Starting phenix.real_space_refine on Wed Jul 30 20:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cm3_30400/07_2025/7cm3_30400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm3_30400/07_2025/7cm3_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_30400/07_2025/7cm3_30400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm3_30400/07_2025/7cm3_30400.map" model { file = "/net/cci-nas-00/data/ceres_data/7cm3_30400/07_2025/7cm3_30400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm3_30400/07_2025/7cm3_30400.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 9 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: 140 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.24, per 1000 atoms: 0.58 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.19 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: 3.69 Time building geometry restraints manager: 3.61 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 - 19.60: 7008 19.60 - 39.21: 508 39.21 - 58.81: 143 58.81 - 78.41: 38 78.41 - 98.02: 9 Dihedral angle restraints: 7706 sinusoidal: 3412 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 7703 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: 0.590 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 28.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 15.850 98.016 4892 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.061 0.011 TRP B 311 HIS 0.013 0.003 HIS B 274 PHE 0.066 0.009 PHE A 997 TYR 0.081 0.009 TYR A 274 ARG 0.012 0.001 ARG A1481 Details of bonding type rmsd link_NAG-ASN : bond 0.03478 ( 4) link_NAG-ASN : angle 11.41754 ( 12) link_BETA1-4 : bond 0.01978 ( 3) link_BETA1-4 : angle 3.50139 ( 9) hydrogen bonds : bond 0.18640 ( 720) hydrogen bonds : angle 6.70007 ( 2109) SS BOND : bond 0.00709 ( 10) SS BOND : angle 1.83607 ( 20) covalent geometry : bond 0.01471 (12719) covalent geometry : angle 1.77018 (17180) *********************** 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 : 1.244 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: 0.2903 time to fit residues: 142.1392 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 : 1.369 ------------------------------------------------------------------------------- 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 122 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3944 r_free = 0.3944 target = 0.150356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116701 restraints weight = 18486.841| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.45 r_work: 0.3367 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12736 Z= 0.168 Angle : 0.693 12.804 17221 Z= 0.354 Chirality : 0.044 0.382 1915 Planarity : 0.005 0.041 2078 Dihedral : 13.521 69.833 2088 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 2.95 % Allowed : 9.46 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1444 helix: 1.14 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 107 HIS 0.004 0.001 HIS A 228 PHE 0.021 0.002 PHE A1530 TYR 0.013 0.001 TYR A1426 ARG 0.007 0.001 ARG B 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00844 ( 4) link_NAG-ASN : angle 6.42055 ( 12) link_BETA1-4 : bond 0.01493 ( 3) link_BETA1-4 : angle 1.84626 ( 9) hydrogen bonds : bond 0.06311 ( 720) hydrogen bonds : angle 4.66951 ( 2109) SS BOND : bond 0.00809 ( 10) SS BOND : angle 1.16728 ( 20) covalent geometry : bond 0.00332 (12719) covalent geometry : angle 0.67071 (17180) *********************** 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 261 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.6892 (ppp) cc_final: 0.6655 (ppp) REVERT: A 892 MET cc_start: 0.7922 (mmt) cc_final: 0.7681 (mmt) REVERT: A 972 MET cc_start: 0.8205 (mmt) cc_final: 0.7998 (mmt) REVERT: A 1506 ASP cc_start: 0.8904 (t0) cc_final: 0.8480 (t0) REVERT: A 1515 MET cc_start: 0.9260 (mmm) cc_final: 0.8925 (mmp) REVERT: A 1536 MET cc_start: 0.8785 (ttp) cc_final: 0.8444 (ttp) REVERT: A 1602 GLN cc_start: 0.6515 (mt0) cc_final: 0.6043 (mt0) REVERT: B 262 ARG cc_start: 0.7868 (tmm-80) cc_final: 0.7628 (tmm-80) REVERT: B 340 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8537 (mtt180) REVERT: B 349 ASP cc_start: 0.8622 (t70) cc_final: 0.8375 (t70) outliers start: 39 outliers final: 25 residues processed: 245 average time/residue: 0.2469 time to fit residues: 87.7044 Evaluate side-chains 211 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 264 ASN Chi-restraints excluded: chain A residue 332 PHE 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 B residue 216 TRP Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 136 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3949 r_free = 0.3949 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116529 restraints weight = 18775.245| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.46 r_work: 0.3368 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2894 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= 0.133 Angle : 0.608 9.749 17221 Z= 0.312 Chirality : 0.041 0.269 1915 Planarity : 0.004 0.041 2078 Dihedral : 12.375 72.998 2084 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.80 % Allowed : 10.60 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1444 helix: 1.45 (0.17), residues: 953 sheet: -4.23 (1.13), residues: 10 loop : -1.20 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1413 HIS 0.004 0.001 HIS B 273 PHE 0.017 0.001 PHE A 72 TYR 0.015 0.001 TYR A1426 ARG 0.004 0.000 ARG A1468 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 4) link_NAG-ASN : angle 5.11665 ( 12) link_BETA1-4 : bond 0.00940 ( 3) link_BETA1-4 : angle 1.55875 ( 9) hydrogen bonds : bond 0.05141 ( 720) hydrogen bonds : angle 4.38630 ( 2109) SS BOND : bond 0.00261 ( 10) SS BOND : angle 1.93491 ( 20) covalent geometry : bond 0.00274 (12719) covalent geometry : angle 0.58857 (17180) *********************** 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 240 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.6911 (ppp) cc_final: 0.6698 (ppp) REVERT: A 393 MET cc_start: 0.6735 (mmp) cc_final: 0.6403 (mmt) REVERT: A 892 MET cc_start: 0.7874 (mmt) cc_final: 0.7587 (mmt) REVERT: A 1302 MET cc_start: 0.7063 (ttt) cc_final: 0.6708 (tmt) REVERT: A 1468 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8446 (ttm-80) REVERT: A 1476 MET cc_start: 0.7755 (ptp) cc_final: 0.7368 (ppp) REVERT: A 1480 LYS cc_start: 0.8511 (mptt) cc_final: 0.8288 (mptt) REVERT: A 1513 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8975 (mmtt) REVERT: A 1515 MET cc_start: 0.9159 (mmm) cc_final: 0.8884 (mmp) REVERT: B 349 ASP cc_start: 0.8474 (t70) cc_final: 0.8201 (t70) outliers start: 37 outliers final: 26 residues processed: 225 average time/residue: 0.2337 time to fit residues: 77.1401 Evaluate side-chains 214 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 468 ASP 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 1494 LEU Chi-restraints excluded: chain A residue 1557 GLU 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 Chi-restraints excluded: chain B residue 350 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 113 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 141 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A1589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117907 restraints weight = 18426.757| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.42 r_work: 0.3388 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3223 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= 0.115 Angle : 0.552 7.871 17221 Z= 0.282 Chirality : 0.039 0.201 1915 Planarity : 0.004 0.042 2078 Dihedral : 11.475 76.388 2082 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.80 % Allowed : 11.58 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1444 helix: 1.64 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -1.26 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1413 HIS 0.003 0.001 HIS B 211 PHE 0.020 0.001 PHE A 72 TYR 0.014 0.001 TYR A1426 ARG 0.013 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 4) link_NAG-ASN : angle 4.05181 ( 12) link_BETA1-4 : bond 0.00761 ( 3) link_BETA1-4 : angle 1.58528 ( 9) hydrogen bonds : bond 0.04409 ( 720) hydrogen bonds : angle 4.17564 ( 2109) SS BOND : bond 0.00180 ( 10) SS BOND : angle 1.59217 ( 20) covalent geometry : bond 0.00231 (12719) covalent geometry : angle 0.53806 (17180) *********************** 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 245 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: A 388 MET cc_start: 0.6903 (ppp) cc_final: 0.6628 (ppp) REVERT: A 393 MET cc_start: 0.6822 (mmp) cc_final: 0.6545 (mmt) REVERT: A 616 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 892 MET cc_start: 0.8070 (mmt) cc_final: 0.7756 (mmt) REVERT: A 1244 MET cc_start: 0.7494 (tpp) cc_final: 0.7262 (mmm) REVERT: A 1302 MET cc_start: 0.7203 (ttt) cc_final: 0.6854 (tmt) REVERT: A 1335 SER cc_start: 0.9320 (p) cc_final: 0.9082 (p) REVERT: A 1468 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8507 (ttm-80) REVERT: A 1480 LYS cc_start: 0.8480 (mptt) cc_final: 0.8244 (mptt) REVERT: A 1513 LYS cc_start: 0.9316 (mmtt) cc_final: 0.9034 (mmtt) REVERT: A 1515 MET cc_start: 0.9249 (mmm) cc_final: 0.8856 (mmp) REVERT: A 1536 MET cc_start: 0.8828 (ttp) cc_final: 0.8466 (ttp) REVERT: B 216 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.4615 (t-100) REVERT: B 233 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: B 262 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.7621 (tmm-80) REVERT: B 270 ASP cc_start: 0.8764 (t70) cc_final: 0.8365 (t0) REVERT: B 349 ASP cc_start: 0.8606 (t70) cc_final: 0.8290 (t70) outliers start: 37 outliers final: 27 residues processed: 229 average time/residue: 0.2672 time to fit residues: 93.3607 Evaluate side-chains 226 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 570 MET 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 1296 ASN Chi-restraints excluded: chain A residue 1494 LEU 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 350 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A1589 GLN A1602 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114058 restraints weight = 18618.358| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.54 r_work: 0.3330 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12736 Z= 0.151 Angle : 0.602 10.717 17221 Z= 0.303 Chirality : 0.046 0.873 1915 Planarity : 0.004 0.043 2078 Dihedral : 11.384 77.558 2080 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 12.34 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1444 helix: 1.62 (0.17), residues: 957 sheet: -4.23 (1.06), residues: 10 loop : -1.38 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1287 HIS 0.004 0.001 HIS A 464 PHE 0.018 0.001 PHE A1530 TYR 0.014 0.001 TYR A1135 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.01476 ( 4) link_NAG-ASN : angle 3.58578 ( 12) link_BETA1-4 : bond 0.00691 ( 3) link_BETA1-4 : angle 1.50809 ( 9) hydrogen bonds : bond 0.04843 ( 720) hydrogen bonds : angle 4.18788 ( 2109) SS BOND : bond 0.00160 ( 10) SS BOND : angle 2.28109 ( 20) covalent geometry : bond 0.00346 (12719) covalent geometry : angle 0.58916 (17180) *********************** 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: 35 poor density : 199 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8026 (tt0) cc_final: 0.7691 (tp30) REVERT: A 388 MET cc_start: 0.6688 (ppp) cc_final: 0.6375 (ppp) REVERT: A 616 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 1302 MET cc_start: 0.7180 (ttt) cc_final: 0.6804 (tmt) REVERT: A 1335 SER cc_start: 0.9288 (p) cc_final: 0.9029 (p) REVERT: A 1424 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 1468 ARG cc_start: 0.8742 (ttm-80) cc_final: 0.8463 (ttm-80) REVERT: A 1480 LYS cc_start: 0.8495 (mptt) cc_final: 0.8265 (mptt) REVERT: A 1513 LYS cc_start: 0.9304 (mmtt) cc_final: 0.9023 (mmtt) REVERT: A 1515 MET cc_start: 0.9248 (mmm) cc_final: 0.8719 (mmp) REVERT: A 1536 MET cc_start: 0.8817 (ttp) cc_final: 0.8408 (ttp) REVERT: B 216 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.7625 (p-90) REVERT: B 262 ARG cc_start: 0.7906 (tmm-80) cc_final: 0.7528 (tmm-80) REVERT: B 270 ASP cc_start: 0.8660 (t70) cc_final: 0.8268 (t0) REVERT: B 280 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 349 ASP cc_start: 0.8418 (t70) cc_final: 0.8118 (t70) outliers start: 35 outliers final: 27 residues processed: 219 average time/residue: 0.2401 time to fit residues: 79.2274 Evaluate side-chains 223 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 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 455 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 468 ASP 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 1218 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 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 351 VAL 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 137 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113155 restraints weight = 18767.278| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.39 r_work: 0.3325 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3548 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= 0.137 Angle : 0.570 8.585 17221 Z= 0.292 Chirality : 0.041 0.286 1915 Planarity : 0.004 0.071 2078 Dihedral : 10.993 77.784 2080 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 13.10 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1444 helix: 1.67 (0.17), residues: 955 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1287 HIS 0.003 0.001 HIS A 228 PHE 0.021 0.001 PHE A 72 TYR 0.015 0.001 TYR A1426 ARG 0.004 0.000 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 4) link_NAG-ASN : angle 3.00758 ( 12) link_BETA1-4 : bond 0.00664 ( 3) link_BETA1-4 : angle 1.46448 ( 9) hydrogen bonds : bond 0.04651 ( 720) hydrogen bonds : angle 4.14220 ( 2109) SS BOND : bond 0.00145 ( 10) SS BOND : angle 1.89463 ( 20) covalent geometry : bond 0.00309 (12719) covalent geometry : angle 0.56091 (17180) *********************** 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 236 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8108 (tt0) cc_final: 0.7741 (tp30) REVERT: A 388 MET cc_start: 0.6737 (ppp) cc_final: 0.6399 (ppp) REVERT: A 616 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 1335 SER cc_start: 0.9298 (p) cc_final: 0.9037 (p) REVERT: A 1424 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 1468 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8486 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9292 (mmtt) cc_final: 0.9021 (mmtt) REVERT: A 1515 MET cc_start: 0.9196 (mmm) cc_final: 0.8711 (mmp) REVERT: A 1536 MET cc_start: 0.8904 (ttp) cc_final: 0.8606 (ttp) REVERT: B 210 LYS cc_start: 0.7878 (tmmt) cc_final: 0.7586 (tmmt) REVERT: B 216 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.4749 (t-100) REVERT: B 262 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7581 (tmm-80) REVERT: B 270 ASP cc_start: 0.8672 (t70) cc_final: 0.8287 (t0) REVERT: B 280 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8477 (mm-30) REVERT: B 349 ASP cc_start: 0.8345 (t70) cc_final: 0.8046 (t70) outliers start: 38 outliers final: 29 residues processed: 218 average time/residue: 0.2263 time to fit residues: 74.5230 Evaluate side-chains 215 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 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 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 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 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 350 GLU 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 56 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3927 r_free = 0.3927 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113928 restraints weight = 18629.872| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.38 r_work: 0.3336 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3636 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= 0.122 Angle : 0.557 8.526 17221 Z= 0.285 Chirality : 0.040 0.206 1915 Planarity : 0.004 0.043 2078 Dihedral : 10.768 76.619 2080 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.73 % Allowed : 13.85 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1444 helix: 1.72 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -1.47 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1287 HIS 0.003 0.001 HIS A1514 PHE 0.025 0.001 PHE A 389 TYR 0.020 0.001 TYR A 415 ARG 0.003 0.000 ARG A1200 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 4) link_NAG-ASN : angle 2.79177 ( 12) link_BETA1-4 : bond 0.00662 ( 3) link_BETA1-4 : angle 1.46288 ( 9) hydrogen bonds : bond 0.04472 ( 720) hydrogen bonds : angle 4.09789 ( 2109) SS BOND : bond 0.00130 ( 10) SS BOND : angle 1.67767 ( 20) covalent geometry : bond 0.00269 (12719) covalent geometry : angle 0.54912 (17180) *********************** 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 230 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8150 (tt0) cc_final: 0.7855 (tp30) REVERT: A 244 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7597 (ptpt) REVERT: A 388 MET cc_start: 0.6719 (ppp) cc_final: 0.6412 (ppp) REVERT: A 616 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 875 TYR cc_start: 0.7364 (m-80) cc_final: 0.7042 (m-80) REVERT: A 1202 LYS cc_start: 0.7530 (pttm) cc_final: 0.6863 (mmmm) REVERT: A 1302 MET cc_start: 0.7120 (ttt) cc_final: 0.6879 (tmt) REVERT: A 1335 SER cc_start: 0.9279 (p) cc_final: 0.9036 (p) REVERT: A 1424 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 1468 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8483 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9289 (mmtt) cc_final: 0.9059 (mmtt) REVERT: A 1515 MET cc_start: 0.9205 (mmm) cc_final: 0.8507 (mmp) REVERT: A 1536 MET cc_start: 0.8885 (ttp) cc_final: 0.8516 (ttp) REVERT: B 210 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7541 (tmmt) REVERT: B 216 TRP cc_start: 0.7595 (OUTLIER) cc_final: 0.4753 (t-100) REVERT: B 262 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7535 (tmm-80) REVERT: B 270 ASP cc_start: 0.8661 (t70) cc_final: 0.8238 (t0) REVERT: B 280 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 349 ASP cc_start: 0.8294 (t70) cc_final: 0.7977 (t70) outliers start: 36 outliers final: 29 residues processed: 217 average time/residue: 0.2388 time to fit residues: 78.1089 Evaluate side-chains 220 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 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 1332 MET 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 1557 GLU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 VAL 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 29 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3944 r_free = 0.3944 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115879 restraints weight = 18729.062| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.38 r_work: 0.3359 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3788 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= 0.108 Angle : 0.535 8.843 17221 Z= 0.273 Chirality : 0.039 0.196 1915 Planarity : 0.004 0.043 2078 Dihedral : 10.422 74.378 2080 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 14.31 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1444 helix: 1.82 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1413 HIS 0.003 0.001 HIS A1514 PHE 0.022 0.001 PHE A 72 TYR 0.015 0.001 TYR A1426 ARG 0.002 0.000 ARG A1468 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 4) link_NAG-ASN : angle 2.62634 ( 12) link_BETA1-4 : bond 0.00701 ( 3) link_BETA1-4 : angle 1.49718 ( 9) hydrogen bonds : bond 0.04048 ( 720) hydrogen bonds : angle 3.99561 ( 2109) SS BOND : bond 0.00116 ( 10) SS BOND : angle 1.50155 ( 20) covalent geometry : bond 0.00227 (12719) covalent geometry : angle 0.52770 (17180) *********************** 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 234 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.660 Fit side-chains REVERT: A 85 GLU cc_start: 0.8206 (tt0) cc_final: 0.7777 (tp30) REVERT: A 244 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7398 (ptpt) REVERT: A 388 MET cc_start: 0.6715 (ppp) cc_final: 0.6382 (ppp) REVERT: A 616 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 875 TYR cc_start: 0.7353 (m-80) cc_final: 0.7061 (m-80) REVERT: A 1105 MET cc_start: 0.8671 (mtp) cc_final: 0.8437 (mtp) REVERT: A 1202 LYS cc_start: 0.7580 (pttm) cc_final: 0.6958 (tppp) REVERT: A 1302 MET cc_start: 0.7068 (ttt) cc_final: 0.6812 (tmt) REVERT: A 1335 SER cc_start: 0.9209 (p) cc_final: 0.8989 (p) REVERT: A 1468 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8458 (ttm-80) REVERT: A 1515 MET cc_start: 0.9198 (mmm) cc_final: 0.8503 (mmp) REVERT: A 1536 MET cc_start: 0.8891 (ttp) cc_final: 0.8521 (ttp) REVERT: B 210 LYS cc_start: 0.7869 (tmmt) cc_final: 0.7530 (tmmt) REVERT: B 216 TRP cc_start: 0.7467 (p-90) cc_final: 0.4773 (t-100) REVERT: B 262 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7486 (tmm-80) REVERT: B 270 ASP cc_start: 0.8609 (t70) cc_final: 0.8213 (t0) REVERT: B 283 GLU cc_start: 0.8446 (pt0) cc_final: 0.8177 (pt0) REVERT: B 349 ASP cc_start: 0.8289 (t70) cc_final: 0.7999 (t70) outliers start: 36 outliers final: 27 residues processed: 222 average time/residue: 0.2727 time to fit residues: 91.6983 Evaluate side-chains 219 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 2.006 ------------------------------------------------------------------------------- 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 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 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 1557 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 VAL 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 122 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3936 r_free = 0.3936 target = 0.149816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115100 restraints weight = 18600.941| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.38 r_work: 0.3352 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.115 Angle : 0.555 8.158 17221 Z= 0.283 Chirality : 0.039 0.189 1915 Planarity : 0.004 0.043 2078 Dihedral : 10.274 71.676 2078 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.50 % Allowed : 14.91 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1444 helix: 1.82 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1413 HIS 0.002 0.001 HIS A1514 PHE 0.021 0.001 PHE A 72 TYR 0.015 0.001 TYR A1426 ARG 0.002 0.000 ARG A1468 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 2.58455 ( 12) link_BETA1-4 : bond 0.00667 ( 3) link_BETA1-4 : angle 1.50273 ( 9) hydrogen bonds : bond 0.04150 ( 720) hydrogen bonds : angle 4.01916 ( 2109) SS BOND : bond 0.00124 ( 10) SS BOND : angle 1.63261 ( 20) covalent geometry : bond 0.00252 (12719) covalent geometry : angle 0.54710 (17180) *********************** 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 225 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8168 (tt0) cc_final: 0.7757 (tp30) REVERT: A 244 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7485 (ptpt) REVERT: A 388 MET cc_start: 0.6698 (ppp) cc_final: 0.6345 (ppp) REVERT: A 616 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 875 TYR cc_start: 0.7418 (m-80) cc_final: 0.7214 (m-80) REVERT: A 1105 MET cc_start: 0.8685 (mtp) cc_final: 0.8445 (mtp) REVERT: A 1202 LYS cc_start: 0.7592 (pttm) cc_final: 0.7066 (tptt) REVERT: A 1302 MET cc_start: 0.7074 (ttt) cc_final: 0.6825 (tmt) REVERT: A 1335 SER cc_start: 0.9212 (p) cc_final: 0.9000 (p) REVERT: A 1468 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8464 (ttm-80) REVERT: A 1513 LYS cc_start: 0.9232 (mmtt) cc_final: 0.9028 (mmtt) REVERT: A 1515 MET cc_start: 0.9200 (mmm) cc_final: 0.8417 (mmp) REVERT: A 1536 MET cc_start: 0.8896 (ttp) cc_final: 0.8524 (ttp) REVERT: A 1557 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 210 LYS cc_start: 0.7836 (tmmt) cc_final: 0.7623 (tmmt) REVERT: B 216 TRP cc_start: 0.7363 (p-90) cc_final: 0.4746 (t-100) REVERT: B 270 ASP cc_start: 0.8620 (t70) cc_final: 0.8222 (t0) REVERT: B 349 ASP cc_start: 0.8310 (t70) cc_final: 0.7996 (t70) outliers start: 33 outliers final: 28 residues processed: 214 average time/residue: 0.3953 time to fit residues: 128.3473 Evaluate side-chains 218 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 3.775 ------------------------------------------------------------------------------- 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 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 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 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 A residue 1589 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 VAL 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 9 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3928 r_free = 0.3928 target = 0.149081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114361 restraints weight = 18669.363| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.38 r_work: 0.3341 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12736 Z= 0.125 Angle : 0.568 9.491 17221 Z= 0.289 Chirality : 0.040 0.237 1915 Planarity : 0.004 0.043 2078 Dihedral : 10.239 69.416 2078 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.35 % Allowed : 15.22 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1444 helix: 1.78 (0.17), residues: 957 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1287 HIS 0.003 0.001 HIS A 464 PHE 0.020 0.001 PHE A 72 TYR 0.014 0.001 TYR A1426 ARG 0.004 0.000 ARG B 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 2.57069 ( 12) link_BETA1-4 : bond 0.00663 ( 3) link_BETA1-4 : angle 1.50427 ( 9) hydrogen bonds : bond 0.04246 ( 720) hydrogen bonds : angle 4.04206 ( 2109) SS BOND : bond 0.00108 ( 10) SS BOND : angle 1.68226 ( 20) covalent geometry : bond 0.00285 (12719) covalent geometry : angle 0.56086 (17180) ********************** 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 221 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8158 (tt0) cc_final: 0.7734 (tp30) REVERT: A 244 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7660 (ptpt) REVERT: A 388 MET cc_start: 0.6722 (ppp) cc_final: 0.6366 (ppp) REVERT: A 616 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 1105 MET cc_start: 0.8683 (mtp) cc_final: 0.8441 (mtp) REVERT: A 1202 LYS cc_start: 0.7610 (pttm) cc_final: 0.7102 (tptt) REVERT: A 1302 MET cc_start: 0.7092 (ttt) cc_final: 0.6841 (tmt) REVERT: A 1335 SER cc_start: 0.9237 (p) cc_final: 0.9011 (p) REVERT: A 1468 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8465 (ttm-80) REVERT: A 1557 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: A 1589 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.6007 (pm20) REVERT: B 210 LYS cc_start: 0.7781 (tmmt) cc_final: 0.7525 (tmmt) REVERT: B 216 TRP cc_start: 0.7254 (p-90) cc_final: 0.4722 (t-100) REVERT: B 270 ASP cc_start: 0.8623 (t70) cc_final: 0.8225 (t0) REVERT: B 349 ASP cc_start: 0.8297 (t70) cc_final: 0.8091 (t70) outliers start: 31 outliers final: 28 residues processed: 212 average time/residue: 0.3153 time to fit residues: 104.6314 Evaluate side-chains 220 residues out of total 1321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 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 1167 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 A residue 1589 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 VAL 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 18 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3939 r_free = 0.3939 target = 0.150046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115390 restraints weight = 18596.820| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.37 r_work: 0.3356 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12736 Z= 0.111 Angle : 0.562 10.541 17221 Z= 0.283 Chirality : 0.039 0.233 1915 Planarity : 0.004 0.042 2078 Dihedral : 10.143 66.781 2078 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.42 % Allowed : 15.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1444 helix: 1.84 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -1.44 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1413 HIS 0.003 0.001 HIS A1514 PHE 0.022 0.001 PHE A 72 TYR 0.014 0.001 TYR A1426 ARG 0.004 0.000 ARG B 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 4) link_NAG-ASN : angle 2.54962 ( 12) link_BETA1-4 : bond 0.00671 ( 3) link_BETA1-4 : angle 1.49672 ( 9) hydrogen bonds : bond 0.04073 ( 720) hydrogen bonds : angle 4.01282 ( 2109) SS BOND : bond 0.00123 ( 10) SS BOND : angle 1.55958 ( 20) covalent geometry : bond 0.00236 (12719) covalent geometry : angle 0.55525 (17180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7307.88 seconds wall clock time: 132 minutes 38.97 seconds (7958.97 seconds total)