Starting phenix.real_space_refine on Wed Sep 25 11:05:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_22422.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_22422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_22422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_22422.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/09_2024/7jpt_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-5461/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: 6.96, per 1000 atoms: 0.68 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 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: 1.36 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: 4.45 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3208 1.35 - 1.47: 2866 1.47 - 1.59: 4381 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 10534 Sorted by residual: bond pdb=" C1 NAG A1802 " pdb=" O5 NAG A1802 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" C THR A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.11e-02 8.12e+03 3.97e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14112 1.69 - 3.38: 223 3.38 - 5.07: 33 5.07 - 6.76: 6 6.76 - 8.45: 2 Bond angle restraints: 14376 Sorted by residual: angle pdb=" C TRP A1025 " pdb=" N THR A1026 " pdb=" CA THR A1026 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" CA CYS A 485 " pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " ideal model delta sigma weight residual 114.40 120.20 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU A 654 " pdb=" CB LEU A 654 " pdb=" CG LEU A 654 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" N LEU A1172 " pdb=" CA LEU A1172 " pdb=" C LEU A1172 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" N THR A 440 " pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 114.04 111.18 2.86 1.24e+00 6.50e-01 5.31e+00 ... (remaining 14371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 5776 22.55 - 45.10: 364 45.10 - 67.66: 54 67.66 - 90.21: 18 90.21 - 112.76: 7 Dihedral angle restraints: 6219 sinusoidal: 2341 harmonic: 3878 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.27 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 0.38 -86.38 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 6216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1315 0.054 - 0.108: 205 0.108 - 0.162: 34 0.162 - 0.216: 0 0.216 - 0.269: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA CYS A1211 " pdb=" N CYS A1211 " pdb=" C CYS A1211 " pdb=" CB CYS A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB ILE A 737 " pdb=" CA ILE A 737 " pdb=" CG1 ILE A 737 " pdb=" CG2 ILE A 737 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1552 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 967 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 968 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 968 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 968 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 813 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 814 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 814 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 814 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 697 " -0.013 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE A 697 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 697 " -0.005 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2673 2.79 - 3.32: 8847 3.32 - 3.85: 16455 3.85 - 4.37: 18978 4.37 - 4.90: 32978 Nonbonded interactions: 79931 Sorted by model distance: nonbonded pdb=" OH TYR A 165 " pdb=" OE1 GLN A1301 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 329 " pdb=" OG SER A 329 " model vdw 2.286 3.040 nonbonded pdb=" O SER A1097 " pdb=" OG SER A1097 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU A1195 " pdb=" N ASP A1210 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG A 160 " pdb=" OD2 ASP A 161 " model vdw 2.324 3.120 ... (remaining 79926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.53 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.173 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: 0.2464 time to fit residues: 77.6609 Evaluate side-chains 144 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2649 (OUTLIER) cc_final: 0.1097 (t) REVERT: A 67 TRP cc_start: 0.7198 (m100) cc_final: 0.6412 (m100) REVERT: A 69 TRP cc_start: 0.8745 (m100) cc_final: 0.8447 (m100) REVERT: A 140 TRP cc_start: 0.6797 (m100) cc_final: 0.6355 (m100) REVERT: A 320 MET cc_start: 0.8075 (ttt) cc_final: 0.7844 (ttt) REVERT: A 326 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7818 (mt) REVERT: A 406 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 590 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5867 (mm-30) REVERT: A 617 PHE cc_start: 0.5343 (t80) cc_final: 0.4999 (t80) REVERT: A 695 LYS cc_start: 0.6422 (mtpt) cc_final: 0.5815 (mmtm) REVERT: A 1136 MET cc_start: 0.7046 (mtt) cc_final: 0.6729 (mtm) REVERT: A 1266 MET cc_start: 0.3562 (tpt) cc_final: 0.2506 (tpt) REVERT: A 1313 MET cc_start: 0.7711 (ttt) cc_final: 0.7199 (ttm) REVERT: A 1361 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 1370 VAL cc_start: 0.8269 (m) cc_final: 0.7826 (t) REVERT: A 1374 GLN cc_start: 0.8160 (mt0) cc_final: 0.7802 (mm-40) outliers start: 54 outliers final: 30 residues processed: 178 average time/residue: 0.2071 time to fit residues: 53.4386 Evaluate side-chains 153 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.8160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10534 Z= 0.227 Angle : 0.587 8.085 14376 Z= 0.298 Chirality : 0.043 0.206 1555 Planarity : 0.004 0.046 1816 Dihedral : 6.561 52.871 1526 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.86 % Allowed : 20.85 % Favored : 73.29 % 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: -2.90 (0.21), residues: 1315 helix: 0.25 (0.34), residues: 211 sheet: -1.67 (0.40), residues: 147 loop : -2.70 (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 0.020 0.002 PHE A1149 TYR 0.016 0.001 TYR A 116 ARG 0.007 0.001 ARG A1015 *********************** 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 196 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3013 (OUTLIER) cc_final: 0.1290 (t) REVERT: A 69 TRP cc_start: 0.8770 (m100) cc_final: 0.8493 (m100) REVERT: A 77 HIS cc_start: 0.7329 (t-90) cc_final: 0.7100 (t-90) REVERT: A 140 TRP cc_start: 0.7035 (m100) cc_final: 0.6416 (m100) REVERT: A 222 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7051 (mtpt) REVERT: A 320 MET cc_start: 0.8124 (ttt) cc_final: 0.7828 (ttt) REVERT: A 406 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6918 (tm-30) REVERT: A 561 ARG cc_start: 0.6463 (ttp-110) cc_final: 0.6237 (ptm-80) REVERT: A 617 PHE cc_start: 0.5420 (t80) cc_final: 0.5010 (t80) REVERT: A 672 GLU cc_start: 0.7887 (tp30) cc_final: 0.7666 (mt-10) REVERT: A 695 LYS cc_start: 0.6561 (mtpt) cc_final: 0.5883 (mmtm) REVERT: A 1033 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7095 (p90) REVERT: A 1146 GLN cc_start: 0.7242 (mt0) cc_final: 0.6971 (mt0) REVERT: A 1313 MET cc_start: 0.7809 (ttt) cc_final: 0.7399 (ttm) REVERT: A 1361 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 1370 VAL cc_start: 0.8218 (m) cc_final: 0.7928 (t) REVERT: A 1374 GLN cc_start: 0.8273 (mt0) cc_final: 0.7884 (mm-40) outliers start: 59 outliers final: 36 residues processed: 189 average time/residue: 0.2159 time to fit residues: 58.9187 Evaluate side-chains 159 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 222 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 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 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 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 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 118 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 369 ASN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN A1065 ASN A1173 ASN A1257 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 10534 Z= 0.376 Angle : 0.696 7.749 14376 Z= 0.356 Chirality : 0.046 0.242 1555 Planarity : 0.005 0.072 1816 Dihedral : 6.828 51.368 1526 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 6.45 % Allowed : 20.56 % Favored : 72.99 % 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: -2.92 (0.21), residues: 1315 helix: 0.27 (0.34), residues: 210 sheet: -1.92 (0.36), residues: 178 loop : -2.69 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 912 HIS 0.005 0.001 HIS A 294 PHE 0.023 0.002 PHE A 846 TYR 0.021 0.002 TYR A 888 ARG 0.007 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 190 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 125 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2856 (OUTLIER) cc_final: 0.2326 (t) REVERT: A 67 TRP cc_start: 0.6912 (m100) cc_final: 0.6565 (m100) REVERT: A 140 TRP cc_start: 0.7229 (m100) cc_final: 0.6478 (m100) REVERT: A 320 MET cc_start: 0.8157 (ttt) cc_final: 0.7841 (ttt) REVERT: A 406 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 466 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6219 (pp) REVERT: A 481 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6477 (pp) REVERT: A 657 TYR cc_start: 0.7618 (m-80) cc_final: 0.7327 (m-80) REVERT: A 672 GLU cc_start: 0.7919 (tp30) cc_final: 0.7498 (mt-10) REVERT: A 695 LYS cc_start: 0.6743 (mtpt) cc_final: 0.6005 (mmtm) REVERT: A 838 LEU cc_start: 0.8891 (mm) cc_final: 0.8395 (mm) REVERT: A 846 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7268 (p90) REVERT: A 1033 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7400 (p90) REVERT: A 1117 ILE cc_start: 0.8897 (mm) cc_final: 0.8576 (mt) REVERT: A 1313 MET cc_start: 0.7824 (ttt) cc_final: 0.7310 (ttm) REVERT: A 1361 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7202 (tm-30) outliers start: 65 outliers final: 49 residues processed: 179 average time/residue: 0.2056 time to fit residues: 53.9519 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 115 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 222 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10534 Z= 0.235 Angle : 0.601 7.882 14376 Z= 0.308 Chirality : 0.043 0.203 1555 Planarity : 0.004 0.069 1816 Dihedral : 6.469 54.650 1525 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 6.36 % Allowed : 20.75 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1315 helix: 0.57 (0.35), residues: 212 sheet: -1.72 (0.36), residues: 182 loop : -2.57 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS A 113 PHE 0.023 0.002 PHE A 697 TYR 0.015 0.001 TYR A 116 ARG 0.003 0.000 ARG A1015 *********************** 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 fitting. rotamer outliers: 64 poor density : 121 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3076 (OUTLIER) cc_final: 0.2272 (t) REVERT: A 67 TRP cc_start: 0.6948 (m100) cc_final: 0.6531 (m100) REVERT: A 140 TRP cc_start: 0.7110 (m100) cc_final: 0.6373 (m100) REVERT: A 222 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7233 (mtpt) REVERT: A 320 MET cc_start: 0.8049 (ttt) cc_final: 0.7670 (ttt) REVERT: A 358 ASP cc_start: 0.7371 (p0) cc_final: 0.7074 (p0) REVERT: A 406 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 481 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6401 (pp) REVERT: A 657 TYR cc_start: 0.7520 (m-80) cc_final: 0.7289 (m-80) REVERT: A 695 LYS cc_start: 0.6762 (mtpt) cc_final: 0.6013 (mmtm) REVERT: A 771 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: A 838 LEU cc_start: 0.8811 (mm) cc_final: 0.8368 (mm) REVERT: A 1033 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7290 (p90) REVERT: A 1117 ILE cc_start: 0.8882 (mm) cc_final: 0.8533 (mt) REVERT: A 1313 MET cc_start: 0.7682 (ttt) cc_final: 0.7154 (ttm) outliers start: 64 outliers final: 43 residues processed: 174 average time/residue: 0.2150 time to fit residues: 53.9797 Evaluate side-chains 157 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 222 LYS Chi-restraints excluded: chain A residue 226 PHE 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 412 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 622 ILE Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 882 ILE 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 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10534 Z= 0.221 Angle : 0.595 7.756 14376 Z= 0.304 Chirality : 0.043 0.196 1555 Planarity : 0.004 0.057 1816 Dihedral : 6.307 54.658 1525 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 6.55 % Allowed : 21.75 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.22), residues: 1315 helix: 0.79 (0.35), residues: 212 sheet: -1.63 (0.36), residues: 181 loop : -2.47 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 912 HIS 0.005 0.001 HIS A 40 PHE 0.030 0.002 PHE A 958 TYR 0.017 0.001 TYR A 548 ARG 0.004 0.001 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 187 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 121 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2985 (OUTLIER) cc_final: 0.2224 (t) REVERT: A 67 TRP cc_start: 0.6915 (m100) cc_final: 0.6505 (m100) REVERT: A 140 TRP cc_start: 0.7048 (m100) cc_final: 0.6422 (m100) REVERT: A 222 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7212 (mtpt) REVERT: A 320 MET cc_start: 0.8018 (ttt) cc_final: 0.7607 (ttt) REVERT: A 333 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: A 358 ASP cc_start: 0.7301 (p0) cc_final: 0.7036 (p0) REVERT: A 406 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 481 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6386 (pp) REVERT: A 657 TYR cc_start: 0.7522 (m-80) cc_final: 0.7300 (m-80) REVERT: A 672 GLU cc_start: 0.7907 (tp30) cc_final: 0.7609 (mt-10) REVERT: A 695 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.5974 (mmtm) REVERT: A 771 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: A 838 LEU cc_start: 0.8801 (mm) cc_final: 0.8409 (mm) REVERT: A 846 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.6961 (p90) REVERT: A 1033 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7275 (p90) REVERT: A 1117 ILE cc_start: 0.8850 (mm) cc_final: 0.8517 (mt) REVERT: A 1313 MET cc_start: 0.7725 (ttt) cc_final: 0.7333 (ttm) outliers start: 66 outliers final: 44 residues processed: 177 average time/residue: 0.2226 time to fit residues: 56.5199 Evaluate side-chains 166 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 114 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 222 LYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 GLU 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 423 ILE Chi-restraints excluded: chain A residue 454 VAL 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 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 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 966 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 A 960 ASN A1065 ASN A1278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10534 Z= 0.206 Angle : 0.591 8.378 14376 Z= 0.300 Chirality : 0.042 0.188 1555 Planarity : 0.004 0.051 1816 Dihedral : 6.195 53.820 1525 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.16 % Allowed : 22.34 % Favored : 71.50 % 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: -2.42 (0.22), residues: 1315 helix: 0.89 (0.35), residues: 213 sheet: -1.59 (0.36), residues: 181 loop : -2.41 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 912 HIS 0.005 0.001 HIS A 113 PHE 0.023 0.002 PHE A 958 TYR 0.016 0.001 TYR A1019 ARG 0.004 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 177 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 115 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3219 (OUTLIER) cc_final: 0.2393 (t) REVERT: A 67 TRP cc_start: 0.6981 (m100) cc_final: 0.6564 (m100) REVERT: A 140 TRP cc_start: 0.7079 (m100) cc_final: 0.6395 (m100) REVERT: A 320 MET cc_start: 0.7987 (ttt) cc_final: 0.7546 (ttt) REVERT: A 406 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6967 (tm-30) REVERT: A 481 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6373 (pp) REVERT: A 657 TYR cc_start: 0.7495 (m-80) cc_final: 0.7279 (m-80) REVERT: A 672 GLU cc_start: 0.7898 (tp30) cc_final: 0.7561 (mt-10) REVERT: A 695 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5950 (mmtm) REVERT: A 771 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: A 838 LEU cc_start: 0.8823 (mm) cc_final: 0.8453 (mm) REVERT: A 1033 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7234 (p90) REVERT: A 1117 ILE cc_start: 0.8840 (mm) cc_final: 0.8503 (mt) REVERT: A 1313 MET cc_start: 0.7723 (ttt) cc_final: 0.7326 (ttm) outliers start: 62 outliers final: 46 residues processed: 171 average time/residue: 0.2229 time to fit residues: 55.4804 Evaluate side-chains 162 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 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 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 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10534 Z= 0.323 Angle : 0.662 8.809 14376 Z= 0.337 Chirality : 0.045 0.228 1555 Planarity : 0.004 0.073 1816 Dihedral : 6.432 53.786 1521 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 6.75 % Allowed : 21.75 % Favored : 71.50 % 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: -2.54 (0.22), residues: 1315 helix: 0.72 (0.35), residues: 212 sheet: -1.67 (0.36), residues: 187 loop : -2.47 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.006 0.001 HIS A 113 PHE 0.027 0.002 PHE A 697 TYR 0.021 0.002 TYR A1019 ARG 0.005 0.001 ARG A 669 *********************** 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 183 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 115 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3104 (OUTLIER) cc_final: 0.2847 (t) REVERT: A 67 TRP cc_start: 0.6986 (m100) cc_final: 0.6621 (m100) REVERT: A 140 TRP cc_start: 0.7317 (m100) cc_final: 0.6532 (m100) REVERT: A 320 MET cc_start: 0.8055 (ttt) cc_final: 0.7593 (ttt) REVERT: A 333 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: A 406 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 481 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6435 (pp) REVERT: A 657 TYR cc_start: 0.7626 (m-80) cc_final: 0.7359 (m-80) REVERT: A 672 GLU cc_start: 0.7962 (tp30) cc_final: 0.7541 (mt-10) REVERT: A 695 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.5977 (mmtm) REVERT: A 771 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: A 838 LEU cc_start: 0.8829 (mm) cc_final: 0.8356 (mm) REVERT: A 846 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7243 (p90) REVERT: A 1033 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7375 (p90) REVERT: A 1117 ILE cc_start: 0.8851 (mm) cc_final: 0.8541 (mt) REVERT: A 1313 MET cc_start: 0.7790 (ttt) cc_final: 0.7345 (ttm) REVERT: A 1374 GLN cc_start: 0.8167 (mt0) cc_final: 0.7919 (mm110) outliers start: 68 outliers final: 50 residues processed: 172 average time/residue: 0.2140 time to fit residues: 53.9760 Evaluate side-chains 167 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 110 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 GLU 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 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 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 832 ASN Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 929 ILE 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN A1065 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10534 Z= 0.256 Angle : 0.630 7.762 14376 Z= 0.322 Chirality : 0.044 0.211 1555 Planarity : 0.004 0.068 1816 Dihedral : 6.311 53.671 1521 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.76 % Allowed : 23.14 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (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: -2.43 (0.22), residues: 1315 helix: 0.85 (0.35), residues: 212 sheet: -1.64 (0.35), residues: 188 loop : -2.40 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 912 HIS 0.006 0.001 HIS A 113 PHE 0.027 0.002 PHE A 697 TYR 0.018 0.001 TYR A1019 ARG 0.003 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 168 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 110 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2824 (t) REVERT: A 67 TRP cc_start: 0.6929 (m100) cc_final: 0.6548 (m100) REVERT: A 140 TRP cc_start: 0.7311 (m100) cc_final: 0.6544 (m100) REVERT: A 320 MET cc_start: 0.8026 (ttt) cc_final: 0.7558 (ttt) REVERT: A 333 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: A 406 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7002 (tm-30) REVERT: A 481 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6385 (pp) REVERT: A 657 TYR cc_start: 0.7584 (m-80) cc_final: 0.7326 (m-80) REVERT: A 672 GLU cc_start: 0.7928 (tp30) cc_final: 0.7521 (mt-10) REVERT: A 673 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 695 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.5974 (mmtm) REVERT: A 771 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: A 838 LEU cc_start: 0.8830 (mm) cc_final: 0.8378 (mm) REVERT: A 846 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7083 (p90) REVERT: A 1033 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7348 (p90) REVERT: A 1117 ILE cc_start: 0.8845 (mm) cc_final: 0.8517 (mt) REVERT: A 1313 MET cc_start: 0.7725 (ttt) cc_final: 0.7304 (ttm) REVERT: A 1374 GLN cc_start: 0.8141 (mt0) cc_final: 0.7884 (mm110) outliers start: 58 outliers final: 48 residues processed: 162 average time/residue: 0.2132 time to fit residues: 49.9695 Evaluate side-chains 163 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 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 134 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 GLU 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 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 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 832 ASN Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 929 ILE 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 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 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 59 optimal weight: 20.0000 chunk 87 optimal weight: 0.0270 chunk 131 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10534 Z= 0.332 Angle : 0.677 8.302 14376 Z= 0.347 Chirality : 0.045 0.242 1555 Planarity : 0.004 0.068 1816 Dihedral : 6.598 52.696 1521 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.96 % Allowed : 23.04 % Favored : 71.00 % 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: -2.53 (0.21), residues: 1315 helix: 0.69 (0.35), residues: 212 sheet: -1.68 (0.35), residues: 188 loop : -2.45 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 912 HIS 0.007 0.001 HIS A 113 PHE 0.028 0.002 PHE A 697 TYR 0.021 0.002 TYR A1019 ARG 0.005 0.001 ARG A 669 ********************** 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 170 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 110 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3297 (OUTLIER) cc_final: 0.2978 (t) REVERT: A 67 TRP cc_start: 0.6953 (m100) cc_final: 0.6649 (m100) REVERT: A 140 TRP cc_start: 0.7507 (m100) cc_final: 0.6721 (m100) REVERT: A 320 MET cc_start: 0.8059 (ttt) cc_final: 0.7559 (ttt) REVERT: A 333 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: A 406 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 481 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6444 (pp) REVERT: A 657 TYR cc_start: 0.7640 (m-80) cc_final: 0.7366 (m-80) REVERT: A 672 GLU cc_start: 0.7954 (tp30) cc_final: 0.7535 (mt-10) REVERT: A 695 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.5949 (mmtm) REVERT: A 771 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: A 838 LEU cc_start: 0.8852 (mm) cc_final: 0.8370 (mm) REVERT: A 846 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7376 (p90) REVERT: A 1033 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7460 (p90) REVERT: A 1117 ILE cc_start: 0.8854 (mm) cc_final: 0.8536 (mt) REVERT: A 1313 MET cc_start: 0.7772 (ttt) cc_final: 0.7196 (ttm) REVERT: A 1374 GLN cc_start: 0.8123 (mt0) cc_final: 0.7865 (mm110) outliers start: 60 outliers final: 48 residues processed: 162 average time/residue: 0.2085 time to fit residues: 50.0227 Evaluate side-chains 157 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 102 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 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 GLU 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 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 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 832 ASN Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 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 96 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 996 GLN ** 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 = 0.4440 r_free = 0.4440 target = 0.194104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162496 restraints weight = 13006.477| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.71 r_work: 0.3959 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10534 Z= 0.201 Angle : 0.612 8.387 14376 Z= 0.314 Chirality : 0.043 0.194 1555 Planarity : 0.004 0.066 1816 Dihedral : 6.277 55.050 1521 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.36 % Allowed : 23.73 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (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: -2.33 (0.22), residues: 1315 helix: 0.96 (0.35), residues: 213 sheet: -1.52 (0.36), residues: 183 loop : -2.34 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 912 HIS 0.006 0.001 HIS A 113 PHE 0.025 0.002 PHE A 697 TYR 0.019 0.001 TYR A1019 ARG 0.004 0.000 ARG A1015 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.22 seconds wall clock time: 41 minutes 43.00 seconds (2503.00 seconds total)