 nonbonded pdb=" NH1 ARG A 542 " pdb=" O14 PC1 A1805 " model vdw 2.225 3.120 nonbonded pdb=" O ASN A1072 " pdb=" ND2 ASN A1072 " model vdw 2.246 3.120 nonbonded pdb=" NH1 ARG A1273 " pdb=" C13 PC1 A1804 " model vdw 2.295 3.540 ... (remaining 96726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.015 0.090 12736 Z= 0.891 Angle : 1.796 27.187 17221 Z= 1.188 Chirality : 0.098 0.911 1915 Planarity : 0.014 0.295 2078 Dihedral : 14.858 90.346 4659 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.85 % Favored : 94.88 % Rotamer: Outliers : 2.12 % Allowed : 4.69 % Favored : 93.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1444 helix: -0.05 (0.15), residues: 934 sheet: None (None), residues: 0 loop : -1.56 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1481 TYR 0.081 0.009 TYR A 274 PHE 0.066 0.009 PHE A 997 TRP 0.061 0.011 TRP B 311 HIS 0.013 0.003 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.01471 / 0.89 (12719) covalent geometry : angle 1.77018 / 1.18 (17180) SS BOND : bond 0.00709 / 0.40 ( 10) SS BOND : angle 1.83607 / 0.88 ( 20) hydrogen bonds : bond 0.18640 / 12.59 ( 720) hydrogen bonds : angle 6.70007 / 4.83 ( 2109) link_BETA1-4 : bond 0.01978 / 0.97 ( 3) link_BETA1-4 : angle 3.50139 / 1.52 ( 9) link_NAG-ASN : bond 0.03478 / 1.74 ( 4) link_NAG-ASN : angle 11.41754 / 5.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 329 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 348 average time/residue: 0.1095 time to fit residues: 54.0146 Evaluate side-chains 203 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 279 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 451 HIS A 569 HIS A1072 ASN A1270 GLN A1460 GLN A1589 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN B 371 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117251 restraints weight = 18623.102| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.47 r_work: 0.3374 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12736 Z= 0.156 Angle : 0.685 11.534 17221 Z= 0.349 Chirality : 0.043 0.353 1915 Planarity : 0.005 0.042 2078 Dihedral : 12.323 68.495 1855 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 3.03 % Allowed : 9.54 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1444 helix: 1.20 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 155 TYR 0.015 0.001 TYR A1426 PHE 0.020 0.002 PHE A1530 TRP 0.025 0.002 TRP A 107 HIS 0.004 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (12719) covalent geometry : angle 0.66449 / 0.35 (17180) SS BOND : bond 0.00254 / 0.13 ( 10) SS BOND : angle 1.14198 / 0.63 ( 20) hydrogen bonds : bond 0.05892 / 3.87 ( 720) hydrogen bonds : angle 4.62902 / 3.34 ( 2109) link_BETA1-4 : bond 0.00926 / 0.47 ( 3) link_BETA1-4 : angle 1.50067 / 0.63 ( 9) link_NAG-ASN : bond 0.00715 / 0.37 ( 4) link_NAG-ASN : angle 6.03979 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8739 (ppp) cc_final: 0.8307 (ppp) REVERT: A 388 MET cc_start: 0.6838 (ppp) cc_final: 0.6570 (ppp) REVERT: A 554 GLU cc_start: 0.8109 (tp30) cc_final: 0.7903 (tp30) REVERT: A 851 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7174 (ttm110) REVERT: A 892 MET cc_start: 0.7893 (mmt) cc_final: 0.7665 (mmt) REVERT: A 972 MET cc_start: 0.8200 (mmt) cc_final: 0.7988 (mmt) REVERT: A 1480 LYS cc_start: 0.8574 (mptt) cc_final: 0.8162 (mptt) REVERT: A 1506 ASP cc_start: 0.8899 (t0) cc_final: 0.8465 (t0) REVERT: A 1515 MET cc_start: 0.9261 (mmm) cc_final: 0.9004 (mmp) REVERT: A 1602 GLN cc_start: 0.6523 (mt0) cc_final: 0.6031 (mt0) REVERT: B 262 ARG cc_start: 0.7850 (tmm-80) cc_final: 0.7609 (tmm-80) REVERT: B 350 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (mp0) outliers start: 40 outliers final: 26 residues processed: 246 average time/residue: 0.1008 time to fit residues: 36.4297 Evaluate side-chains 213 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 350 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 71 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1460 GLN A1589 GLN B 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115041 restraints weight = 18743.955| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.45 r_work: 0.3346 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12736 Z= 0.153 Angle : 0.616 9.838 17221 Z= 0.318 Chirality : 0.041 0.210 1915 Planarity : 0.004 0.042 2078 Dihedral : 11.635 66.479 1851 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.88 % Allowed : 11.13 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.22), residues: 1444 helix: 1.40 (0.17), residues: 952 sheet: -4.06 (1.13), residues: 10 loop : -1.22 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 951 TYR 0.015 0.001 TYR A1426 PHE 0.018 0.002 PHE A1530 TRP 0.010 0.001 TRP A 119 HIS 0.004 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (12719) covalent geometry : angle 0.59733 / 0.31 (17180) SS BOND : bond 0.00375 / 0.20 ( 10) SS BOND : angle 2.28101 / 1.13 ( 20) hydrogen bonds : bond 0.05372 / 3.52 ( 720) hydrogen bonds : angle 4.42237 / 3.19 ( 2109) link_BETA1-4 : bond 0.00696 / 0.35 ( 3) link_BETA1-4 : angle 1.14471 / 0.53 ( 9) link_NAG-ASN : bond 0.00765 / 0.38 ( 4) link_NAG-ASN : angle 4.97029 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.6920 (ppp) cc_final: 0.6698 (ppp) REVERT: A 393 MET cc_start: 0.6780 (mmp) cc_final: 0.6446 (mmt) REVERT: A 892 MET cc_start: 0.7905 (mmt) cc_final: 0.7592 (mmt) REVERT: A 1476 MET cc_start: 0.7775 (ptp) cc_final: 0.7421 (ppp) REVERT: A 1513 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8971 (mmtt) REVERT: A 1515 MET cc_start: 0.9129 (mmm) cc_final: 0.8669 (mmp) REVERT: B 340 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8446 (mtt90) outliers start: 38 outliers final: 28 residues processed: 221 average time/residue: 0.0981 time to fit residues: 32.2173 Evaluate side-chains 208 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 136 optimal weight: 0.0970 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN A 334 GLN A1589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116594 restraints weight = 18622.938| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.46 r_work: 0.3371 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12736 Z= 0.117 Angle : 0.563 8.027 17221 Z= 0.289 Chirality : 0.039 0.197 1915 Planarity : 0.004 0.043 2078 Dihedral : 10.916 64.433 1849 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.73 % Allowed : 11.96 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1444 helix: 1.59 (0.17), residues: 955 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 152 TYR 0.014 0.001 TYR A1426 PHE 0.020 0.001 PHE A 72 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (12719) covalent geometry : angle 0.55018 / 0.29 (17180) SS BOND : bond 0.00169 / 0.10 ( 10) SS BOND : angle 1.63398 / 0.87 ( 20) hydrogen bonds : bond 0.04538 / 2.96 ( 720) hydrogen bonds : angle 4.21243 / 3.03 ( 2109) link_BETA1-4 : bond 0.00619 / 0.31 ( 3) link_BETA1-4 : angle 1.24137 / 0.58 ( 9) link_NAG-ASN : bond 0.00362 / 0.18 ( 4) link_NAG-ASN : angle 4.02437 / 1.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8533 (mm) cc_final: 0.8267 (mt) REVERT: A 388 MET cc_start: 0.6706 (ppp) cc_final: 0.6467 (ppp) REVERT: A 393 MET cc_start: 0.6703 (mmp) cc_final: 0.6424 (mmt) REVERT: A 616 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 1202 LYS cc_start: 0.7561 (pttp) cc_final: 0.6825 (tppp) REVERT: A 1302 MET cc_start: 0.7009 (ttt) cc_final: 0.6698 (tmt) REVERT: A 1335 SER cc_start: 0.9253 (p) cc_final: 0.8997 (p) REVERT: A 1424 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 1468 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8418 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9275 (mmtt) cc_final: 0.9028 (mmtt) REVERT: A 1515 MET cc_start: 0.9237 (mmm) cc_final: 0.8707 (mmp) REVERT: A 1536 MET cc_start: 0.8788 (ttp) cc_final: 0.8421 (ttp) REVERT: B 216 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.4565 (t-100) REVERT: B 233 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: B 262 ARG cc_start: 0.7812 (tmm-80) cc_final: 0.7510 (tmm-80) REVERT: B 270 ASP cc_start: 0.8637 (t70) cc_final: 0.8230 (t0) REVERT: B 327 THR cc_start: 0.7545 (p) cc_final: 0.7302 (m) outliers start: 36 outliers final: 26 residues processed: 222 average time/residue: 0.0950 time to fit residues: 31.8287 Evaluate side-chains 219 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1184 ILE Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1589 GLN A1602 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112419 restraints weight = 18784.855| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.53 r_work: 0.3310 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12736 Z= 0.157 Angle : 0.597 7.834 17221 Z= 0.307 Chirality : 0.041 0.202 1915 Planarity : 0.004 0.044 2078 Dihedral : 10.575 64.615 1847 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.18 % Allowed : 12.79 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1444 helix: 1.54 (0.17), residues: 960 sheet: -4.13 (1.10), residues: 10 loop : -1.42 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.014 0.001 TYR A 415 PHE 0.020 0.002 PHE A 72 TRP 0.012 0.001 TRP A 119 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12719) covalent geometry : angle 0.58484 / 0.30 (17180) SS BOND : bond 0.00164 / 0.09 ( 10) SS BOND : angle 2.19810 / 1.11 ( 20) hydrogen bonds : bond 0.05060 / 3.33 ( 720) hydrogen bonds : angle 4.23746 / 3.06 ( 2109) link_BETA1-4 : bond 0.00561 / 0.28 ( 3) link_BETA1-4 : angle 1.25021 / 0.60 ( 9) link_NAG-ASN : bond 0.00231 / 0.11 ( 4) link_NAG-ASN : angle 3.62520 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8127 (tt0) cc_final: 0.7742 (tp30) REVERT: A 388 MET cc_start: 0.6698 (ppp) cc_final: 0.6398 (ppp) REVERT: A 393 MET cc_start: 0.6909 (mmp) cc_final: 0.6696 (mmt) REVERT: A 616 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 912 VAL cc_start: 0.8197 (m) cc_final: 0.7982 (p) REVERT: A 1202 LYS cc_start: 0.7614 (pttp) cc_final: 0.6978 (tptt) REVERT: A 1209 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6446 (t-90) REVERT: A 1302 MET cc_start: 0.7131 (ttt) cc_final: 0.6782 (tmt) REVERT: A 1513 LYS cc_start: 0.9304 (mmtt) cc_final: 0.9022 (mmtt) REVERT: A 1515 MET cc_start: 0.9236 (mmm) cc_final: 0.8812 (mmp) REVERT: A 1536 MET cc_start: 0.8878 (ttp) cc_final: 0.8560 (ttp) REVERT: B 216 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.4783 (t-100) REVERT: B 233 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: B 262 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7563 (tmm-80) REVERT: B 270 ASP cc_start: 0.8696 (t70) cc_final: 0.8298 (t0) REVERT: B 280 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8483 (mm-30) outliers start: 42 outliers final: 31 residues processed: 215 average time/residue: 0.0907 time to fit residues: 29.5494 Evaluate side-chains 217 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1209 HIS Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114571 restraints weight = 18644.107| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.52 r_work: 0.3337 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.121 Angle : 0.581 9.151 17221 Z= 0.292 Chirality : 0.045 0.946 1915 Planarity : 0.004 0.044 2078 Dihedral : 10.356 63.809 1847 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.95 % Allowed : 13.25 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1444 helix: 1.68 (0.17), residues: 959 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.015 0.001 TYR A1426 PHE 0.020 0.001 PHE A 72 TRP 0.012 0.001 TRP A 119 HIS 0.004 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12719) covalent geometry : angle 0.57038 / 0.29 (17180) SS BOND : bond 0.00148 / 0.08 ( 10) SS BOND : angle 1.83578 / 0.97 ( 20) hydrogen bonds : bond 0.04499 / 2.94 ( 720) hydrogen bonds : angle 4.11733 / 2.97 ( 2109) link_BETA1-4 : bond 0.00559 / 0.28 ( 3) link_BETA1-4 : angle 1.25313 / 0.60 ( 9) link_NAG-ASN : bond 0.00826 / 0.41 ( 4) link_NAG-ASN : angle 3.48316 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8093 (tt0) cc_final: 0.7807 (tp30) REVERT: A 388 MET cc_start: 0.6787 (ppp) cc_final: 0.6473 (ppp) REVERT: A 393 MET cc_start: 0.6812 (mmp) cc_final: 0.6611 (mmt) REVERT: A 616 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 1202 LYS cc_start: 0.7613 (pttp) cc_final: 0.7023 (tptt) REVERT: A 1302 MET cc_start: 0.7102 (ttt) cc_final: 0.6760 (tmt) REVERT: A 1335 SER cc_start: 0.9253 (p) cc_final: 0.9005 (p) REVERT: A 1424 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 1468 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8539 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9294 (mmtt) cc_final: 0.9027 (mmtt) REVERT: A 1515 MET cc_start: 0.9208 (mmm) cc_final: 0.8722 (mmp) REVERT: A 1536 MET cc_start: 0.8871 (ttp) cc_final: 0.8556 (ttp) REVERT: B 210 LYS cc_start: 0.7827 (tmmt) cc_final: 0.7509 (tmmt) REVERT: B 216 TRP cc_start: 0.7835 (OUTLIER) cc_final: 0.7571 (p-90) REVERT: B 233 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: B 262 ARG cc_start: 0.7924 (tmm-80) cc_final: 0.7515 (tmm-80) REVERT: B 270 ASP cc_start: 0.8657 (t70) cc_final: 0.8258 (t0) REVERT: B 280 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8435 (mm-30) outliers start: 39 outliers final: 33 residues processed: 218 average time/residue: 0.0963 time to fit residues: 32.1832 Evaluate side-chains 222 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 133 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 136 optimal weight: 0.4980 chunk 118 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114762 restraints weight = 18649.002| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.52 r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12736 Z= 0.120 Angle : 0.552 8.521 17221 Z= 0.282 Chirality : 0.040 0.331 1915 Planarity : 0.004 0.043 2078 Dihedral : 9.979 63.129 1847 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.03 % Allowed : 13.85 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1444 helix: 1.74 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.49 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1468 TYR 0.020 0.001 TYR A 415 PHE 0.022 0.001 PHE A 72 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12719) covalent geometry : angle 0.54545 / 0.28 (17180) SS BOND : bond 0.00114 / 0.07 ( 10) SS BOND : angle 1.70060 / 0.92 ( 20) hydrogen bonds : bond 0.04337 / 2.83 ( 720) hydrogen bonds : angle 4.07278 / 2.93 ( 2109) link_BETA1-4 : bond 0.00542 / 0.27 ( 3) link_BETA1-4 : angle 1.29649 / 0.62 ( 9) link_NAG-ASN : bond 0.00837 / 0.42 ( 4) link_NAG-ASN : angle 2.45417 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8176 (tt0) cc_final: 0.7860 (tp30) REVERT: A 244 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7490 (ptpt) REVERT: A 388 MET cc_start: 0.6737 (ppp) cc_final: 0.6311 (ppp) REVERT: A 393 MET cc_start: 0.6830 (mmp) cc_final: 0.6621 (mmt) REVERT: A 616 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 875 TYR cc_start: 0.7363 (m-80) cc_final: 0.7032 (m-80) REVERT: A 1244 MET cc_start: 0.7328 (tpp) cc_final: 0.7128 (mmm) REVERT: A 1302 MET cc_start: 0.7127 (ttt) cc_final: 0.6803 (tmt) REVERT: A 1335 SER cc_start: 0.9238 (p) cc_final: 0.9009 (p) REVERT: A 1424 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 1468 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8458 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9270 (mmtt) cc_final: 0.9039 (mmtt) REVERT: A 1515 MET cc_start: 0.9198 (mmm) cc_final: 0.8484 (mmp) REVERT: A 1536 MET cc_start: 0.8882 (ttp) cc_final: 0.8484 (ttp) REVERT: B 210 LYS cc_start: 0.7881 (tmmt) cc_final: 0.7484 (tmmt) REVERT: B 216 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.4783 (t-100) REVERT: B 233 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: B 262 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7522 (tmm-80) REVERT: B 270 ASP cc_start: 0.8640 (t70) cc_final: 0.8103 (t0) REVERT: B 283 GLU cc_start: 0.8457 (pt0) cc_final: 0.8052 (pt0) outliers start: 40 outliers final: 26 residues processed: 220 average time/residue: 0.0993 time to fit residues: 33.5581 Evaluate side-chains 216 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 5.9990 chunk 132 optimal weight: 0.0470 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111809 restraints weight = 18553.985| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.36 r_work: 0.3305 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12736 Z= 0.154 Angle : 0.586 8.656 17221 Z= 0.301 Chirality : 0.041 0.235 1915 Planarity : 0.004 0.044 2078 Dihedral : 9.948 63.561 1847 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 14.53 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1444 helix: 1.62 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.014 0.001 TYR A1426 PHE 0.020 0.001 PHE A 72 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (12719) covalent geometry : angle 0.57867 / 0.30 (17180) SS BOND : bond 0.00323 / 0.16 ( 10) SS BOND : angle 1.99215 / 1.02 ( 20) hydrogen bonds : bond 0.04814 / 3.16 ( 720) hydrogen bonds : angle 4.17728 / 3.01 ( 2109) link_BETA1-4 : bond 0.00512 / 0.25 ( 3) link_BETA1-4 : angle 1.28164 / 0.62 ( 9) link_NAG-ASN : bond 0.00467 / 0.23 ( 4) link_NAG-ASN : angle 2.49233 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8177 (tt0) cc_final: 0.7711 (tp30) REVERT: A 244 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7702 (ptpt) REVERT: A 274 TYR cc_start: 0.8675 (t80) cc_final: 0.8439 (t80) REVERT: A 335 MET cc_start: 0.7976 (tmm) cc_final: 0.7497 (tmm) REVERT: A 388 MET cc_start: 0.6829 (ppp) cc_final: 0.6447 (ppp) REVERT: A 393 MET cc_start: 0.7055 (mmp) cc_final: 0.6845 (mmt) REVERT: A 616 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 875 TYR cc_start: 0.7480 (m-80) cc_final: 0.7214 (m-80) REVERT: A 1202 LYS cc_start: 0.7557 (pttm) cc_final: 0.7071 (tptt) REVERT: A 1335 SER cc_start: 0.9300 (p) cc_final: 0.9036 (p) REVERT: A 1513 LYS cc_start: 0.9299 (mmtt) cc_final: 0.9065 (mmtt) REVERT: A 1515 MET cc_start: 0.9180 (mmm) cc_final: 0.8683 (mmp) REVERT: A 1536 MET cc_start: 0.8921 (ttp) cc_final: 0.8675 (ttp) REVERT: B 210 LYS cc_start: 0.7893 (tmmt) cc_final: 0.7679 (tmmt) REVERT: B 233 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: B 270 ASP cc_start: 0.8683 (t70) cc_final: 0.8359 (t0) outliers start: 37 outliers final: 29 residues processed: 210 average time/residue: 0.0948 time to fit residues: 30.4334 Evaluate side-chains 214 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.148775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113912 restraints weight = 18730.738| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.38 r_work: 0.3343 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12736 Z= 0.114 Angle : 0.555 8.280 17221 Z= 0.283 Chirality : 0.039 0.197 1915 Planarity : 0.004 0.043 2078 Dihedral : 9.669 62.661 1847 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.50 % Allowed : 14.61 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1444 helix: 1.75 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1468 TYR 0.015 0.001 TYR A1426 PHE 0.022 0.001 PHE A 72 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12719) covalent geometry : angle 0.54799 / 0.28 (17180) SS BOND : bond 0.00208 / 0.09 ( 10) SS BOND : angle 1.77656 / 0.95 ( 20) hydrogen bonds : bond 0.04252 / 2.77 ( 720) hydrogen bonds : angle 4.07911 / 2.93 ( 2109) link_BETA1-4 : bond 0.00536 / 0.27 ( 3) link_BETA1-4 : angle 1.31278 / 0.63 ( 9) link_NAG-ASN : bond 0.00555 / 0.28 ( 4) link_NAG-ASN : angle 2.38566 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8118 (tt0) cc_final: 0.7695 (tp30) REVERT: A 244 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7610 (ptpt) REVERT: A 274 TYR cc_start: 0.8669 (t80) cc_final: 0.8403 (t80) REVERT: A 388 MET cc_start: 0.6777 (ppp) cc_final: 0.6340 (ppp) REVERT: A 454 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 616 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 875 TYR cc_start: 0.7380 (m-80) cc_final: 0.7179 (m-80) REVERT: A 1202 LYS cc_start: 0.7555 (pttm) cc_final: 0.7040 (tptt) REVERT: A 1302 MET cc_start: 0.6975 (ttt) cc_final: 0.6762 (tmt) REVERT: A 1335 SER cc_start: 0.9235 (p) cc_final: 0.9010 (p) REVERT: A 1468 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8539 (ttm-80) REVERT: A 1536 MET cc_start: 0.8907 (ttp) cc_final: 0.8658 (ttp) REVERT: A 1557 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 210 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7587 (tmmt) REVERT: B 216 TRP cc_start: 0.7493 (p-90) cc_final: 0.4896 (t-100) REVERT: B 233 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: B 270 ASP cc_start: 0.8648 (t70) cc_final: 0.8257 (t0) outliers start: 33 outliers final: 26 residues processed: 219 average time/residue: 0.0953 time to fit residues: 32.2519 Evaluate side-chains 211 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1547 SER Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1589 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 143 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114598 restraints weight = 18550.373| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.31 r_work: 0.3353 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12736 Z= 0.110 Angle : 0.559 9.929 17221 Z= 0.283 Chirality : 0.039 0.241 1915 Planarity : 0.004 0.042 2078 Dihedral : 9.470 61.983 1845 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.35 % Allowed : 15.14 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1444 helix: 1.83 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 262 TYR 0.015 0.001 TYR A1426 PHE 0.022 0.001 PHE A 72 TRP 0.022 0.001 TRP A 119 HIS 0.003 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12719) covalent geometry : angle 0.55293 / 0.28 (17180) SS BOND : bond 0.00141 / 0.08 ( 10) SS BOND : angle 1.58953 / 0.86 ( 20) hydrogen bonds : bond 0.04044 / 2.64 ( 720) hydrogen bonds : angle 4.04779 / 2.91 ( 2109) link_BETA1-4 : bond 0.00583 / 0.29 ( 3) link_BETA1-4 : angle 1.33171 / 0.63 ( 9) link_NAG-ASN : bond 0.00499 / 0.25 ( 4) link_NAG-ASN : angle 2.36004 / 1.10 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8128 (tt0) cc_final: 0.7727 (tp30) REVERT: A 244 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7689 (ptpt) REVERT: A 388 MET cc_start: 0.6798 (ppp) cc_final: 0.6336 (ppp) REVERT: A 565 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8378 (p0) REVERT: A 616 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 1202 LYS cc_start: 0.7516 (pttm) cc_final: 0.7033 (tptt) REVERT: A 1263 MET cc_start: 0.6331 (ptp) cc_final: 0.5919 (ptp) REVERT: A 1302 MET cc_start: 0.7035 (ttt) cc_final: 0.6832 (tmt) REVERT: A 1335 SER cc_start: 0.9210 (p) cc_final: 0.8991 (p) REVERT: A 1468 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8546 (ttm-80) REVERT: A 1536 MET cc_start: 0.8893 (ttp) cc_final: 0.8668 (ttp) REVERT: A 1557 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: B 210 LYS cc_start: 0.7780 (tmmt) cc_final: 0.7476 (tmmt) REVERT: B 216 TRP cc_start: 0.7309 (p-90) cc_final: 0.4845 (t-100) REVERT: B 233 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: B 270 ASP cc_start: 0.8609 (t70) cc_final: 0.8190 (t0) outliers start: 31 outliers final: 27 residues processed: 213 average time/residue: 0.0922 time to fit residues: 30.1476 Evaluate side-chains 217 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1589 GLN Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 110 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114288 restraints weight = 18516.500| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.31 r_work: 0.3351 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.115 Angle : 0.568 10.869 17221 Z= 0.287 Chirality : 0.040 0.236 1915 Planarity : 0.004 0.041 2078 Dihedral : 9.396 61.764 1845 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.42 % Allowed : 15.29 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1444 helix: 1.82 (0.17), residues: 955 sheet: None (None), residues: 0 loop : -1.47 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 262 TYR 0.015 0.001 TYR A1426 PHE 0.022 0.001 PHE A 72 TRP 0.024 0.001 TRP A 119 HIS 0.003 0.001 HIS A1514 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12719) covalent geometry : angle 0.56152 / 0.28 (17180) SS BOND : bond 0.00120 / 0.07 ( 10) SS BOND : angle 1.61115 / 0.87 ( 20) hydrogen bonds : bond 0.04093 / 2.67 ( 720) hydrogen bonds : angle 4.04731 / 2.91 ( 2109) link_BETA1-4 : bond 0.00509 / 0.25 ( 3) link_BETA1-4 : angle 1.33003 / 0.63 ( 9) link_NAG-ASN : bond 0.00474 / 0.24 ( 4) link_NAG-ASN : angle 2.33684 / 1.09 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.97 seconds wall clock time: 49 minutes 57.12 seconds (2997.12 seconds total)