Starting phenix.real_space_refine on Fri Feb 14 12:39:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpt_22422/02_2025/7jpt_22422.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpt_22422/02_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_22422/02_2025/7jpt_22422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpt_22422/02_2025/7jpt_22422.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpt_22422/02_2025/7jpt_22422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpt_22422/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.06, per 1000 atoms: 0.59 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 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: 1.81 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: 4.04 Time building geometry restraints manager: 2.96 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- 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 10534 Z= 0.162 Angle : 0.548 8.452 14376 Z= 0.292 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.986 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: 0.2499 time to fit residues: 78.6204 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 : 1.174 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.202120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.170860 restraints weight = 12881.179| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.58 r_work: 0.4033 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 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 = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10534 Z= 0.243 Angle : 0.618 8.576 14376 Z= 0.312 Chirality : 0.043 0.190 1555 Planarity : 0.004 0.046 1816 Dihedral : 8.011 56.755 1543 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 5.36 % Allowed : 20.56 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.34 (0.20), residues: 1315 helix: -0.33 (0.33), residues: 212 sheet: -2.02 (0.38), residues: 142 loop : -2.94 (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 0.015 0.002 PHE A 276 TYR 0.016 0.001 TYR A 116 ARG 0.007 0.001 ARG A1186 *********************** 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 184 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2594 (OUTLIER) cc_final: 0.1027 (t) REVERT: A 67 TRP cc_start: 0.7240 (m100) cc_final: 0.6594 (m100) REVERT: A 69 TRP cc_start: 0.8704 (m100) cc_final: 0.8442 (m100) REVERT: A 140 TRP cc_start: 0.6976 (m100) cc_final: 0.6519 (m100) REVERT: A 326 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7924 (mt) REVERT: A 406 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 590 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: A 617 PHE cc_start: 0.5783 (t80) cc_final: 0.5434 (t80) REVERT: A 695 LYS cc_start: 0.6683 (mtpt) cc_final: 0.6021 (mmtm) REVERT: A 1136 MET cc_start: 0.7325 (mtt) cc_final: 0.7071 (mtm) REVERT: A 1266 MET cc_start: 0.3807 (tpt) cc_final: 0.2700 (tpt) REVERT: A 1313 MET cc_start: 0.8047 (ttt) cc_final: 0.7621 (ttm) REVERT: A 1361 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 1370 VAL cc_start: 0.8407 (m) cc_final: 0.7973 (t) outliers start: 54 outliers final: 30 residues processed: 178 average time/residue: 0.2207 time to fit residues: 56.5631 Evaluate side-chains 152 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 590 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 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 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1042 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 0.0970 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 A 510 HIS A1065 ASN A1084 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.199318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.167683 restraints weight = 13091.710| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.67 r_work: 0.4006 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10534 Z= 0.241 Angle : 0.596 8.099 14376 Z= 0.303 Chirality : 0.043 0.215 1555 Planarity : 0.004 0.046 1816 Dihedral : 6.628 52.433 1526 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 6.16 % Allowed : 20.56 % Favored : 73.29 % 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: -2.91 (0.21), residues: 1315 helix: 0.22 (0.34), residues: 211 sheet: -1.68 (0.40), residues: 147 loop : -2.71 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 880 HIS 0.007 0.001 HIS A 113 PHE 0.022 0.002 PHE A1149 TYR 0.016 0.001 TYR A 116 ARG 0.007 0.001 ARG A 561 *********************** 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 194 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2980 (OUTLIER) cc_final: 0.1266 (t) REVERT: A 67 TRP cc_start: 0.7183 (m100) cc_final: 0.6584 (m100) REVERT: A 140 TRP cc_start: 0.7194 (m100) cc_final: 0.6475 (m100) REVERT: A 141 LYS cc_start: 0.7742 (mmmt) cc_final: 0.6378 (mttt) REVERT: A 406 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 617 PHE cc_start: 0.5913 (t80) cc_final: 0.5487 (t80) REVERT: A 695 LYS cc_start: 0.6854 (mtpt) cc_final: 0.6088 (mmtm) REVERT: A 1033 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.7002 (p90) REVERT: A 1313 MET cc_start: 0.8128 (ttt) cc_final: 0.7788 (ttm) REVERT: A 1361 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7559 (tm-30) outliers start: 62 outliers final: 41 residues processed: 186 average time/residue: 0.2016 time to fit residues: 54.6569 Evaluate side-chains 155 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 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 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 319 ARG Chi-restraints excluded: chain A residue 331 SER 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 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 832 ASN Chi-restraints excluded: chain A residue 907 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.198378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.167834 restraints weight = 12906.333| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.39 r_work: 0.3990 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10534 Z= 0.238 Angle : 0.596 8.046 14376 Z= 0.304 Chirality : 0.043 0.191 1555 Planarity : 0.004 0.069 1816 Dihedral : 6.259 53.357 1522 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.26 % Allowed : 21.65 % Favored : 73.09 % 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: -2.74 (0.21), residues: 1315 helix: 0.59 (0.35), residues: 210 sheet: -1.80 (0.37), residues: 167 loop : -2.61 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 912 HIS 0.003 0.001 HIS A 40 PHE 0.019 0.002 PHE A 697 TYR 0.016 0.001 TYR A 548 ARG 0.006 0.001 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2226 (OUTLIER) cc_final: 0.1751 (t) REVERT: A 67 TRP cc_start: 0.7032 (m100) cc_final: 0.6641 (m100) REVERT: A 140 TRP cc_start: 0.7150 (m100) cc_final: 0.6540 (m100) REVERT: A 406 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7223 (tm-30) REVERT: A 481 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (pp) REVERT: A 617 PHE cc_start: 0.5904 (t80) cc_final: 0.5486 (t80) REVERT: A 695 LYS cc_start: 0.6904 (mtpt) cc_final: 0.6114 (mmtm) REVERT: A 838 LEU cc_start: 0.9052 (mm) cc_final: 0.8719 (mm) REVERT: A 1033 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.7123 (p90) REVERT: A 1136 MET cc_start: 0.7722 (mtt) cc_final: 0.7260 (mtm) REVERT: A 1266 MET cc_start: 0.2807 (tpt) cc_final: 0.2584 (mmt) REVERT: A 1313 MET cc_start: 0.8075 (ttt) cc_final: 0.7684 (ttm) REVERT: A 1361 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7573 (tm-30) outliers start: 53 outliers final: 38 residues processed: 165 average time/residue: 0.2048 time to fit residues: 49.6382 Evaluate side-chains 149 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 331 SER 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 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 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 832 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 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 = 0.4433 r_free = 0.4433 target = 0.193349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.162854 restraints weight = 13008.274| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.54 r_work: 0.3949 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- 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 = 0.19 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 = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10534 Z= 0.316 Angle : 0.649 7.782 14376 Z= 0.333 Chirality : 0.045 0.222 1555 Planarity : 0.004 0.067 1816 Dihedral : 6.412 52.177 1521 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.45 % Allowed : 21.15 % Favored : 72.39 % 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: -2.69 (0.21), residues: 1315 helix: 0.56 (0.35), residues: 211 sheet: -1.76 (0.37), residues: 176 loop : -2.56 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.005 0.001 HIS A 294 PHE 0.037 0.002 PHE A 958 TYR 0.017 0.002 TYR A 888 ARG 0.004 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 120 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3227 (OUTLIER) cc_final: 0.2332 (t) REVERT: A 67 TRP cc_start: 0.7036 (m100) cc_final: 0.6783 (m100) REVERT: A 140 TRP cc_start: 0.7294 (m100) cc_final: 0.6623 (m100) REVERT: A 320 MET cc_start: 0.8051 (ttt) cc_final: 0.7825 (ttt) REVERT: A 358 ASP cc_start: 0.7742 (p0) cc_final: 0.7401 (p0) REVERT: A 406 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 466 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6402 (pp) REVERT: A 481 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7073 (pp) REVERT: A 512 GLU cc_start: 0.6546 (tp30) cc_final: 0.6332 (tm-30) REVERT: A 695 LYS cc_start: 0.7057 (mtpt) cc_final: 0.6253 (mmtm) REVERT: A 771 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: A 838 LEU cc_start: 0.9080 (mm) cc_final: 0.8678 (mm) REVERT: A 846 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7601 (p90) REVERT: A 1033 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.7306 (p90) REVERT: A 1117 ILE cc_start: 0.8890 (mm) cc_final: 0.8505 (mt) REVERT: A 1313 MET cc_start: 0.8113 (ttt) cc_final: 0.7658 (ttm) REVERT: A 1361 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7585 (tm-30) outliers start: 65 outliers final: 46 residues processed: 175 average time/residue: 0.2127 time to fit residues: 53.7675 Evaluate side-chains 166 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 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 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165977 restraints weight = 13054.000| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.80 r_work: 0.3988 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4004 r_free = 0.4004 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4004 r_free = 0.4004 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10534 Z= 0.158 Angle : 0.564 8.186 14376 Z= 0.290 Chirality : 0.042 0.172 1555 Planarity : 0.004 0.066 1816 Dihedral : 6.045 55.283 1521 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.36 % Allowed : 22.34 % Favored : 72.29 % 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: -2.42 (0.22), residues: 1315 helix: 0.93 (0.35), residues: 212 sheet: -1.61 (0.37), residues: 177 loop : -2.41 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS A 40 PHE 0.046 0.001 PHE A 958 TYR 0.019 0.001 TYR A1019 ARG 0.003 0.000 ARG A1015 *********************** 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 176 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2638 (OUTLIER) cc_final: 0.1871 (t) REVERT: A 67 TRP cc_start: 0.6901 (m100) cc_final: 0.6637 (m100) REVERT: A 140 TRP cc_start: 0.7125 (m100) cc_final: 0.6364 (m100) REVERT: A 141 LYS cc_start: 0.7680 (mmmt) cc_final: 0.6611 (mttp) REVERT: A 358 ASP cc_start: 0.7514 (p0) cc_final: 0.7169 (p0) REVERT: A 406 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 481 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6944 (pp) REVERT: A 695 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6095 (mmtm) REVERT: A 838 LEU cc_start: 0.9056 (mm) cc_final: 0.8737 (mm) REVERT: A 1033 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7168 (p90) REVERT: A 1117 ILE cc_start: 0.8879 (mm) cc_final: 0.8487 (mt) REVERT: A 1313 MET cc_start: 0.8033 (ttt) cc_final: 0.7717 (ttm) outliers start: 54 outliers final: 33 residues processed: 168 average time/residue: 0.2036 time to fit residues: 50.0199 Evaluate side-chains 152 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 319 ARG Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 474 VAL 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 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 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 542 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 = 0.4494 r_free = 0.4494 target = 0.199173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.167168 restraints weight = 13154.840| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.82 r_work: 0.3994 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10534 Z= 0.177 Angle : 0.579 8.957 14376 Z= 0.294 Chirality : 0.042 0.171 1555 Planarity : 0.004 0.067 1816 Dihedral : 5.908 53.776 1521 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.97 % Allowed : 22.94 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (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: -2.29 (0.22), residues: 1315 helix: 1.08 (0.35), residues: 212 sheet: -1.53 (0.38), residues: 175 loop : -2.33 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 912 HIS 0.007 0.001 HIS A 40 PHE 0.036 0.001 PHE A 958 TYR 0.019 0.001 TYR A1019 ARG 0.005 0.001 ARG A1015 *********************** 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 170 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3396 (OUTLIER) cc_final: 0.2487 (t) REVERT: A 67 TRP cc_start: 0.6901 (m100) cc_final: 0.6647 (m100) REVERT: A 140 TRP cc_start: 0.7054 (m100) cc_final: 0.6528 (m100) REVERT: A 358 ASP cc_start: 0.7527 (p0) cc_final: 0.7209 (p0) REVERT: A 406 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 481 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6918 (pp) REVERT: A 695 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6051 (mmtm) REVERT: A 771 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: A 838 LEU cc_start: 0.9100 (mm) cc_final: 0.8761 (mm) REVERT: A 994 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6421 (mp) REVERT: A 1033 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7071 (p90) REVERT: A 1313 MET cc_start: 0.8033 (ttt) cc_final: 0.7722 (ttm) outliers start: 50 outliers final: 37 residues processed: 164 average time/residue: 0.2093 time to fit residues: 50.1543 Evaluate side-chains 156 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 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 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 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 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 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 7 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 960 ASN A1065 ASN A1153 GLN A1278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.194873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.164671 restraints weight = 13184.117| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.55 r_work: 0.3957 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10534 Z= 0.270 Angle : 0.624 10.705 14376 Z= 0.318 Chirality : 0.044 0.243 1555 Planarity : 0.004 0.068 1816 Dihedral : 6.156 52.374 1521 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.86 % Allowed : 22.14 % 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: -2.35 (0.22), residues: 1315 helix: 0.97 (0.35), residues: 211 sheet: -1.59 (0.36), residues: 183 loop : -2.34 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 571 HIS 0.004 0.001 HIS A 40 PHE 0.031 0.002 PHE A 958 TYR 0.018 0.001 TYR A1019 ARG 0.004 0.001 ARG A1015 *********************** 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 173 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3119 (OUTLIER) cc_final: 0.2681 (t) REVERT: A 140 TRP cc_start: 0.7212 (m100) cc_final: 0.6469 (m100) REVERT: A 141 LYS cc_start: 0.7676 (mmmt) cc_final: 0.6073 (mttp) REVERT: A 358 ASP cc_start: 0.7487 (p0) cc_final: 0.7234 (p0) REVERT: A 406 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 481 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6919 (pp) REVERT: A 695 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6109 (mmtm) REVERT: A 771 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 838 LEU cc_start: 0.9066 (mm) cc_final: 0.8650 (mm) REVERT: A 1033 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7257 (p90) REVERT: A 1117 ILE cc_start: 0.8870 (mm) cc_final: 0.8516 (mt) REVERT: A 1313 MET cc_start: 0.8062 (ttt) cc_final: 0.7715 (ttm) outliers start: 59 outliers final: 41 residues processed: 166 average time/residue: 0.1880 time to fit residues: 46.1957 Evaluate side-chains 157 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL 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 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 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 123 optimal weight: 0.0010 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4457 r_free = 0.4457 target = 0.195383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.165352 restraints weight = 13207.001| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.48 r_work: 0.3973 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10534 Z= 0.231 Angle : 0.610 10.290 14376 Z= 0.311 Chirality : 0.043 0.222 1555 Planarity : 0.004 0.068 1816 Dihedral : 6.095 53.519 1521 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.46 % Allowed : 22.34 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.22), residues: 1315 helix: 1.04 (0.35), residues: 211 sheet: -1.49 (0.37), residues: 175 loop : -2.28 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 67 HIS 0.005 0.001 HIS A 40 PHE 0.030 0.002 PHE A 958 TYR 0.018 0.001 TYR A1019 ARG 0.004 0.001 ARG A1015 *********************** 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 167 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3358 (OUTLIER) cc_final: 0.2913 (t) REVERT: A 140 TRP cc_start: 0.7274 (m100) cc_final: 0.6499 (m100) REVERT: A 141 LYS cc_start: 0.7682 (mmmt) cc_final: 0.6156 (mttp) REVERT: A 358 ASP cc_start: 0.7480 (p0) cc_final: 0.7259 (p0) REVERT: A 406 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 481 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6971 (pp) REVERT: A 695 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6116 (mmtm) REVERT: A 771 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: A 838 LEU cc_start: 0.9117 (mm) cc_final: 0.8735 (mm) REVERT: A 846 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 1033 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7335 (p90) REVERT: A 1117 ILE cc_start: 0.8847 (mm) cc_final: 0.8484 (mt) REVERT: A 1313 MET cc_start: 0.8059 (ttt) cc_final: 0.7715 (ttm) outliers start: 55 outliers final: 43 residues processed: 160 average time/residue: 0.1914 time to fit residues: 45.8334 Evaluate side-chains 160 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 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 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 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 792 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 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.198534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164437 restraints weight = 13138.409| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.66 r_work: 0.4012 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10534 Z= 0.168 Angle : 0.590 10.038 14376 Z= 0.301 Chirality : 0.043 0.190 1555 Planarity : 0.004 0.066 1816 Dihedral : 5.898 54.286 1521 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.17 % Allowed : 23.63 % Favored : 72.19 % 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: -2.08 (0.22), residues: 1315 helix: 1.16 (0.35), residues: 212 sheet: -1.30 (0.39), residues: 167 loop : -2.17 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 67 HIS 0.005 0.001 HIS A 40 PHE 0.038 0.002 PHE A1149 TYR 0.019 0.001 TYR A1019 ARG 0.004 0.000 ARG A1015 ********************** 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 : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2922 (OUTLIER) cc_final: 0.2497 (t) REVERT: A 140 TRP cc_start: 0.7309 (m100) cc_final: 0.6464 (m100) REVERT: A 141 LYS cc_start: 0.7353 (mmmt) cc_final: 0.5915 (mttp) REVERT: A 406 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 481 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6795 (pp) REVERT: A 695 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.5966 (mmtm) REVERT: A 771 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: A 838 LEU cc_start: 0.9083 (mm) cc_final: 0.8752 (mm) REVERT: A 1033 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7198 (p90) REVERT: A 1266 MET cc_start: 0.2275 (OUTLIER) cc_final: 0.1974 (tpp) REVERT: A 1313 MET cc_start: 0.8010 (ttt) cc_final: 0.7671 (ttm) outliers start: 42 outliers final: 36 residues processed: 152 average time/residue: 0.2060 time to fit residues: 46.1373 Evaluate side-chains 154 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 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 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 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 792 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1022 ILE 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 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1266 MET 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: 0.0670 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 A1278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.202596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168869 restraints weight = 13015.568| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.64 r_work: 0.4043 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10534 Z= 0.145 Angle : 0.578 9.565 14376 Z= 0.294 Chirality : 0.042 0.167 1555 Planarity : 0.004 0.063 1816 Dihedral : 5.477 54.308 1519 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.18 % Allowed : 25.32 % Favored : 71.50 % 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: -1.91 (0.22), residues: 1315 helix: 1.37 (0.35), residues: 212 sheet: -1.31 (0.37), residues: 178 loop : -2.06 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 912 HIS 0.005 0.000 HIS A 40 PHE 0.030 0.001 PHE A 958 TYR 0.019 0.001 TYR A 548 ARG 0.004 0.000 ARG A1015 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.07 seconds wall clock time: 84 minutes 25.02 seconds (5065.02 seconds total)