Starting phenix.real_space_refine on Thu Jul 2 20:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2026/7jpt_22422.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6576 2.51 5 N 1728 2.21 5 O 1850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10153 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 1260} Chain breaks: 5 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 865 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 24, 'GLU:plan': 47, 'ARG:plan': 19, 'ASN:plan1': 13, 'GLN:plan1': 5, 'HIS:plan': 6, 'TYR:plan': 5, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 500 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10220 At special positions: 0 Unit cell: (86.92, 99.64, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1850 8.00 N 1728 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 100 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 623 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 922 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1060 " - pdb=" SG CYS A1080 " distance=2.03 Simple disulfide: pdb=" SG CYS A1131 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1197 " - pdb=" SG CYS A1211 " distance=2.03 Simple disulfide: pdb=" SG CYS A1239 " - pdb=" SG CYS A1255 " distance=2.03 Simple disulfide: pdb=" SG CYS A1277 " - pdb=" SG CYS A1380 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1801 " - " ASN A1253 " " NAG B 1 " - " ASN A1076 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 320.8 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 28 sheets defined 19.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.017A pdb=" N ASP A 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.800A pdb=" N GLN A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.599A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.771A pdb=" N VAL A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.557A pdb=" N GLU A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.357A pdb=" N GLU A 505 " --> pdb=" O PRO A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 534 through 549 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.540A pdb=" N LEU A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 removed outlier: 4.104A pdb=" N ILE A 694 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 852 through 867 Processing helix chain 'A' and resid 973 through 983 removed outlier: 3.968A pdb=" N ASP A 978 " --> pdb=" O SER A 974 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 983 " --> pdb=" O THR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.604A pdb=" N GLN A 996 " --> pdb=" O SER A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1123 through 1134 Processing helix chain 'A' and resid 1143 through 1158 Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 3.719A pdb=" N HIS A1274 " --> pdb=" O GLN A1270 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1281 " --> pdb=" O CYS A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1304 removed outlier: 3.605A pdb=" N TYR A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1322 removed outlier: 3.689A pdb=" N LYS A1321 " --> pdb=" O TYR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1368 Processing helix chain 'A' and resid 1369 through 1375 removed outlier: 3.598A pdb=" N HIS A1375 " --> pdb=" O TYR A1371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.573A pdb=" N ARG A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.479A pdb=" N ILE A 208 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 162 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 206 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 238 removed outlier: 3.993A pdb=" N ASN A 233 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 338 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN A 235 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU A 336 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 3.853A pdb=" N TYR A 483 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 378 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 481 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 421 " --> pdb=" O TYR A 465 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 423 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 463 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 425 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 461 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 462 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.541A pdb=" N VAL A 598 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.932A pdb=" N PHE A 780 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 716 removed outlier: 4.923A pdb=" N ALA A 753 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 823 through 831 removed outlier: 7.722A pdb=" N ASP A 828 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N LEU A 926 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC1, first strand: chain 'A' and resid 956 through 958 Processing sheet with id=AC2, first strand: chain 'A' and resid 970 through 972 Processing sheet with id=AC3, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC4, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC5, first strand: chain 'A' and resid 1108 through 1110 Processing sheet with id=AC6, first strand: chain 'A' and resid 1161 through 1162 Processing sheet with id=AC7, first strand: chain 'A' and resid 1165 through 1167 Processing sheet with id=AC8, first strand: chain 'A' and resid 1249 through 1250 Processing sheet with id=AC9, first strand: chain 'A' and resid 1258 through 1259 removed outlier: 3.842A pdb=" N LEU A1378 " --> pdb=" O ILE A1259 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA A1379 " --> pdb=" O MET A1313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1316 through 1317 274 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3208 1.35 - 1.47: 2866 1.47 - 1.59: 4381 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 10534 Sorted by residual: bond pdb=" C1 NAG A1802 " pdb=" O5 NAG A1802 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" C THR A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.11e-02 8.12e+03 3.97e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14112 1.69 - 3.38: 223 3.38 - 5.07: 33 5.07 - 6.76: 6 6.76 - 8.45: 2 Bond angle restraints: 14376 Sorted by residual: angle pdb=" C TRP A1025 " pdb=" N THR A1026 " pdb=" CA THR A1026 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" CA CYS A 485 " pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " ideal model delta sigma weight residual 114.40 120.20 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU A 654 " pdb=" CB LEU A 654 " pdb=" CG LEU A 654 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" N LEU A1172 " pdb=" CA LEU A1172 " pdb=" C LEU A1172 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" N THR A 440 " pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 114.04 111.18 2.86 1.24e+00 6.50e-01 5.31e+00 ... (remaining 14371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5538 17.70 - 35.41: 431 35.41 - 53.11: 121 53.11 - 70.81: 17 70.81 - 88.52: 9 Dihedral angle restraints: 6116 sinusoidal: 2238 harmonic: 3878 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.27 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 0.38 -86.38 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 6113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1315 0.054 - 0.108: 205 0.108 - 0.162: 34 0.162 - 0.216: 0 0.216 - 0.269: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA CYS A1211 " pdb=" N CYS A1211 " pdb=" C CYS A1211 " pdb=" CB CYS A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB ILE A 737 " pdb=" CA ILE A 737 " pdb=" CG1 ILE A 737 " pdb=" CG2 ILE A 737 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1552 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 967 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 968 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 968 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 968 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 813 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 814 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 814 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 814 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 697 " -0.013 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE A 697 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 697 " -0.005 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2673 2.79 - 3.32: 8847 3.32 - 3.85: 16455 3.85 - 4.37: 18978 4.37 - 4.90: 32978 Nonbonded interactions: 79931 Sorted by model distance: nonbonded pdb=" OH TYR A 165 " pdb=" OE1 GLN A1301 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 329 " pdb=" OG SER A 329 " model vdw 2.286 3.040 nonbonded pdb=" O SER A1097 " pdb=" OG SER A1097 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU A1195 " pdb=" N ASP A1210 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG A 160 " pdb=" OD2 ASP A 161 " model vdw 2.324 3.120 ... (remaining 79926 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=0.53 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10561 Z= 0.122 Angle : 0.552 8.452 14434 Z= 0.294 Chirality : 0.042 0.269 1555 Planarity : 0.003 0.036 1816 Dihedral : 13.654 88.517 3539 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 3.48 % Allowed : 18.97 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.19), residues: 1315 helix: -1.24 (0.30), residues: 208 sheet: -2.36 (0.36), residues: 150 loop : -3.33 (0.16), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 796 TYR 0.009 0.001 TYR A 116 PHE 0.024 0.001 PHE A 697 TRP 0.008 0.001 TRP A1025 HIS 0.003 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10534) covalent geometry : angle 0.54759 / 0.29 (14376) SS BOND : bond 0.00235 / 0.16 ( 23) SS BOND : angle 1.22295 / 0.94 ( 46) hydrogen bonds : bond 0.14778 / 10.18 ( 271) hydrogen bonds : angle 6.22724 / 4.11 ( 705) link_BETA1-4 : bond 0.00311 / 0.15 ( 2) link_BETA1-4 : angle 1.12007 / 0.60 ( 6) link_NAG-ASN : bond 0.00221 / 0.12 ( 2) link_NAG-ASN : angle 0.92706 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2372 (OUTLIER) cc_final: 0.1033 (t) REVERT: A 109 LYS cc_start: 0.6901 (tptt) cc_final: 0.6623 (tptt) REVERT: A 140 TRP cc_start: 0.6619 (m100) cc_final: 0.6344 (m100) REVERT: A 222 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6619 (ttpm) REVERT: A 695 LYS cc_start: 0.5972 (mtpt) cc_final: 0.5410 (mmtm) REVERT: A 771 ASP cc_start: 0.7619 (m-30) cc_final: 0.7192 (m-30) REVERT: A 910 LYS cc_start: 0.8137 (ttpm) cc_final: 0.7843 (ttpp) REVERT: A 911 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7894 (p) REVERT: A 996 GLN cc_start: 0.8435 (tp40) cc_final: 0.7982 (tm-30) REVERT: A 1021 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6732 (ptpt) REVERT: A 1117 ILE cc_start: 0.8628 (mm) cc_final: 0.8421 (mm) REVERT: A 1136 MET cc_start: 0.7211 (mtt) cc_final: 0.6982 (mtm) REVERT: A 1266 MET cc_start: 0.3358 (tpt) cc_final: 0.2535 (tpt) REVERT: A 1313 MET cc_start: 0.7704 (ttt) cc_final: 0.7210 (ttm) REVERT: A 1361 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 1370 VAL cc_start: 0.8401 (m) cc_final: 0.8156 (t) outliers start: 35 outliers final: 19 residues processed: 230 average time/residue: 0.0947 time to fit residues: 30.1113 Evaluate side-chains 144 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1362 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 231 GLN A 529 ASN A 538 GLN A 542 ASN A 861 ASN A 993 GLN A1059 HIS A1065 ASN A1173 ASN A1274 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.205735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.174718 restraints weight = 13062.243| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.64 r_work: 0.4082 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10561 Z= 0.126 Angle : 0.582 8.427 14434 Z= 0.296 Chirality : 0.042 0.181 1555 Planarity : 0.004 0.044 1816 Dihedral : 5.755 55.031 1440 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.87 % Allowed : 21.05 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.20), residues: 1315 helix: -0.25 (0.33), residues: 212 sheet: -1.96 (0.37), residues: 155 loop : -2.96 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1186 TYR 0.015 0.001 TYR A 116 PHE 0.012 0.001 PHE A 998 TRP 0.010 0.001 TRP A 912 HIS 0.006 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10534) covalent geometry : angle 0.57571 / 0.29 (14376) SS BOND : bond 0.00309 / 0.22 ( 23) SS BOND : angle 1.51962 / 1.07 ( 46) hydrogen bonds : bond 0.03226 / 2.25 ( 271) hydrogen bonds : angle 5.03130 / 3.38 ( 705) link_BETA1-4 : bond 0.00250 / 0.12 ( 2) link_BETA1-4 : angle 1.66490 / 0.88 ( 6) link_NAG-ASN : bond 0.00025 / 0.01 ( 2) link_NAG-ASN : angle 1.10714 / 0.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2488 (OUTLIER) cc_final: 0.0946 (t) REVERT: A 67 TRP cc_start: 0.7163 (m100) cc_final: 0.6528 (m100) REVERT: A 140 TRP cc_start: 0.6869 (m100) cc_final: 0.6465 (m100) REVERT: A 406 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7096 (tm-30) REVERT: A 529 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.7015 (p0) REVERT: A 561 ARG cc_start: 0.6195 (ttp-110) cc_final: 0.5935 (ptm-80) REVERT: A 590 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6170 (mm-30) REVERT: A 617 PHE cc_start: 0.5718 (t80) cc_final: 0.5422 (t80) REVERT: A 695 LYS cc_start: 0.6489 (mtpt) cc_final: 0.5875 (mmtm) REVERT: A 1136 MET cc_start: 0.7333 (mtt) cc_final: 0.7097 (mtm) REVERT: A 1266 MET cc_start: 0.3685 (tpt) cc_final: 0.3013 (tpt) REVERT: A 1313 MET cc_start: 0.8059 (ttt) cc_final: 0.7660 (ttm) REVERT: A 1370 VAL cc_start: 0.8365 (m) cc_final: 0.7938 (t) REVERT: A 1374 GLN cc_start: 0.8004 (mt0) cc_final: 0.7789 (mm-40) outliers start: 49 outliers final: 22 residues processed: 171 average time/residue: 0.0868 time to fit residues: 21.5631 Evaluate side-chains 143 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 510 HIS A 529 ASN A 661 HIS A1065 ASN A1084 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.203591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.172258 restraints weight = 13016.571| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.59 r_work: 0.4058 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10561 Z= 0.127 Angle : 0.572 8.227 14434 Z= 0.292 Chirality : 0.042 0.199 1555 Planarity : 0.004 0.049 1816 Dihedral : 5.404 51.817 1422 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.06 % Allowed : 20.85 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.21), residues: 1315 helix: 0.27 (0.34), residues: 211 sheet: -1.79 (0.39), residues: 152 loop : -2.75 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1015 TYR 0.015 0.001 TYR A 116 PHE 0.025 0.001 PHE A1149 TRP 0.009 0.001 TRP A 880 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10534) covalent geometry : angle 0.56543 / 0.29 (14376) SS BOND : bond 0.00432 / 0.31 ( 23) SS BOND : angle 1.52550 / 1.03 ( 46) hydrogen bonds : bond 0.03073 / 2.16 ( 271) hydrogen bonds : angle 4.83567 / 3.28 ( 705) link_BETA1-4 : bond 0.00369 / 0.18 ( 2) link_BETA1-4 : angle 1.37889 / 0.78 ( 6) link_NAG-ASN : bond 0.00015 / 0.01 ( 2) link_NAG-ASN : angle 1.13992 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2696 (OUTLIER) cc_final: 0.0991 (t) REVERT: A 67 TRP cc_start: 0.7073 (m100) cc_final: 0.6461 (m100) REVERT: A 69 TRP cc_start: 0.8687 (m100) cc_final: 0.8413 (m100) REVERT: A 140 TRP cc_start: 0.7053 (m100) cc_final: 0.6357 (m100) REVERT: A 141 LYS cc_start: 0.7842 (mmmt) cc_final: 0.6351 (mttp) REVERT: A 406 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7113 (tm-30) REVERT: A 561 ARG cc_start: 0.6452 (ttp-110) cc_final: 0.6208 (ptm-80) REVERT: A 617 PHE cc_start: 0.5775 (t80) cc_final: 0.5438 (t80) REVERT: A 1266 MET cc_start: 0.3767 (tpt) cc_final: 0.3113 (tpt) REVERT: A 1313 MET cc_start: 0.8099 (ttt) cc_final: 0.7804 (ttm) REVERT: A 1370 VAL cc_start: 0.8346 (m) cc_final: 0.7994 (t) REVERT: A 1374 GLN cc_start: 0.8136 (mt0) cc_final: 0.7894 (mm-40) outliers start: 51 outliers final: 32 residues processed: 179 average time/residue: 0.0842 time to fit residues: 21.7935 Evaluate side-chains 149 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1025 TRP Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.199614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.167740 restraints weight = 13081.433| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.55 r_work: 0.4002 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10561 Z= 0.153 Angle : 0.596 8.066 14434 Z= 0.304 Chirality : 0.043 0.189 1555 Planarity : 0.004 0.076 1816 Dihedral : 5.595 50.695 1418 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.77 % Allowed : 21.55 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.21), residues: 1315 helix: 0.58 (0.35), residues: 211 sheet: -1.59 (0.40), residues: 142 loop : -2.63 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1015 TYR 0.018 0.001 TYR A1019 PHE 0.017 0.002 PHE A 958 TRP 0.011 0.001 TRP A 880 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (10534) covalent geometry : angle 0.58874 / 0.30 (14376) SS BOND : bond 0.00408 / 0.29 ( 23) SS BOND : angle 1.61754 / 1.17 ( 46) hydrogen bonds : bond 0.03138 / 2.19 ( 271) hydrogen bonds : angle 4.83408 / 3.28 ( 705) link_BETA1-4 : bond 0.00555 / 0.27 ( 2) link_BETA1-4 : angle 1.42584 / 0.79 ( 6) link_NAG-ASN : bond 0.00058 / 0.03 ( 2) link_NAG-ASN : angle 1.27963 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2301 (OUTLIER) cc_final: 0.1683 (t) REVERT: A 67 TRP cc_start: 0.7037 (m100) cc_final: 0.6698 (m100) REVERT: A 69 TRP cc_start: 0.8714 (m100) cc_final: 0.8458 (m100) REVERT: A 140 TRP cc_start: 0.7096 (m100) cc_final: 0.6552 (m100) REVERT: A 406 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 481 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6942 (pp) REVERT: A 617 PHE cc_start: 0.5910 (t80) cc_final: 0.5543 (t80) REVERT: A 1033 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.7032 (p90) REVERT: A 1136 MET cc_start: 0.7699 (mtt) cc_final: 0.7394 (mtm) REVERT: A 1313 MET cc_start: 0.8103 (ttt) cc_final: 0.7741 (ttm) REVERT: A 1370 VAL cc_start: 0.8357 (m) cc_final: 0.8055 (t) REVERT: A 1374 GLN cc_start: 0.8222 (mt0) cc_final: 0.7969 (mm-40) outliers start: 48 outliers final: 35 residues processed: 165 average time/residue: 0.0866 time to fit residues: 21.5529 Evaluate side-chains 151 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1025 TRP Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 538 GLN A 542 ASN A 832 ASN A1065 ASN A1173 ASN A1257 ASN A1278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.191719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161301 restraints weight = 13207.412| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.44 r_work: 0.3913 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 10561 Z= 0.259 Angle : 0.712 8.056 14434 Z= 0.364 Chirality : 0.046 0.243 1555 Planarity : 0.005 0.071 1816 Dihedral : 6.161 53.338 1417 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 6.16 % Allowed : 21.15 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1315 helix: 0.37 (0.34), residues: 210 sheet: -1.82 (0.36), residues: 180 loop : -2.64 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.021 0.002 TYR A 888 PHE 0.041 0.003 PHE A 958 TRP 0.019 0.002 TRP A 912 HIS 0.006 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 (10534) covalent geometry : angle 0.70284 / 0.36 (14376) SS BOND : bond 0.00441 / 0.31 ( 23) SS BOND : angle 2.01923 / 1.46 ( 46) hydrogen bonds : bond 0.03853 / 2.69 ( 271) hydrogen bonds : angle 5.24577 / 3.55 ( 705) link_BETA1-4 : bond 0.00638 / 0.31 ( 2) link_BETA1-4 : angle 1.75366 / 0.94 ( 6) link_NAG-ASN : bond 0.00258 / 0.13 ( 2) link_NAG-ASN : angle 1.59127 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2834 (OUTLIER) cc_final: 0.2062 (t) REVERT: A 67 TRP cc_start: 0.7163 (m100) cc_final: 0.6840 (m100) REVERT: A 140 TRP cc_start: 0.7342 (m100) cc_final: 0.6632 (m100) REVERT: A 358 ASP cc_start: 0.7708 (p0) cc_final: 0.7404 (p0) REVERT: A 406 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 481 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7033 (pp) REVERT: A 838 LEU cc_start: 0.9112 (mm) cc_final: 0.8659 (mm) REVERT: A 846 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7605 (p90) REVERT: A 1033 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7287 (p90) REVERT: A 1313 MET cc_start: 0.8078 (ttt) cc_final: 0.7618 (ttm) REVERT: A 1361 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7200 (tm-30) outliers start: 62 outliers final: 46 residues processed: 174 average time/residue: 0.0885 time to fit residues: 23.0416 Evaluate side-chains 159 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1065 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.197186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.166570 restraints weight = 13163.889| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.49 r_work: 0.4023 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10561 Z= 0.122 Angle : 0.587 8.093 14434 Z= 0.300 Chirality : 0.042 0.184 1555 Planarity : 0.004 0.071 1816 Dihedral : 5.733 58.541 1416 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.76 % Allowed : 22.05 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.21), residues: 1315 helix: 0.75 (0.35), residues: 212 sheet: -1.61 (0.37), residues: 174 loop : -2.51 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 319 TYR 0.016 0.001 TYR A 548 PHE 0.031 0.002 PHE A 958 TRP 0.012 0.001 TRP A 220 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10534) covalent geometry : angle 0.58176 / 0.30 (14376) SS BOND : bond 0.00292 / 0.21 ( 23) SS BOND : angle 1.37677 / 0.98 ( 46) hydrogen bonds : bond 0.02966 / 2.03 ( 271) hydrogen bonds : angle 4.90381 / 3.36 ( 705) link_BETA1-4 : bond 0.00336 / 0.17 ( 2) link_BETA1-4 : angle 1.24246 / 0.65 ( 6) link_NAG-ASN : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : angle 1.10242 / 0.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2523 (OUTLIER) cc_final: 0.1659 (t) REVERT: A 67 TRP cc_start: 0.7025 (m100) cc_final: 0.6809 (m100) REVERT: A 140 TRP cc_start: 0.7248 (m100) cc_final: 0.6571 (m100) REVERT: A 406 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 481 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7106 (pp) REVERT: A 778 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8324 (ttm-80) REVERT: A 838 LEU cc_start: 0.9114 (mm) cc_final: 0.8797 (mm) REVERT: A 1033 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7248 (p90) REVERT: A 1117 ILE cc_start: 0.8932 (mm) cc_final: 0.8550 (mt) REVERT: A 1313 MET cc_start: 0.8079 (ttt) cc_final: 0.7664 (ttm) outliers start: 58 outliers final: 36 residues processed: 174 average time/residue: 0.0805 time to fit residues: 21.1248 Evaluate side-chains 155 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1065 ASN A1153 GLN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.195195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.165608 restraints weight = 13081.491| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.43 r_work: 0.3959 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10561 Z= 0.169 Angle : 0.626 7.892 14434 Z= 0.319 Chirality : 0.044 0.202 1555 Planarity : 0.004 0.070 1816 Dihedral : 5.846 59.735 1416 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.46 % Allowed : 22.64 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.22), residues: 1315 helix: 0.80 (0.35), residues: 212 sheet: -1.72 (0.36), residues: 192 loop : -2.47 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.016 0.001 TYR A 548 PHE 0.032 0.002 PHE A 958 TRP 0.028 0.001 TRP A 912 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (10534) covalent geometry : angle 0.61845 / 0.32 (14376) SS BOND : bond 0.00321 / 0.24 ( 23) SS BOND : angle 1.65546 / 1.23 ( 46) hydrogen bonds : bond 0.03217 / 2.23 ( 271) hydrogen bonds : angle 4.91955 / 3.37 ( 705) link_BETA1-4 : bond 0.00585 / 0.28 ( 2) link_BETA1-4 : angle 1.48519 / 0.80 ( 6) link_NAG-ASN : bond 0.00056 / 0.03 ( 2) link_NAG-ASN : angle 1.29489 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3086 (OUTLIER) cc_final: 0.2176 (t) REVERT: A 67 TRP cc_start: 0.7025 (m100) cc_final: 0.6795 (m100) REVERT: A 140 TRP cc_start: 0.7311 (m100) cc_final: 0.6637 (m100) REVERT: A 406 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 481 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7085 (pp) REVERT: A 695 LYS cc_start: 0.6880 (mmmt) cc_final: 0.5822 (mmmt) REVERT: A 771 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: A 838 LEU cc_start: 0.9170 (mm) cc_final: 0.8828 (mm) REVERT: A 1033 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7261 (p90) REVERT: A 1117 ILE cc_start: 0.8950 (mm) cc_final: 0.8599 (mt) REVERT: A 1313 MET cc_start: 0.8082 (ttt) cc_final: 0.7629 (ttm) REVERT: A 1318 TYR cc_start: 0.7305 (t80) cc_final: 0.7047 (t80) outliers start: 55 outliers final: 41 residues processed: 164 average time/residue: 0.0829 time to fit residues: 20.7712 Evaluate side-chains 159 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 ASN A1065 ASN A1153 GLN A1278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.196065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.162651 restraints weight = 13143.963| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.57 r_work: 0.3969 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10561 Z= 0.143 Angle : 0.607 8.898 14434 Z= 0.309 Chirality : 0.043 0.189 1555 Planarity : 0.004 0.072 1816 Dihedral : 5.737 55.593 1416 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.16 % Allowed : 23.14 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.22), residues: 1315 helix: 0.96 (0.35), residues: 212 sheet: -1.68 (0.35), residues: 192 loop : -2.39 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 778 TYR 0.017 0.001 TYR A 548 PHE 0.028 0.002 PHE A 958 TRP 0.024 0.001 TRP A 912 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10534) covalent geometry : angle 0.60138 / 0.31 (14376) SS BOND : bond 0.00301 / 0.22 ( 23) SS BOND : angle 1.49737 / 1.10 ( 46) hydrogen bonds : bond 0.02989 / 2.06 ( 271) hydrogen bonds : angle 4.87412 / 3.34 ( 705) link_BETA1-4 : bond 0.00479 / 0.23 ( 2) link_BETA1-4 : angle 1.35305 / 0.72 ( 6) link_NAG-ASN : bond 0.00069 / 0.04 ( 2) link_NAG-ASN : angle 1.17372 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2747 (OUTLIER) cc_final: 0.2313 (t) REVERT: A 140 TRP cc_start: 0.7183 (m100) cc_final: 0.6530 (m100) REVERT: A 406 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 481 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7000 (pp) REVERT: A 695 LYS cc_start: 0.6811 (mmmt) cc_final: 0.5795 (mmmt) REVERT: A 771 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 838 LEU cc_start: 0.9091 (mm) cc_final: 0.8746 (mm) REVERT: A 1033 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7314 (p90) REVERT: A 1117 ILE cc_start: 0.8876 (mm) cc_final: 0.8535 (mt) REVERT: A 1313 MET cc_start: 0.8048 (ttt) cc_final: 0.7709 (ttm) REVERT: A 1318 TYR cc_start: 0.7276 (t80) cc_final: 0.7046 (t80) outliers start: 52 outliers final: 42 residues processed: 163 average time/residue: 0.0843 time to fit residues: 20.8996 Evaluate side-chains 161 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 45 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 ASN A1065 ASN A1278 GLN ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.191824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.162263 restraints weight = 13107.744| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.42 r_work: 0.3930 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10561 Z= 0.216 Angle : 0.681 8.499 14434 Z= 0.348 Chirality : 0.045 0.226 1555 Planarity : 0.004 0.072 1816 Dihedral : 6.046 54.299 1416 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 5.46 % Allowed : 22.94 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.22), residues: 1315 helix: 0.73 (0.35), residues: 210 sheet: -1.60 (0.36), residues: 190 loop : -2.41 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 669 TYR 0.017 0.002 TYR A 116 PHE 0.025 0.002 PHE A 697 TRP 0.038 0.002 TRP A 67 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (10534) covalent geometry : angle 0.67346 / 0.35 (14376) SS BOND : bond 0.00363 / 0.26 ( 23) SS BOND : angle 1.82854 / 1.35 ( 46) hydrogen bonds : bond 0.03463 / 2.41 ( 271) hydrogen bonds : angle 5.11657 / 3.48 ( 705) link_BETA1-4 : bond 0.00594 / 0.29 ( 2) link_BETA1-4 : angle 1.59880 / 0.85 ( 6) link_NAG-ASN : bond 0.00160 / 0.08 ( 2) link_NAG-ASN : angle 1.44801 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2979 (OUTLIER) cc_final: 0.2511 (t) REVERT: A 140 TRP cc_start: 0.7324 (m100) cc_final: 0.6593 (m100) REVERT: A 406 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 481 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7112 (pp) REVERT: A 695 LYS cc_start: 0.6984 (mmmt) cc_final: 0.5982 (mmmt) REVERT: A 771 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: A 838 LEU cc_start: 0.9117 (mm) cc_final: 0.8700 (mm) REVERT: A 1033 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7374 (p90) REVERT: A 1117 ILE cc_start: 0.8883 (mm) cc_final: 0.8547 (mt) REVERT: A 1222 TYR cc_start: 0.7847 (t80) cc_final: 0.7629 (t80) REVERT: A 1313 MET cc_start: 0.8043 (ttt) cc_final: 0.7553 (ttm) REVERT: A 1318 TYR cc_start: 0.7391 (t80) cc_final: 0.7122 (t80) outliers start: 55 outliers final: 42 residues processed: 162 average time/residue: 0.0872 time to fit residues: 21.1761 Evaluate side-chains 157 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 ASN A 996 GLN A1065 ASN A1278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163962 restraints weight = 12893.163| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.62 r_work: 0.3992 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10561 Z= 0.110 Angle : 0.602 8.359 14434 Z= 0.308 Chirality : 0.042 0.167 1555 Planarity : 0.004 0.073 1816 Dihedral : 5.713 51.220 1416 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.67 % Allowed : 25.22 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1315 helix: 0.93 (0.35), residues: 212 sheet: -1.43 (0.36), residues: 187 loop : -2.26 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1015 TYR 0.020 0.001 TYR A 548 PHE 0.032 0.001 PHE A1149 TRP 0.031 0.001 TRP A 67 HIS 0.008 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10534) covalent geometry : angle 0.59757 / 0.31 (14376) SS BOND : bond 0.00261 / 0.19 ( 23) SS BOND : angle 1.26748 / 0.92 ( 46) hydrogen bonds : bond 0.02772 / 1.89 ( 271) hydrogen bonds : angle 4.88900 / 3.36 ( 705) link_BETA1-4 : bond 0.00471 / 0.23 ( 2) link_BETA1-4 : angle 1.30612 / 0.67 ( 6) link_NAG-ASN : bond 0.00197 / 0.10 ( 2) link_NAG-ASN : angle 1.03888 / 0.57 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2749 (OUTLIER) cc_final: 0.2453 (t) REVERT: A 140 TRP cc_start: 0.7087 (m100) cc_final: 0.6474 (m100) REVERT: A 406 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 481 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6897 (pp) REVERT: A 688 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7637 (p90) REVERT: A 695 LYS cc_start: 0.6790 (mmmt) cc_final: 0.5826 (mmmt) REVERT: A 771 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 778 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: A 838 LEU cc_start: 0.9066 (mm) cc_final: 0.8726 (mm) REVERT: A 994 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6563 (mp) REVERT: A 1033 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7283 (p90) REVERT: A 1266 MET cc_start: 0.3716 (mtt) cc_final: 0.2528 (mtp) REVERT: A 1313 MET cc_start: 0.7991 (ttt) cc_final: 0.7679 (ttm) outliers start: 37 outliers final: 29 residues processed: 156 average time/residue: 0.0821 time to fit residues: 19.1648 Evaluate side-chains 152 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1326 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 94 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 960 ASN A1065 ASN A1278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.200623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167550 restraints weight = 13064.229| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.60 r_work: 0.4022 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.4037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10561 Z= 0.105 Angle : 0.582 8.262 14434 Z= 0.298 Chirality : 0.041 0.145 1555 Planarity : 0.004 0.066 1816 Dihedral : 5.451 55.689 1416 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.57 % Allowed : 25.32 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.22), residues: 1315 helix: 1.24 (0.36), residues: 213 sheet: -1.39 (0.36), residues: 190 loop : -2.17 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1015 TYR 0.018 0.001 TYR A 548 PHE 0.028 0.001 PHE A1348 TRP 0.027 0.001 TRP A 912 HIS 0.009 0.001 HIS A1373 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10534) covalent geometry : angle 0.57803 / 0.30 (14376) SS BOND : bond 0.00243 / 0.17 ( 23) SS BOND : angle 1.17641 / 0.85 ( 46) hydrogen bonds : bond 0.02588 / 1.77 ( 271) hydrogen bonds : angle 4.70806 / 3.22 ( 705) link_BETA1-4 : bond 0.00452 / 0.22 ( 2) link_BETA1-4 : angle 1.27642 / 0.68 ( 6) link_NAG-ASN : bond 0.00142 / 0.07 ( 2) link_NAG-ASN : angle 1.04663 / 0.57 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.24 seconds wall clock time: 40 minutes 28.18 seconds (2428.18 seconds total)