Starting phenix.real_space_refine on Mon Jul 28 09:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpt_22422/07_2025/7jpt_22422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpt_22422/07_2025/7jpt_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_2025/7jpt_22422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2025/7jpt_22422.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2025/7jpt_22422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpt_22422/07_2025/7jpt_22422.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 5, 'ASP:plan': 24, 'TYR:plan': 5, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 47, 'ARG:plan': 19} 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.70, per 1000 atoms: 0.56 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: 2.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.41 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: 4.02 Time building geometry restraints manager: 2.69 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 - 22.55: 5776 22.55 - 45.10: 364 45.10 - 67.66: 54 67.66 - 90.21: 18 90.21 - 112.76: 7 Dihedral angle restraints: 6219 sinusoidal: 2341 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 6216 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 15.001 112.760 3642 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP A1025 HIS 0.003 0.000 HIS A 40 PHE 0.024 0.001 PHE A 697 TYR 0.009 0.001 TYR A 116 ARG 0.001 0.000 ARG A 796 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 2) link_NAG-ASN : angle 0.92706 ( 6) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.12007 ( 6) hydrogen bonds : bond 0.14778 ( 271) hydrogen bonds : angle 6.22724 ( 705) SS BOND : bond 0.00235 ( 23) SS BOND : angle 1.22295 ( 46) covalent geometry : bond 0.00249 (10534) covalent geometry : angle 0.54759 (14376) *********************** 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 : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2372 (OUTLIER) cc_final: 0.1032 (t) REVERT: A 109 LYS cc_start: 0.6901 (tptt) cc_final: 0.6624 (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: 0.6620 (ttpm) REVERT: A 561 ARG cc_start: 0.4794 (ptm160) cc_final: 0.4588 (ptm160) 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: 0.7893 (p) REVERT: A 996 GLN cc_start: 0.8435 (tp40) cc_final: 0.7983 (tm-30) REVERT: A 1021 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6721 (mtmt) 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: 0.3359 (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: 0.8155 (t) outliers start: 35 outliers final: 19 residues processed: 230 average time/residue: 0.2575 time to fit residues: 82.0669 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 : 1.185 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.0270 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 231 GLN A 510 HIS A 529 ASN A 538 GLN A 542 ASN A 861 ASN A 993 GLN A1059 HIS A1065 ASN A1173 ASN A1274 HIS A1306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.201756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.170000 restraints weight = 12873.777| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.72 r_work: 0.4029 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10561 Z= 0.158 Angle : 0.630 9.110 14434 Z= 0.317 Chirality : 0.044 0.190 1555 Planarity : 0.004 0.046 1816 Dihedral : 7.851 53.946 1543 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.36 % Allowed : 20.75 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.20), residues: 1315 helix: -0.35 (0.32), residues: 212 sheet: -2.02 (0.38), residues: 142 loop : -2.92 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 912 HIS 0.006 0.001 HIS A 40 PHE 0.013 0.002 PHE A 276 TYR 0.016 0.001 TYR A 116 ARG 0.006 0.001 ARG A1290 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 2) link_NAG-ASN : angle 1.15947 ( 6) link_BETA1-4 : bond 0.00344 ( 2) link_BETA1-4 : angle 2.52266 ( 6) hydrogen bonds : bond 0.03436 ( 271) hydrogen bonds : angle 5.12218 ( 705) SS BOND : bond 0.00293 ( 23) SS BOND : angle 1.65995 ( 46) covalent geometry : bond 0.00371 (10534) covalent geometry : angle 0.62160 (14376) *********************** 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 187 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2619 (OUTLIER) cc_final: 0.1043 (t) REVERT: A 67 TRP cc_start: 0.7166 (m100) cc_final: 0.6551 (m100) REVERT: A 69 TRP cc_start: 0.8702 (m100) cc_final: 0.8439 (m100) REVERT: A 140 TRP cc_start: 0.7007 (m100) cc_final: 0.6535 (m100) REVERT: A 326 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 406 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 617 PHE cc_start: 0.5827 (t80) cc_final: 0.5463 (t80) REVERT: A 695 LYS cc_start: 0.6694 (mtpt) cc_final: 0.6024 (mmtm) REVERT: A 1136 MET cc_start: 0.7332 (mtt) cc_final: 0.7070 (mtm) REVERT: A 1169 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7657 (t0) REVERT: A 1266 MET cc_start: 0.3815 (tpt) cc_final: 0.2698 (tpt) REVERT: A 1313 MET cc_start: 0.8020 (ttt) cc_final: 0.7594 (ttm) REVERT: A 1361 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 1370 VAL cc_start: 0.8412 (m) cc_final: 0.7987 (t) outliers start: 54 outliers final: 28 residues processed: 180 average time/residue: 0.2068 time to fit residues: 53.8726 Evaluate side-chains 148 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 622 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 852 SER 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 1042 SER Chi-restraints excluded: chain A residue 1169 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS A1065 ASN A1084 HIS A1173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.197976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166826 restraints weight = 13140.367| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.41 r_work: 0.4005 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10561 Z= 0.175 Angle : 0.616 8.020 14434 Z= 0.312 Chirality : 0.044 0.193 1555 Planarity : 0.004 0.049 1816 Dihedral : 6.628 52.245 1524 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.26 % Allowed : 20.36 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.21), residues: 1315 helix: 0.23 (0.34), residues: 210 sheet: -1.68 (0.39), residues: 147 loop : -2.73 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.007 0.001 HIS A 113 PHE 0.020 0.002 PHE A1149 TYR 0.016 0.001 TYR A 116 ARG 0.007 0.001 ARG A1015 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 2) link_NAG-ASN : angle 1.21198 ( 6) link_BETA1-4 : bond 0.00609 ( 2) link_BETA1-4 : angle 2.04180 ( 6) hydrogen bonds : bond 0.03468 ( 271) hydrogen bonds : angle 5.02797 ( 705) SS BOND : bond 0.00459 ( 23) SS BOND : angle 1.69190 ( 46) covalent geometry : bond 0.00416 (10534) covalent geometry : angle 0.60776 (14376) *********************** 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 188 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.7211 (m100) cc_final: 0.6984 (m100) REVERT: A 140 TRP cc_start: 0.7135 (m100) cc_final: 0.6433 (m100) REVERT: A 141 LYS cc_start: 0.7677 (mmmt) cc_final: 0.6362 (mttt) REVERT: A 406 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 617 PHE cc_start: 0.5978 (t80) cc_final: 0.5545 (t80) REVERT: A 695 LYS cc_start: 0.6951 (mtpt) cc_final: 0.6171 (mmtm) REVERT: A 1033 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7068 (p90) REVERT: A 1313 MET cc_start: 0.8122 (ttt) cc_final: 0.7761 (ttm) REVERT: A 1361 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7565 (tm-30) outliers start: 63 outliers final: 42 residues processed: 180 average time/residue: 0.2148 time to fit residues: 56.7458 Evaluate side-chains 154 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 105 MET 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 361 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 476 SER 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 832 ASN 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 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 1169 ASP 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 1382 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.200372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.168661 restraints weight = 12891.507| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.67 r_work: 0.4008 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10561 Z= 0.122 Angle : 0.579 8.055 14434 Z= 0.294 Chirality : 0.042 0.201 1555 Planarity : 0.004 0.070 1816 Dihedral : 6.004 54.386 1519 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.57 % Allowed : 22.05 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1315 helix: 0.67 (0.35), residues: 210 sheet: -1.75 (0.37), residues: 172 loop : -2.58 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 912 HIS 0.004 0.001 HIS A 40 PHE 0.018 0.001 PHE A 697 TYR 0.015 0.001 TYR A 116 ARG 0.005 0.001 ARG A1015 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.03609 ( 6) link_BETA1-4 : bond 0.00441 ( 2) link_BETA1-4 : angle 1.70404 ( 6) hydrogen bonds : bond 0.02994 ( 271) hydrogen bonds : angle 4.87218 ( 705) SS BOND : bond 0.00358 ( 23) SS BOND : angle 1.46139 ( 46) covalent geometry : bond 0.00288 (10534) covalent geometry : angle 0.57268 (14376) *********************** 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 171 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2065 (OUTLIER) cc_final: 0.1635 (t) REVERT: A 67 TRP cc_start: 0.7019 (m100) cc_final: 0.6592 (m100) REVERT: A 140 TRP cc_start: 0.7130 (m100) cc_final: 0.6467 (m100) REVERT: A 141 LYS cc_start: 0.7682 (mmmt) cc_final: 0.6522 (mttp) REVERT: A 142 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7193 (ttpt) REVERT: A 406 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 481 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6921 (pp) REVERT: A 617 PHE cc_start: 0.5844 (t80) cc_final: 0.5403 (t80) REVERT: A 673 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 695 LYS cc_start: 0.6831 (mtpt) cc_final: 0.6047 (mmtm) REVERT: A 838 LEU cc_start: 0.9063 (mm) cc_final: 0.8770 (mm) REVERT: A 1033 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 1136 MET cc_start: 0.7742 (mtt) cc_final: 0.7407 (mtm) REVERT: A 1313 MET cc_start: 0.8081 (ttt) cc_final: 0.7702 (ttm) REVERT: A 1361 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7563 (tm-30) outliers start: 46 outliers final: 29 residues processed: 165 average time/residue: 0.2099 time to fit residues: 50.3813 Evaluate side-chains 140 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 142 LYS 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 517 ILE Chi-restraints excluded: chain A residue 589 LEU 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 775 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER 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 1033 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 0.0270 chunk 131 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 538 GLN A 542 ASN A 832 ASN A1065 ASN A1146 GLN A1278 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.193038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.161856 restraints weight = 13010.598| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.58 r_work: 0.3931 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10561 Z= 0.216 Angle : 0.663 7.616 14434 Z= 0.339 Chirality : 0.045 0.227 1555 Planarity : 0.004 0.070 1816 Dihedral : 6.310 51.546 1518 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 6.26 % Allowed : 20.85 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1315 helix: 0.56 (0.35), residues: 211 sheet: -1.81 (0.36), residues: 176 loop : -2.58 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.006 0.001 HIS A 113 PHE 0.036 0.002 PHE A 958 TYR 0.020 0.002 TYR A1019 ARG 0.004 0.001 ARG A 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.36405 ( 6) link_BETA1-4 : bond 0.00571 ( 2) link_BETA1-4 : angle 2.05465 ( 6) hydrogen bonds : bond 0.03570 ( 271) hydrogen bonds : angle 5.08773 ( 705) SS BOND : bond 0.00409 ( 23) SS BOND : angle 1.83068 ( 46) covalent geometry : bond 0.00517 (10534) covalent geometry : angle 0.65453 (14376) *********************** 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 179 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 116 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3039 (OUTLIER) cc_final: 0.2444 (t) REVERT: A 67 TRP cc_start: 0.7062 (m100) cc_final: 0.6789 (m100) REVERT: A 140 TRP cc_start: 0.7416 (m100) cc_final: 0.6645 (m100) REVERT: A 141 LYS cc_start: 0.7636 (mmmt) cc_final: 0.6544 (mttp) REVERT: A 406 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 481 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7045 (pp) REVERT: A 695 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6222 (mmtm) REVERT: A 838 LEU cc_start: 0.9118 (mm) cc_final: 0.8684 (mm) REVERT: A 846 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7576 (p90) REVERT: A 1033 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7280 (p90) REVERT: A 1313 MET cc_start: 0.8062 (ttt) cc_final: 0.7612 (ttm) REVERT: A 1361 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 63 outliers final: 47 residues processed: 167 average time/residue: 0.2135 time to fit residues: 52.0321 Evaluate side-chains 160 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 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 907 MET 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 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 115 optimal weight: 0.9990 chunk 50 optimal weight: 0.0010 chunk 118 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 99 optimal weight: 0.0870 chunk 7 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.9968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.198924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.167183 restraints weight = 13046.759| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.69 r_work: 0.4016 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10561 Z= 0.113 Angle : 0.573 7.799 14434 Z= 0.294 Chirality : 0.042 0.174 1555 Planarity : 0.004 0.067 1816 Dihedral : 5.893 55.202 1518 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.36 % Allowed : 21.85 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1315 helix: 0.88 (0.35), residues: 213 sheet: -1.61 (0.37), residues: 177 loop : -2.45 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS A 40 PHE 0.050 0.001 PHE A 958 TYR 0.020 0.001 TYR A1019 ARG 0.004 0.001 ARG A1015 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 2) link_NAG-ASN : angle 1.09401 ( 6) link_BETA1-4 : bond 0.00510 ( 2) link_BETA1-4 : angle 1.59136 ( 6) hydrogen bonds : bond 0.02857 ( 271) hydrogen bonds : angle 4.79988 ( 705) SS BOND : bond 0.00276 ( 23) SS BOND : angle 1.31156 ( 46) covalent geometry : bond 0.00264 (10534) covalent geometry : angle 0.56782 (14376) *********************** 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 170 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2532 (OUTLIER) cc_final: 0.2010 (t) REVERT: A 67 TRP cc_start: 0.6980 (m100) cc_final: 0.6663 (m100) REVERT: A 140 TRP cc_start: 0.7286 (m100) cc_final: 0.6533 (m100) REVERT: A 141 LYS cc_start: 0.7467 (mmmt) cc_final: 0.6628 (mttp) REVERT: A 406 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 481 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7011 (pp) REVERT: A 688 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7404 (p90) REVERT: A 695 LYS cc_start: 0.6957 (mtpt) cc_final: 0.6150 (mmtm) REVERT: A 771 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: A 838 LEU cc_start: 0.9060 (mm) cc_final: 0.8728 (mm) REVERT: A 1033 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7144 (p90) REVERT: A 1313 MET cc_start: 0.8050 (ttt) cc_final: 0.7741 (ttm) outliers start: 54 outliers final: 35 residues processed: 161 average time/residue: 0.1937 time to fit residues: 46.7161 Evaluate side-chains 152 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS 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 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 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 852 SER Chi-restraints excluded: chain A residue 878 SER 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 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 97 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 960 ASN A1065 ASN A1257 ASN A1278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.193017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.161954 restraints weight = 13248.366| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.48 r_work: 0.3931 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10561 Z= 0.196 Angle : 0.656 7.885 14434 Z= 0.334 Chirality : 0.044 0.221 1555 Planarity : 0.004 0.069 1816 Dihedral : 6.161 51.426 1518 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 6.65 % Allowed : 21.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1315 helix: 0.78 (0.35), residues: 211 sheet: -1.80 (0.35), residues: 190 loop : -2.42 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 912 HIS 0.005 0.001 HIS A1265 PHE 0.035 0.002 PHE A 958 TYR 0.019 0.002 TYR A1019 ARG 0.004 0.001 ARG A 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 2) link_NAG-ASN : angle 1.43291 ( 6) link_BETA1-4 : bond 0.00482 ( 2) link_BETA1-4 : angle 1.95282 ( 6) hydrogen bonds : bond 0.03400 ( 271) hydrogen bonds : angle 4.98467 ( 705) SS BOND : bond 0.00354 ( 23) SS BOND : angle 1.71129 ( 46) covalent geometry : bond 0.00467 (10534) covalent geometry : angle 0.64816 (14376) *********************** 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 177 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 110 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3188 (OUTLIER) cc_final: 0.2540 (t) REVERT: A 67 TRP cc_start: 0.7085 (m100) cc_final: 0.6837 (m100) REVERT: A 140 TRP cc_start: 0.7592 (m100) cc_final: 0.6777 (m100) REVERT: A 141 LYS cc_start: 0.7612 (mmmt) cc_final: 0.6788 (mttp) REVERT: A 406 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 481 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7040 (pp) REVERT: A 688 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7589 (p90) REVERT: A 695 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6209 (mmtm) REVERT: A 771 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: A 838 LEU cc_start: 0.9073 (mm) cc_final: 0.8659 (mm) REVERT: A 846 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7513 (p90) REVERT: A 1033 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7304 (p90) REVERT: A 1117 ILE cc_start: 0.8880 (mm) cc_final: 0.8505 (mt) REVERT: A 1313 MET cc_start: 0.8088 (ttt) cc_final: 0.7743 (ttm) outliers start: 67 outliers final: 49 residues processed: 165 average time/residue: 0.1862 time to fit residues: 45.6608 Evaluate side-chains 160 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 104 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR 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 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS 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 846 PHE 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 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 995 GLU 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 1237 VAL 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 7 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN 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 = 0.4414 r_free = 0.4414 target = 0.191404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160072 restraints weight = 13199.649| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.60 r_work: 0.3920 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3384 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= 0.211 Angle : 0.665 8.260 14434 Z= 0.340 Chirality : 0.045 0.239 1555 Planarity : 0.004 0.072 1816 Dihedral : 6.376 53.163 1518 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 6.26 % Allowed : 22.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1315 helix: 0.74 (0.35), residues: 211 sheet: -1.71 (0.36), residues: 188 loop : -2.41 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 912 HIS 0.004 0.001 HIS A 40 PHE 0.029 0.002 PHE A 697 TYR 0.019 0.002 TYR A1019 ARG 0.005 0.001 ARG A 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 2) link_NAG-ASN : angle 1.51429 ( 6) link_BETA1-4 : bond 0.00606 ( 2) link_BETA1-4 : angle 1.88700 ( 6) hydrogen bonds : bond 0.03440 ( 271) hydrogen bonds : angle 5.09857 ( 705) SS BOND : bond 0.00383 ( 23) SS BOND : angle 1.73722 ( 46) covalent geometry : bond 0.00503 (10534) covalent geometry : angle 0.65696 (14376) *********************** 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 175 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 112 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6994 (m100) cc_final: 0.6772 (m100) REVERT: A 140 TRP cc_start: 0.7665 (m100) cc_final: 0.6854 (m100) REVERT: A 141 LYS cc_start: 0.7534 (mmmt) cc_final: 0.6912 (mttp) REVERT: A 406 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 466 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6508 (pp) REVERT: A 481 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7061 (pp) REVERT: A 688 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7534 (p90) REVERT: A 695 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6176 (mmtm) REVERT: A 771 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: A 838 LEU cc_start: 0.9084 (mm) cc_final: 0.8666 (mm) REVERT: A 846 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7752 (p90) REVERT: A 1033 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7384 (p90) REVERT: A 1117 ILE cc_start: 0.8878 (mm) cc_final: 0.8522 (mt) REVERT: A 1222 TYR cc_start: 0.7837 (t80) cc_final: 0.7606 (t80) REVERT: A 1313 MET cc_start: 0.8042 (ttt) cc_final: 0.7581 (ttm) outliers start: 63 outliers final: 44 residues processed: 168 average time/residue: 0.1889 time to fit residues: 47.6534 Evaluate side-chains 155 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 105 MET Chi-restraints excluded: chain A residue 185 LEU 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 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR 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 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS 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 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER 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 1237 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 123 optimal weight: 0.0770 chunk 111 optimal weight: 0.4980 chunk 59 optimal weight: 0.0040 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN A 996 GLN ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN A1373 HIS A1375 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.198923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165568 restraints weight = 13139.151| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.61 r_work: 0.4000 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10561 Z= 0.105 Angle : 0.582 8.077 14434 Z= 0.298 Chirality : 0.042 0.159 1555 Planarity : 0.004 0.067 1816 Dihedral : 5.858 55.742 1518 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.07 % Allowed : 23.93 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.22), residues: 1315 helix: 1.06 (0.35), residues: 212 sheet: -1.41 (0.38), residues: 173 loop : -2.22 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 912 HIS 0.005 0.001 HIS A 40 PHE 0.029 0.001 PHE A 958 TYR 0.019 0.001 TYR A 548 ARG 0.004 0.000 ARG A1015 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 2) link_NAG-ASN : angle 1.10444 ( 6) link_BETA1-4 : bond 0.00541 ( 2) link_BETA1-4 : angle 1.52157 ( 6) hydrogen bonds : bond 0.02761 ( 271) hydrogen bonds : angle 4.83138 ( 705) SS BOND : bond 0.00275 ( 23) SS BOND : angle 1.33200 ( 46) covalent geometry : bond 0.00238 (10534) covalent geometry : angle 0.57656 (14376) *********************** 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 161 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6771 (m100) cc_final: 0.6524 (m100) REVERT: A 140 TRP cc_start: 0.7553 (m100) cc_final: 0.6729 (m100) REVERT: A 141 LYS cc_start: 0.7432 (mmmt) cc_final: 0.6802 (mttp) REVERT: A 406 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 466 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6478 (pp) REVERT: A 481 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6891 (pp) REVERT: A 688 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7595 (p90) REVERT: A 695 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6004 (mmtm) REVERT: A 771 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 838 LEU cc_start: 0.9056 (mm) cc_final: 0.8741 (mm) REVERT: A 994 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6614 (mp) REVERT: A 1033 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7167 (p90) REVERT: A 1313 MET cc_start: 0.7986 (ttt) cc_final: 0.7660 (ttm) REVERT: A 1326 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7524 (t80) outliers start: 41 outliers final: 27 residues processed: 156 average time/residue: 0.2286 time to fit residues: 52.6419 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 : 1.056 ------------------------------------------------------------------------------- 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 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 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 466 LEU 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 622 ILE 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 695 LYS 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 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 1079 SER Chi-restraints excluded: chain A residue 1140 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 91 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 59 optimal weight: 40.0000 chunk 118 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 130 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.194155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.164321 restraints weight = 13169.788| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.41 r_work: 0.3944 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10561 Z= 0.174 Angle : 0.635 8.066 14434 Z= 0.325 Chirality : 0.044 0.205 1555 Planarity : 0.004 0.063 1816 Dihedral : 6.004 52.259 1518 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.17 % Allowed : 24.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.22), residues: 1315 helix: 0.95 (0.35), residues: 212 sheet: -1.49 (0.37), residues: 178 loop : -2.23 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 571 HIS 0.005 0.001 HIS A 77 PHE 0.025 0.002 PHE A 697 TYR 0.019 0.002 TYR A1019 ARG 0.004 0.001 ARG A1337 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 1.43743 ( 6) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 1.80608 ( 6) hydrogen bonds : bond 0.03215 ( 271) hydrogen bonds : angle 4.94275 ( 705) SS BOND : bond 0.00314 ( 23) SS BOND : angle 1.63848 ( 46) covalent geometry : bond 0.00415 (10534) covalent geometry : angle 0.62784 (14376) ********************** 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 159 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.7026 (m100) cc_final: 0.6762 (m100) REVERT: A 97 MET cc_start: 0.8182 (mmt) cc_final: 0.7683 (mtt) REVERT: A 140 TRP cc_start: 0.7698 (m100) cc_final: 0.6845 (m100) REVERT: A 141 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6895 (mttp) REVERT: A 406 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 466 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6423 (pp) REVERT: A 481 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 688 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7605 (p90) REVERT: A 695 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6084 (mmtm) REVERT: A 771 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: A 838 LEU cc_start: 0.9113 (mm) cc_final: 0.8701 (mm) REVERT: A 1033 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7313 (p90) REVERT: A 1313 MET cc_start: 0.8041 (ttt) cc_final: 0.7717 (ttm) REVERT: A 1326 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7589 (t80) outliers start: 42 outliers final: 32 residues processed: 154 average time/residue: 0.1962 time to fit residues: 44.9087 Evaluate side-chains 150 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 466 LEU 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 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS 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 792 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 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 1079 SER Chi-restraints excluded: chain A residue 1140 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 74 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.190597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159209 restraints weight = 13090.577| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.63 r_work: 0.3923 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10561 Z= 0.214 Angle : 0.684 8.366 14434 Z= 0.351 Chirality : 0.045 0.239 1555 Planarity : 0.004 0.064 1816 Dihedral : 6.361 52.988 1518 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.57 % Allowed : 24.23 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1315 helix: 0.78 (0.35), residues: 211 sheet: -1.55 (0.36), residues: 188 loop : -2.31 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 912 HIS 0.008 0.001 HIS A1373 PHE 0.026 0.002 PHE A 697 TYR 0.019 0.002 TYR A1019 ARG 0.004 0.001 ARG A 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 1.53296 ( 6) link_BETA1-4 : bond 0.00605 ( 2) link_BETA1-4 : angle 1.91263 ( 6) hydrogen bonds : bond 0.03567 ( 271) hydrogen bonds : angle 5.20736 ( 705) SS BOND : bond 0.00360 ( 23) SS BOND : angle 1.85992 ( 46) covalent geometry : bond 0.00509 (10534) covalent geometry : angle 0.67526 (14376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4905.27 seconds wall clock time: 84 minutes 54.59 seconds (5094.59 seconds total)