Starting phenix.real_space_refine on Wed Feb 4 21:46:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qj5_53199/02_2026/9qj5_53199.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 65 5.16 5 C 8171 2.51 5 N 2260 2.21 5 O 2453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5012 Classifications: {'peptide': 651} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 605} Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2241 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 269} Chain: "B" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2531 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 3123 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3114 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 382} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 404, 3114 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 382} Chain breaks: 2 bond proxies already assigned to first conformer: 3173 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.55, per 1000 atoms: 0.27 Number of scatterers: 12950 At special positions: 0 Unit cell: (85.272, 107.844, 158.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 1 11.99 O 2453 8.00 N 2260 7.00 C 8171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.05 Simple disulfide: pdb=" SG CYS C1566 " - pdb=" SG CYS B1394 " distance=2.03 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.05 Simple disulfide: pdb=" SG CYS C1590 " - pdb=" SG CYS B 876 " distance=2.03 Simple disulfide: pdb=" SG CYS C1595 " - pdb=" SG CYS C1673 " distance=2.03 Simple disulfide: pdb=" SG CYS C1618 " - pdb=" SG CYS C1742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1718 " - pdb=" SG CYS C1727 " distance=2.04 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 89 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 204 " 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 NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 633.3 milliseconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3052 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 29 sheets defined 14.5% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.574A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.641A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.515A pdb=" N VAL A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 3.719A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'C' and resid 1611 through 1619 Processing helix chain 'C' and resid 1722 through 1740 removed outlier: 4.424A pdb=" N ALA C1726 " --> pdb=" O ARG C1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 882 removed outlier: 3.993A pdb=" N GLY B 880 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 881 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 882 " --> pdb=" O GLY B 879 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 877 through 882' Processing helix chain 'B' and resid 952 through 955 Processing helix chain 'D' and resid 212 through 229 Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 266 through 287 removed outlier: 3.529A pdb=" N PHE D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.667A pdb=" N SER D 313 " --> pdb=" O ASN D 310 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 314 " --> pdb=" O ASP D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 310 through 314' Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 338 through 358 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 385 through 397 removed outlier: 3.581A pdb=" N VAL D 389 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.955A pdb=" N ASP D 404 " --> pdb=" O LYS D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 419 through 427 Processing helix chain 'D' and resid 441 through 451 removed outlier: 3.540A pdb=" N HIS D 451 " --> pdb=" O GLN D 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 removed outlier: 3.518A pdb=" N ALA A 83 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.609A pdb=" N GLN A 109 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 76 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 54 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 removed outlier: 6.623A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 247 removed outlier: 3.915A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.492A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 293 through 295 current: chain 'A' and resid 352 through 357 Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AA9, first strand: chain 'A' and resid 417 through 424 Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 476 Processing sheet with id=AB2, first strand: chain 'A' and resid 514 through 522 removed outlier: 6.680A pdb=" N ILE A 509 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N MET A 518 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR A 507 " --> pdb=" O MET A 518 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG A 520 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR A 505 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 549 " --> pdb=" O HIS A 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 571 through 575 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 781 through 782 current: chain 'B' and resid 819 through 821 Processing sheet with id=AB4, first strand: chain 'C' and resid 1465 through 1474 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1516 through 1518 removed outlier: 4.553A pdb=" N SER C1553 " --> pdb=" O THR C1489 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C1556 " --> pdb=" O CYS C1566 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS C1566 " --> pdb=" O LEU C1556 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1581 through 1584 removed outlier: 4.101A pdb=" N SER C1584 " --> pdb=" O VAL C1587 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1701 through 1702 removed outlier: 3.546A pdb=" N VAL C1669 " --> pdb=" O ARG C1641 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS C1646 " --> pdb=" O VAL C1631 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL C1631 " --> pdb=" O LYS C1646 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C1648 " --> pdb=" O VAL C1629 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL C1629 " --> pdb=" O THR C1648 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C1650 " --> pdb=" O PHE C1627 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE C1627 " --> pdb=" O VAL C1650 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS C1652 " --> pdb=" O TYR C1625 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR C1625 " --> pdb=" O HIS C1652 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 774 through 775 Processing sheet with id=AB9, first strand: chain 'B' and resid 833 through 837 removed outlier: 3.598A pdb=" N HIS B 834 " --> pdb=" O TYR B 856 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AC2, first strand: chain 'B' and resid 909 through 910 Processing sheet with id=AC3, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.709A pdb=" N ASN B 975 " --> pdb=" O THR B1383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 957 through 960 removed outlier: 4.208A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B1331 " --> pdb=" O HIS B1342 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B1342 " --> pdb=" O LEU B1331 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B1340 " --> pdb=" O SER B1333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 34 through 37 Processing sheet with id=AC6, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC7, first strand: chain 'D' and resid 98 through 101 removed outlier: 3.587A pdb=" N ILE D 99 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 116 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.794A pdb=" N ILE D 122 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AD1, first strand: chain 'D' and resid 182 through 184 Processing sheet with id=AD2, first strand: chain 'D' and resid 303 through 304 removed outlier: 6.557A pdb=" N LEU D 253 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA D 294 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 255 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE D 296 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU D 257 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE D 298 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU D 259 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASP D 407 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS D 369 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR D 409 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 371 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE D 411 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU D 373 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 413 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR D 375 " --> pdb=" O VAL D 413 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1110 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: 1.94 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4329 1.35 - 1.47: 3080 1.47 - 1.60: 5724 1.60 - 1.72: 0 1.72 - 1.85: 97 Bond restraints: 13230 Sorted by residual: bond pdb=" CB ASN A 307 " pdb=" CG ASN A 307 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.55e+00 bond pdb=" CB CYS C1583 " pdb=" SG CYS C1583 " ideal model delta sigma weight residual 1.808 1.848 -0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB ASP A 561 " pdb=" CG ASP A 561 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.42e+00 bond pdb=" CB GLU B 769 " pdb=" CG GLU B 769 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CA ASN A 307 " pdb=" CB ASN A 307 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.36e-02 5.41e+03 1.37e+00 ... (remaining 13225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 17630 2.33 - 4.66: 258 4.66 - 7.00: 33 7.00 - 9.33: 12 9.33 - 11.66: 3 Bond angle restraints: 17936 Sorted by residual: angle pdb=" CA CYS C1588 " pdb=" CB CYS C1588 " pdb=" SG CYS C1588 " ideal model delta sigma weight residual 114.40 123.48 -9.08 2.30e+00 1.89e-01 1.56e+01 angle pdb=" CA GLU B 769 " pdb=" CB GLU B 769 " pdb=" CG GLU B 769 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C GLU B1418 " pdb=" N ASP B1419 " pdb=" CA ASP B1419 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N SER B1374 " pdb=" CA SER B1374 " pdb=" C SER B1374 " ideal model delta sigma weight residual 107.88 112.85 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" CB ARG D 355 " pdb=" CG ARG D 355 " pdb=" CD ARG D 355 " ideal model delta sigma weight residual 111.30 119.37 -8.07 2.30e+00 1.89e-01 1.23e+01 ... (remaining 17931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7027 17.79 - 35.57: 767 35.57 - 53.36: 186 53.36 - 71.15: 63 71.15 - 88.94: 12 Dihedral angle restraints: 8055 sinusoidal: 3297 harmonic: 4758 Sorted by residual: dihedral pdb=" CB CYS C1618 " pdb=" SG CYS C1618 " pdb=" SG CYS C1742 " pdb=" CB CYS C1742 " ideal model delta sinusoidal sigma weight residual 93.00 169.89 -76.89 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS D 117 " pdb=" SG CYS D 117 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 150.84 -57.84 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 38.83 54.17 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 8052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1728 0.069 - 0.137: 261 0.137 - 0.206: 6 0.206 - 0.274: 0 0.274 - 0.343: 1 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CG LEU D 279 " pdb=" CB LEU D 279 " pdb=" CD1 LEU D 279 " pdb=" CD2 LEU D 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL C1623 " pdb=" CA VAL C1623 " pdb=" CG1 VAL C1623 " pdb=" CG2 VAL C1623 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA CYS C1583 " pdb=" N CYS C1583 " pdb=" C CYS C1583 " pdb=" CB CYS C1583 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1993 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 769 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLU B 769 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU B 769 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 770 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 307 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C ASN A 307 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 307 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY A 308 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 769 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" CD GLU B 769 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 769 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 769 " 0.015 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 198 2.65 - 3.21: 11464 3.21 - 3.77: 19245 3.77 - 4.34: 26002 4.34 - 4.90: 44454 Nonbonded interactions: 101363 Sorted by model distance: nonbonded pdb=" OG SER D 262 " pdb="MG MG D 801 " model vdw 2.087 2.170 nonbonded pdb=" OG SER D 264 " pdb="MG MG D 801 " model vdw 2.139 2.170 nonbonded pdb=" OD2 ASP A 81 " pdb=" OH TYR A 506 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP A 200 " pdb=" N ASP A 201 " model vdw 2.220 3.120 nonbonded pdb=" O THR C1489 " pdb=" OH TYR C1570 " model vdw 2.231 3.040 ... (remaining 101358 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.930 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.003 0.040 13249 Z= 0.130 Angle : 0.695 11.661 17977 Z= 0.343 Chirality : 0.045 0.343 1996 Planarity : 0.004 0.035 2345 Dihedral : 16.123 88.936 4955 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.56 % Allowed : 23.16 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1644 helix: 1.04 (0.38), residues: 187 sheet: 0.29 (0.22), residues: 552 loop : -0.65 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1724 TYR 0.022 0.001 TYR A 548 PHE 0.017 0.001 PHE B1360 TRP 0.033 0.001 TRP D 364 HIS 0.008 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00301 (13230) covalent geometry : angle 0.68863 (17936) SS BOND : bond 0.00666 ( 16) SS BOND : angle 1.38029 ( 32) hydrogen bonds : bond 0.23543 ( 415) hydrogen bonds : angle 9.21276 ( 1110) link_NAG-ASN : bond 0.00282 ( 3) link_NAG-ASN : angle 3.61278 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6136 (mtt-85) cc_final: 0.5453 (mtt-85) REVERT: A 180 ASN cc_start: 0.8366 (p0) cc_final: 0.8051 (p0) REVERT: A 184 LEU cc_start: 0.8923 (mp) cc_final: 0.8625 (mp) REVERT: A 360 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7562 (t60) REVERT: C 1584 SER cc_start: 0.7495 (p) cc_final: 0.7224 (m) REVERT: C 1612 TYR cc_start: 0.7054 (t80) cc_final: 0.6533 (t80) REVERT: B 940 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6400 (t-90) REVERT: B 959 GLU cc_start: 0.7336 (pp20) cc_final: 0.7050 (pt0) REVERT: B 1357 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7793 (tt0) outliers start: 8 outliers final: 5 residues processed: 185 average time/residue: 0.1024 time to fit residues: 27.8084 Evaluate side-chains 166 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain C residue 1509 ASP Chi-restraints excluded: chain B residue 764 GLU Chi-restraints excluded: chain B residue 940 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136855 restraints weight = 30589.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139032 restraints weight = 21365.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139671 restraints weight = 19719.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142292 restraints weight = 11362.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142503 restraints weight = 9168.698| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13249 Z= 0.232 Angle : 0.702 13.096 17977 Z= 0.357 Chirality : 0.047 0.313 1996 Planarity : 0.005 0.048 2345 Dihedral : 6.010 57.892 1882 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.56 % Allowed : 18.81 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1644 helix: 0.68 (0.35), residues: 202 sheet: 0.23 (0.22), residues: 593 loop : -0.75 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 283 TYR 0.018 0.002 TYR D 208 PHE 0.018 0.002 PHE C1627 TRP 0.030 0.002 TRP D 364 HIS 0.010 0.002 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00554 (13230) covalent geometry : angle 0.69556 (17936) SS BOND : bond 0.00728 ( 16) SS BOND : angle 1.70879 ( 32) hydrogen bonds : bond 0.04310 ( 415) hydrogen bonds : angle 6.45588 ( 1110) link_NAG-ASN : bond 0.00275 ( 3) link_NAG-ASN : angle 3.02750 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6259 (mtt-85) cc_final: 0.5781 (mtt-85) REVERT: A 59 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7135 (mtm110) REVERT: A 107 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: A 262 MET cc_start: 0.8124 (mpp) cc_final: 0.7798 (mtm) REVERT: A 307 ASN cc_start: 0.8524 (t0) cc_final: 0.8258 (t0) REVERT: A 336 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7823 (mt) REVERT: B 844 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7945 (tpp-160) REVERT: B 919 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 940 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6522 (t-90) REVERT: B 1357 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7748 (tt0) REVERT: D 208 TYR cc_start: 0.8114 (p90) cc_final: 0.7663 (p90) outliers start: 65 outliers final: 35 residues processed: 213 average time/residue: 0.0952 time to fit residues: 29.9596 Evaluate side-chains 189 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1492 SER Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 104 optimal weight: 0.0040 chunk 59 optimal weight: 8.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 128 GLN A 151 ASN A 419 GLN B 793 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.173019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138794 restraints weight = 35891.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142559 restraints weight = 24917.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143338 restraints weight = 17012.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146255 restraints weight = 10491.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146825 restraints weight = 8240.984| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13249 Z= 0.129 Angle : 0.620 11.721 17977 Z= 0.309 Chirality : 0.045 0.245 1996 Planarity : 0.004 0.046 2345 Dihedral : 5.472 53.278 1875 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.72 % Allowed : 20.07 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1644 helix: 0.81 (0.35), residues: 205 sheet: 0.22 (0.21), residues: 593 loop : -0.68 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 132 TYR 0.012 0.001 TYR D 175 PHE 0.016 0.001 PHE D 273 TRP 0.023 0.001 TRP D 364 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00306 (13230) covalent geometry : angle 0.61251 (17936) SS BOND : bond 0.00573 ( 16) SS BOND : angle 1.92883 ( 32) hydrogen bonds : bond 0.03568 ( 415) hydrogen bonds : angle 5.94135 ( 1110) link_NAG-ASN : bond 0.00346 ( 3) link_NAG-ASN : angle 2.64569 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6946 (mtm110) REVERT: A 107 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 262 MET cc_start: 0.8122 (mpp) cc_final: 0.7716 (mtm) REVERT: A 300 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.5962 (mp0) REVERT: A 307 ASN cc_start: 0.8483 (t0) cc_final: 0.8202 (t0) REVERT: C 1501 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 919 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7455 (t80) REVERT: B 940 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6577 (t-90) REVERT: B 1357 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7664 (tt0) REVERT: D 208 TYR cc_start: 0.7995 (p90) cc_final: 0.7627 (p90) outliers start: 53 outliers final: 38 residues processed: 213 average time/residue: 0.1109 time to fit residues: 34.2163 Evaluate side-chains 197 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1404 LYS Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 793 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137321 restraints weight = 27729.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138755 restraints weight = 15244.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139990 restraints weight = 13835.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140681 restraints weight = 9961.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141226 restraints weight = 9102.521| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13249 Z= 0.140 Angle : 0.605 11.122 17977 Z= 0.301 Chirality : 0.045 0.334 1996 Planarity : 0.004 0.049 2345 Dihedral : 5.391 52.767 1875 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.77 % Allowed : 19.30 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1644 helix: 0.80 (0.35), residues: 205 sheet: 0.16 (0.22), residues: 585 loop : -0.68 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 132 TYR 0.017 0.001 TYR D 175 PHE 0.022 0.001 PHE C1733 TRP 0.020 0.001 TRP D 364 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00336 (13230) covalent geometry : angle 0.59932 (17936) SS BOND : bond 0.00593 ( 16) SS BOND : angle 1.65979 ( 32) hydrogen bonds : bond 0.03229 ( 415) hydrogen bonds : angle 5.66678 ( 1110) link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 2.37358 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 0.459 Fit side-chains REVERT: A 59 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6888 (mtm110) REVERT: A 107 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 262 MET cc_start: 0.8139 (mpp) cc_final: 0.7810 (mtm) REVERT: A 300 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: A 307 ASN cc_start: 0.8482 (t0) cc_final: 0.8186 (t0) REVERT: A 590 HIS cc_start: 0.7074 (m170) cc_final: 0.6856 (m170) REVERT: B 919 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 940 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6546 (t-90) REVERT: D 208 TYR cc_start: 0.8028 (p90) cc_final: 0.7722 (p90) outliers start: 68 outliers final: 45 residues processed: 217 average time/residue: 0.0976 time to fit residues: 31.4612 Evaluate side-chains 197 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1492 SER Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1360 PHE Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135784 restraints weight = 41077.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137815 restraints weight = 31937.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139977 restraints weight = 17775.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143188 restraints weight = 10925.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143715 restraints weight = 8852.131| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13249 Z= 0.188 Angle : 0.651 11.610 17977 Z= 0.323 Chirality : 0.046 0.310 1996 Planarity : 0.004 0.050 2345 Dihedral : 5.455 52.335 1873 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.91 % Allowed : 19.16 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1644 helix: 0.65 (0.35), residues: 205 sheet: 0.07 (0.21), residues: 596 loop : -0.73 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 22 TYR 0.017 0.002 TYR A 505 PHE 0.015 0.002 PHE D 273 TRP 0.020 0.001 TRP D 364 HIS 0.006 0.001 HIS C1652 Details of bonding type rmsd covalent geometry : bond 0.00454 (13230) covalent geometry : angle 0.64469 (17936) SS BOND : bond 0.00554 ( 16) SS BOND : angle 1.95407 ( 32) hydrogen bonds : bond 0.03294 ( 415) hydrogen bonds : angle 5.68421 ( 1110) link_NAG-ASN : bond 0.00200 ( 3) link_NAG-ASN : angle 2.25384 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 152 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6971 (mtm110) REVERT: A 107 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 187 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6855 (ttt-90) REVERT: A 262 MET cc_start: 0.8064 (mpp) cc_final: 0.7799 (mtm) REVERT: A 300 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: A 628 MET cc_start: 0.8061 (mtp) cc_final: 0.7751 (mtt) REVERT: C 1501 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8113 (mt) REVERT: B 850 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: B 919 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7320 (t80) REVERT: B 940 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6756 (t-90) REVERT: B 1356 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 1357 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7574 (tt0) REVERT: D 208 TYR cc_start: 0.8069 (p90) cc_final: 0.7842 (p90) outliers start: 70 outliers final: 51 residues processed: 208 average time/residue: 0.1053 time to fit residues: 32.6229 Evaluate side-chains 196 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1647 ILE Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1734 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 850 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1360 PHE Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 424 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.170081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135869 restraints weight = 32926.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139816 restraints weight = 20784.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140241 restraints weight = 16493.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142705 restraints weight = 9865.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142982 restraints weight = 8148.483| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13249 Z= 0.144 Angle : 0.631 12.482 17977 Z= 0.309 Chirality : 0.045 0.398 1996 Planarity : 0.004 0.050 2345 Dihedral : 5.369 51.878 1873 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.63 % Allowed : 19.51 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1644 helix: 0.68 (0.35), residues: 204 sheet: 0.05 (0.21), residues: 596 loop : -0.69 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1613 TYR 0.016 0.001 TYR A 505 PHE 0.013 0.001 PHE D 273 TRP 0.018 0.001 TRP D 364 HIS 0.004 0.001 HIS C1652 Details of bonding type rmsd covalent geometry : bond 0.00348 (13230) covalent geometry : angle 0.62589 (17936) SS BOND : bond 0.00541 ( 16) SS BOND : angle 1.59346 ( 32) hydrogen bonds : bond 0.03062 ( 415) hydrogen bonds : angle 5.52848 ( 1110) link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 2.13388 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6846 (mtm110) REVERT: A 107 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 187 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6812 (ttt-90) REVERT: A 262 MET cc_start: 0.8090 (mpp) cc_final: 0.7813 (mtm) REVERT: A 300 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: C 1533 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6277 (ttm-80) REVERT: B 919 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 940 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6780 (t-90) outliers start: 66 outliers final: 50 residues processed: 203 average time/residue: 0.1054 time to fit residues: 32.1544 Evaluate side-chains 190 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1533 ARG Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1647 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1360 PHE Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 424 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 159 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136629 restraints weight = 22662.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138530 restraints weight = 13288.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139516 restraints weight = 11535.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140331 restraints weight = 9110.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143647 restraints weight = 8599.708| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13249 Z= 0.137 Angle : 0.634 13.131 17977 Z= 0.310 Chirality : 0.045 0.383 1996 Planarity : 0.004 0.051 2345 Dihedral : 5.300 51.846 1873 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.77 % Allowed : 19.65 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1644 helix: 0.76 (0.35), residues: 204 sheet: 0.03 (0.21), residues: 604 loop : -0.64 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1613 TYR 0.020 0.001 TYR D 208 PHE 0.013 0.001 PHE D 273 TRP 0.016 0.001 TRP D 364 HIS 0.004 0.001 HIS C1652 Details of bonding type rmsd covalent geometry : bond 0.00334 (13230) covalent geometry : angle 0.62789 (17936) SS BOND : bond 0.00556 ( 16) SS BOND : angle 1.96664 ( 32) hydrogen bonds : bond 0.02991 ( 415) hydrogen bonds : angle 5.40237 ( 1110) link_NAG-ASN : bond 0.00221 ( 3) link_NAG-ASN : angle 2.04654 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 150 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6880 (mtm110) REVERT: A 107 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 187 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6808 (ttt-90) REVERT: A 262 MET cc_start: 0.8123 (mpp) cc_final: 0.7837 (mtt) REVERT: A 300 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: A 352 MET cc_start: 0.8057 (tpp) cc_final: 0.7791 (tpt) REVERT: C 1501 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8044 (mt) REVERT: C 1534 GLU cc_start: 0.7589 (pm20) cc_final: 0.7265 (pm20) REVERT: B 850 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: B 919 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7253 (t80) REVERT: B 940 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6774 (t-90) REVERT: B 1356 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7075 (mt-10) REVERT: D 208 TYR cc_start: 0.7980 (p90) cc_final: 0.7663 (p90) outliers start: 68 outliers final: 50 residues processed: 204 average time/residue: 0.1034 time to fit residues: 31.1012 Evaluate side-chains 196 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1734 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 850 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1366 ILE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 424 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.169729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135540 restraints weight = 33211.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138229 restraints weight = 20026.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138898 restraints weight = 17571.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141853 restraints weight = 10617.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142132 restraints weight = 8437.734| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13249 Z= 0.149 Angle : 0.641 13.154 17977 Z= 0.315 Chirality : 0.045 0.397 1996 Planarity : 0.004 0.051 2345 Dihedral : 5.331 51.926 1873 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.91 % Allowed : 19.86 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1644 helix: 0.74 (0.35), residues: 204 sheet: 0.00 (0.21), residues: 609 loop : -0.65 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1613 TYR 0.016 0.001 TYR D 208 PHE 0.013 0.001 PHE D 273 TRP 0.015 0.001 TRP D 364 HIS 0.004 0.001 HIS C1652 Details of bonding type rmsd covalent geometry : bond 0.00359 (13230) covalent geometry : angle 0.63533 (17936) SS BOND : bond 0.00558 ( 16) SS BOND : angle 1.85198 ( 32) hydrogen bonds : bond 0.03249 ( 415) hydrogen bonds : angle 5.33225 ( 1110) link_NAG-ASN : bond 0.00190 ( 3) link_NAG-ASN : angle 2.01307 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6841 (mtm110) REVERT: A 107 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: A 167 MET cc_start: 0.8727 (mtt) cc_final: 0.8427 (mtm) REVERT: A 187 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6858 (ttt-90) REVERT: A 262 MET cc_start: 0.8041 (mpp) cc_final: 0.7794 (mtt) REVERT: A 300 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: A 307 ASN cc_start: 0.8436 (t0) cc_final: 0.8188 (t0) REVERT: A 352 MET cc_start: 0.8012 (tpp) cc_final: 0.7772 (tpt) REVERT: A 590 HIS cc_start: 0.7151 (m170) cc_final: 0.6928 (m170) REVERT: C 1501 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8048 (mp) REVERT: C 1534 GLU cc_start: 0.7529 (pm20) cc_final: 0.7081 (pm20) REVERT: B 850 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 919 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 940 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6796 (t-90) REVERT: D 208 TYR cc_start: 0.8029 (p90) cc_final: 0.7737 (p90) outliers start: 70 outliers final: 54 residues processed: 205 average time/residue: 0.1098 time to fit residues: 33.8055 Evaluate side-chains 203 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1523 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1734 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 850 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1360 PHE Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 424 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 137 optimal weight: 0.8980 chunk 117 optimal weight: 0.0070 chunk 54 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136925 restraints weight = 26709.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137287 restraints weight = 16582.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139301 restraints weight = 13388.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140168 restraints weight = 9155.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140853 restraints weight = 8699.486| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13249 Z= 0.123 Angle : 0.639 13.787 17977 Z= 0.313 Chirality : 0.045 0.414 1996 Planarity : 0.004 0.052 2345 Dihedral : 5.179 51.873 1873 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.93 % Allowed : 20.98 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1644 helix: 0.78 (0.36), residues: 204 sheet: 0.03 (0.21), residues: 606 loop : -0.58 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1613 TYR 0.017 0.001 TYR C1737 PHE 0.013 0.001 PHE C1627 TRP 0.015 0.001 TRP D 364 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00294 (13230) covalent geometry : angle 0.63333 (17936) SS BOND : bond 0.00588 ( 16) SS BOND : angle 1.85924 ( 32) hydrogen bonds : bond 0.03124 ( 415) hydrogen bonds : angle 5.21391 ( 1110) link_NAG-ASN : bond 0.00215 ( 3) link_NAG-ASN : angle 1.95146 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6951 (mtm110) REVERT: A 107 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 167 MET cc_start: 0.8711 (mtt) cc_final: 0.8389 (mtm) REVERT: A 262 MET cc_start: 0.8065 (mpp) cc_final: 0.7800 (mtt) REVERT: A 307 ASN cc_start: 0.8482 (t0) cc_final: 0.8230 (t0) REVERT: A 352 MET cc_start: 0.7971 (tpp) cc_final: 0.7686 (tpt) REVERT: C 1501 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 1534 GLU cc_start: 0.7681 (pm20) cc_final: 0.7098 (pm20) REVERT: B 850 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 919 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7202 (t80) REVERT: B 940 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6798 (t-90) REVERT: B 944 LEU cc_start: 0.7995 (pp) cc_final: 0.7757 (tp) REVERT: D 208 TYR cc_start: 0.7960 (p90) cc_final: 0.7715 (p90) outliers start: 56 outliers final: 42 residues processed: 192 average time/residue: 0.1133 time to fit residues: 33.2002 Evaluate side-chains 187 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1734 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 850 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 HIS B 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135684 restraints weight = 34158.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139093 restraints weight = 21757.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140232 restraints weight = 15225.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141824 restraints weight = 10013.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142680 restraints weight = 8882.214| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13249 Z= 0.156 Angle : 0.667 14.046 17977 Z= 0.329 Chirality : 0.046 0.403 1996 Planarity : 0.004 0.052 2345 Dihedral : 5.246 52.111 1873 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.79 % Allowed : 21.47 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1644 helix: 0.73 (0.36), residues: 204 sheet: -0.04 (0.21), residues: 615 loop : -0.61 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 132 TYR 0.015 0.001 TYR A 505 PHE 0.014 0.001 PHE D 121 TRP 0.014 0.001 TRP D 364 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00377 (13230) covalent geometry : angle 0.66132 (17936) SS BOND : bond 0.00556 ( 16) SS BOND : angle 1.92806 ( 32) hydrogen bonds : bond 0.03244 ( 415) hydrogen bonds : angle 5.25083 ( 1110) link_NAG-ASN : bond 0.00204 ( 3) link_NAG-ASN : angle 1.96052 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6853 (mtm110) REVERT: A 107 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 167 MET cc_start: 0.8691 (mtt) cc_final: 0.8406 (mtm) REVERT: A 187 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6172 (ttt-90) REVERT: A 262 MET cc_start: 0.8063 (mpp) cc_final: 0.7811 (mtt) REVERT: A 307 ASN cc_start: 0.8515 (t0) cc_final: 0.8261 (t0) REVERT: A 352 MET cc_start: 0.7951 (tpp) cc_final: 0.7702 (tpt) REVERT: C 1501 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8023 (mp) REVERT: C 1534 GLU cc_start: 0.7531 (pm20) cc_final: 0.7031 (pm20) REVERT: B 850 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 919 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 940 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: B 944 LEU cc_start: 0.7976 (pp) cc_final: 0.7621 (tp) REVERT: B 1345 GLN cc_start: 0.7099 (tt0) cc_final: 0.6863 (tt0) REVERT: B 1356 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7117 (mt-10) REVERT: D 208 TYR cc_start: 0.8013 (p90) cc_final: 0.7800 (p90) outliers start: 54 outliers final: 45 residues processed: 187 average time/residue: 0.1173 time to fit residues: 32.6074 Evaluate side-chains 190 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1734 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 850 GLU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 940 HIS Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1358 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1415 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN D 97 ASN D 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132129 restraints weight = 24399.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132657 restraints weight = 15157.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134588 restraints weight = 13577.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134956 restraints weight = 9114.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135488 restraints weight = 8723.254| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13249 Z= 0.218 Angle : 0.711 14.999 17977 Z= 0.353 Chirality : 0.047 0.369 1996 Planarity : 0.004 0.050 2345 Dihedral : 5.531 52.098 1873 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.07 % Allowed : 21.33 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1644 helix: 0.42 (0.35), residues: 209 sheet: -0.13 (0.21), residues: 620 loop : -0.77 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 895 TYR 0.018 0.002 TYR A 505 PHE 0.016 0.002 PHE C1627 TRP 0.015 0.001 TRP D 364 HIS 0.007 0.001 HIS C1652 Details of bonding type rmsd covalent geometry : bond 0.00526 (13230) covalent geometry : angle 0.70489 (17936) SS BOND : bond 0.00632 ( 16) SS BOND : angle 2.06092 ( 32) hydrogen bonds : bond 0.03484 ( 415) hydrogen bonds : angle 5.51173 ( 1110) link_NAG-ASN : bond 0.00131 ( 3) link_NAG-ASN : angle 2.07714 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.53 seconds wall clock time: 38 minutes 0.20 seconds (2280.20 seconds total)