Starting phenix.real_space_refine on Thu Feb 5 06:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.map" model { file = "/net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qj4_53198/02_2026/9qj4_53198.cif" } resolution = 3.9 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= 0.012 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 81 5.16 5 C 9626 2.51 5 N 2675 2.21 5 O 2871 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s 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: 15254 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: 5427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 695, 5418 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 695, 5418 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 5532 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS D 65 " occ=0.20 ... (16 atoms not shown) pdb=" NZ BLYS D 65 " occ=0.80 Time building chain proxies: 4.35, per 1000 atoms: 0.29 Number of scatterers: 15254 At special positions: 0 Unit cell: (85.272, 130.416, 159.676, 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 81 16.00 Mg 1 11.99 O 2871 8.00 N 2675 7.00 C 9626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, 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=2.04 Simple disulfide: pdb=" SG CYS C1566 " - pdb=" SG CYS B1394 " distance=2.03 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 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=2.03 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 Simple disulfide: pdb=" SG CYS D 463 " - pdb=" SG CYS D 581 " distance=2.03 Simple disulfide: pdb=" SG CYS D 492 " - pdb=" SG CYS D 508 " distance=2.03 Simple disulfide: pdb=" SG CYS D 584 " - pdb=" SG CYS D 600 " distance=2.02 Simple disulfide: pdb=" SG CYS D 638 " - pdb=" SG CYS D 665 " distance=2.03 Simple disulfide: pdb=" SG CYS D 675 " - pdb=" SG CYS D 725 " 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: 0.91 Conformation dependent library (CDL) restraints added in 701.6 milliseconds 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3596 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 34 sheets defined 15.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.630A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.577A 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: 3.703A 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 1720 through 1722 No H-bonds generated for 'chain 'C' and resid 1720 through 1722' Processing helix chain 'C' and resid 1723 through 1740 Processing helix chain 'B' and resid 877 through 881 removed outlier: 4.098A pdb=" N GLY B 880 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 881 " --> pdb=" O ALA B 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 877 through 881' 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: 3.633A pdb=" N PHE D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.597A pdb=" N SER D 313 " --> pdb=" O ASN D 310 " (cutoff:3.500A) removed outlier: 3.664A 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 Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.959A 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 removed outlier: 4.458A pdb=" N LEU D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 451 removed outlier: 3.554A pdb=" N HIS D 451 " --> pdb=" O GLN D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.643A pdb=" N CYS D 508 " --> pdb=" O ALA D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.657A pdb=" N LEU D 517 " --> pdb=" O ASP D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 585 through 592 Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 632 through 640 removed outlier: 3.976A pdb=" N THR D 636 " --> pdb=" O GLY D 632 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER D 637 " --> pdb=" O VAL D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 645 removed outlier: 3.653A pdb=" N GLN D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 675 through 679 Processing helix chain 'D' and resid 755 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 removed outlier: 8.010A 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: 5.940A pdb=" N VAL A 31 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 109 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.829A pdb=" N LEU A 76 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 removed outlier: 7.023A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.057A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.451A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, 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=AA9, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB1, first strand: chain 'A' and resid 417 through 424 Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 476 Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 522 removed outlier: 6.657A pdb=" N ILE A 509 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 518 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR A 507 " --> pdb=" O MET A 518 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ARG A 520 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 505 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB4, 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 818 through 821 Processing sheet with id=AB5, first strand: chain 'C' and resid 1465 through 1474 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 1516 through 1518 removed outlier: 4.522A pdb=" N SER C1553 " --> pdb=" O THR C1489 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C1556 " --> pdb=" O CYS C1566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS C1566 " --> pdb=" O LEU C1556 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1581 through 1584 Processing sheet with id=AB8, first strand: chain 'C' and resid 1625 through 1631 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1625 through 1631 current: chain 'C' and resid 1640 through 1653 removed outlier: 3.509A pdb=" N VAL C1669 " --> pdb=" O ARG C1641 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 774 through 775 Processing sheet with id=AC1, first strand: chain 'B' and resid 833 through 837 removed outlier: 3.571A pdb=" N HIS B 834 " --> pdb=" O TYR B 856 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AC3, first strand: chain 'B' and resid 909 through 910 Processing sheet with id=AC4, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.615A pdb=" N ASN B 975 " --> pdb=" O THR B1383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 957 through 960 removed outlier: 4.285A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B1340 " --> pdb=" O SER B1333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 37 Processing sheet with id=AC7, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC8, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AC9, first strand: chain 'D' and resid 98 through 101 removed outlier: 3.651A pdb=" N ILE D 99 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 116 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.837A pdb=" N ILE D 122 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AD3, first strand: chain 'D' and resid 182 through 184 Processing sheet with id=AD4, first strand: chain 'D' and resid 303 through 304 removed outlier: 3.629A pdb=" N LYS D 303 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 297 " --> pdb=" O LYS D 303 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU D 253 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA D 294 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 255 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE D 296 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 257 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE D 298 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU D 259 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ASP D 407 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS D 369 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR D 409 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE D 371 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE D 411 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU D 373 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 413 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR D 375 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 527 through 533 removed outlier: 6.015A pdb=" N TRP D 529 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP D 524 " --> pdb=" O TRP D 529 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 522 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY D 523 " --> pdb=" O HIS D 481 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N HIS D 481 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 537 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 612 through 618 Processing sheet with id=AD7, first strand: chain 'D' and resid 663 through 666 removed outlier: 5.732A pdb=" N ILE D 750 " --> pdb=" O VAL D 717 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 717 " --> pdb=" O ILE D 750 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN D 693 " --> pdb=" O LEU D 685 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 685 " --> pdb=" O GLN D 693 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1218 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: 3.24 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5097 1.34 - 1.46: 3401 1.46 - 1.58: 6972 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 15589 Sorted by residual: bond pdb=" CG LYS D 378 " pdb=" CD LYS D 378 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS D 378 " pdb=" CG LYS D 378 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB GLU A 190 " pdb=" CG GLU A 190 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CA ASN D 333 " pdb=" CB ASN D 333 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.32e-02 5.74e+03 1.60e+00 bond pdb=" CG ARG D 355 " pdb=" CD ARG D 355 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 ... (remaining 15584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 20740 2.69 - 5.38: 314 5.38 - 8.07: 64 8.07 - 10.76: 10 10.76 - 13.45: 3 Bond angle restraints: 21131 Sorted by residual: angle pdb=" CB MET D 631 " pdb=" CG MET D 631 " pdb=" SD MET D 631 " ideal model delta sigma weight residual 112.70 125.47 -12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB LYS D 378 " pdb=" CG LYS D 378 " pdb=" CD LYS D 378 " ideal model delta sigma weight residual 111.30 120.67 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" CA LEU A 526 " pdb=" CB LEU A 526 " pdb=" CG LEU A 526 " ideal model delta sigma weight residual 116.30 129.75 -13.45 3.50e+00 8.16e-02 1.48e+01 angle pdb=" CB LYS D 443 " pdb=" CG LYS D 443 " pdb=" CD LYS D 443 " ideal model delta sigma weight residual 111.30 120.11 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA GLU B 769 " pdb=" CB GLU B 769 " pdb=" CG GLU B 769 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 ... (remaining 21126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8192 17.93 - 35.86: 1002 35.86 - 53.79: 233 53.79 - 71.72: 57 71.72 - 89.65: 11 Dihedral angle restraints: 9495 sinusoidal: 3901 harmonic: 5594 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 93.00 166.01 -73.01 1 1.00e+01 1.00e-02 6.79e+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 93.00 152.71 -59.71 1 1.00e+01 1.00e-02 4.76e+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 38.98 54.02 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 9492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2096 0.081 - 0.161: 243 0.161 - 0.242: 3 0.242 - 0.323: 0 0.323 - 0.403: 1 Chirality restraints: 2343 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 -2.19 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE D 395 " pdb=" CA ILE D 395 " pdb=" CG1 ILE D 395 " pdb=" CG2 ILE D 395 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 2340 not shown) Planarity restraints: 2766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C1620 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C1621 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C1621 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1621 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 364 " 0.015 2.00e-02 2.50e+03 1.21e-02 3.67e+00 pdb=" CG TRP D 364 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 364 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 364 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 364 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 364 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 364 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 364 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 364 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 364 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 397 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASN D 397 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN D 397 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE D 398 " -0.010 2.00e-02 2.50e+03 ... (remaining 2763 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 20 2.56 - 3.14: 11912 3.14 - 3.73: 23464 3.73 - 4.31: 31519 4.31 - 4.90: 53264 Nonbonded interactions: 120179 Sorted by model distance: nonbonded pdb=" OG SER D 262 " pdb="MG MG D 801 " model vdw 1.972 2.170 nonbonded pdb=" OG SER D 264 " pdb="MG MG D 801 " model vdw 2.191 2.170 nonbonded pdb=" OG1 THR D 337 " pdb="MG MG D 801 " model vdw 2.277 2.170 nonbonded pdb=" N GLU A 209 " pdb=" OE1 GLU A 209 " model vdw 2.441 3.120 nonbonded pdb=" O CYS C1727 " pdb=" OD1 ASN C1731 " model vdw 2.474 3.040 ... (remaining 120174 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=0.20 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: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.580 Find NCS groups from input model: 0.100 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.004 0.067 15613 Z= 0.164 Angle : 0.837 13.445 21182 Z= 0.405 Chirality : 0.047 0.403 2343 Planarity : 0.005 0.062 2763 Dihedral : 16.293 89.651 5836 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.48 % Allowed : 28.57 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.56 (0.19), residues: 1933 helix: 0.23 (0.33), residues: 239 sheet: 0.12 (0.21), residues: 621 loop : -0.77 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 484 TYR 0.011 0.001 TYR A 281 PHE 0.026 0.002 PHE B1360 TRP 0.033 0.002 TRP D 364 HIS 0.013 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00391 (15589) covalent geometry : angle 0.83185 (21131) SS BOND : bond 0.00353 ( 21) SS BOND : angle 1.62688 ( 42) hydrogen bonds : bond 0.21780 ( 461) hydrogen bonds : angle 9.13694 ( 1218) link_NAG-ASN : bond 0.00319 ( 3) link_NAG-ASN : angle 3.57299 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8234 (mm) cc_final: 0.7709 (mm) REVERT: A 259 LEU cc_start: 0.8436 (tp) cc_final: 0.7822 (mm) REVERT: A 270 TYR cc_start: 0.8000 (m-80) cc_final: 0.7554 (m-80) REVERT: A 272 TYR cc_start: 0.8294 (p90) cc_final: 0.7406 (p90) REVERT: A 287 LEU cc_start: 0.8319 (tt) cc_final: 0.8098 (tt) REVERT: C 1473 TRP cc_start: 0.7443 (p90) cc_final: 0.7195 (p90) REVERT: C 1704 ASP cc_start: 0.8240 (p0) cc_final: 0.7911 (p0) REVERT: D 46 LEU cc_start: 0.7946 (tp) cc_final: 0.7236 (pp) REVERT: D 306 MET cc_start: 0.7835 (tpp) cc_final: 0.6857 (tmm) REVERT: D 350 MET cc_start: 0.6194 (ppp) cc_final: 0.5192 (mtt) REVERT: D 360 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6838 (mp0) REVERT: D 386 LYS cc_start: 0.8134 (tmmt) cc_final: 0.7563 (tttp) REVERT: D 443 LYS cc_start: 0.8628 (tppt) cc_final: 0.8062 (tptt) REVERT: D 447 GLN cc_start: 0.9049 (tp40) cc_final: 0.8793 (tp40) REVERT: D 489 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6938 (pt0) REVERT: D 518 TRP cc_start: 0.5195 (m-10) cc_final: 0.4713 (m-10) REVERT: D 670 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5470 (mm-30) REVERT: D 684 PHE cc_start: 0.5918 (p90) cc_final: 0.5502 (p90) REVERT: D 721 LEU cc_start: 0.5911 (tp) cc_final: 0.5422 (mm) REVERT: D 735 LYS cc_start: 0.3816 (OUTLIER) cc_final: 0.2061 (pptt) outliers start: 8 outliers final: 4 residues processed: 200 average time/residue: 0.1170 time to fit residues: 35.5487 Evaluate side-chains 181 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1550 GLN Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 147 GLN A 419 GLN A 422 GLN A 552 HIS ** C1652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.138044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105448 restraints weight = 59144.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107516 restraints weight = 32089.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107639 restraints weight = 29260.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109542 restraints weight = 18721.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110401 restraints weight = 15092.071| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 15613 Z= 0.208 Angle : 0.739 11.967 21182 Z= 0.361 Chirality : 0.047 0.316 2343 Planarity : 0.005 0.046 2763 Dihedral : 5.643 55.522 2194 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.88 % Allowed : 22.20 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.68 (0.19), residues: 1933 helix: 0.39 (0.32), residues: 245 sheet: -0.04 (0.21), residues: 643 loop : -0.89 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1724 TYR 0.012 0.002 TYR A 281 PHE 0.026 0.002 PHE B1360 TRP 0.031 0.002 TRP D 364 HIS 0.006 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00486 (15589) covalent geometry : angle 0.73514 (21131) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.36640 ( 42) hydrogen bonds : bond 0.04079 ( 461) hydrogen bonds : angle 6.60122 ( 1218) link_NAG-ASN : bond 0.00175 ( 3) link_NAG-ASN : angle 3.02948 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 192 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6973 (tm-30) REVERT: A 160 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (t) REVERT: A 373 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7844 (mtmt) REVERT: A 548 TYR cc_start: 0.8016 (m-80) cc_final: 0.7734 (m-80) REVERT: C 1704 ASP cc_start: 0.8073 (p0) cc_final: 0.7724 (p0) REVERT: B 1360 PHE cc_start: 0.2906 (t80) cc_final: 0.2199 (t80) REVERT: D 162 ARG cc_start: 0.8668 (ttp-170) cc_final: 0.8139 (ttt-90) REVERT: D 260 ASP cc_start: 0.6613 (t70) cc_final: 0.6163 (t0) REVERT: D 306 MET cc_start: 0.8075 (tpp) cc_final: 0.7388 (tmm) REVERT: D 320 ILE cc_start: 0.9153 (tp) cc_final: 0.8937 (pt) REVERT: D 386 LYS cc_start: 0.8228 (tmmt) cc_final: 0.7700 (tttp) REVERT: D 443 LYS cc_start: 0.8540 (tppt) cc_final: 0.8062 (tptt) REVERT: D 670 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.5278 (mm-30) REVERT: D 721 LEU cc_start: 0.5562 (tp) cc_final: 0.5255 (mm) REVERT: D 735 LYS cc_start: 0.4226 (OUTLIER) cc_final: 0.2285 (pptt) outliers start: 82 outliers final: 41 residues processed: 262 average time/residue: 0.1200 time to fit residues: 47.8368 Evaluate side-chains 221 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1488 VAL Chi-restraints excluded: chain C residue 1497 LEU 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 1627 PHE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1395 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 76 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS A 147 GLN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1550 GLN C1652 HIS ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103308 restraints weight = 54353.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103493 restraints weight = 27430.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103973 restraints weight = 28327.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105125 restraints weight = 18662.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106360 restraints weight = 15985.898| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 15613 Z= 0.240 Angle : 0.742 10.723 21182 Z= 0.364 Chirality : 0.047 0.271 2343 Planarity : 0.005 0.039 2763 Dihedral : 5.793 56.159 2191 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.30 % Allowed : 20.71 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.93 (0.19), residues: 1933 helix: 0.10 (0.32), residues: 254 sheet: -0.15 (0.20), residues: 652 loop : -1.08 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1622 TYR 0.023 0.002 TYR D 208 PHE 0.021 0.002 PHE B1360 TRP 0.027 0.002 TRP D 420 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00564 (15589) covalent geometry : angle 0.73788 (21131) SS BOND : bond 0.00945 ( 21) SS BOND : angle 1.43213 ( 42) hydrogen bonds : bond 0.04233 ( 461) hydrogen bonds : angle 6.40374 ( 1218) link_NAG-ASN : bond 0.00133 ( 3) link_NAG-ASN : angle 2.87718 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 193 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TRP cc_start: 0.7012 (t60) cc_final: 0.6762 (t60) REVERT: A 131 ASN cc_start: 0.8211 (m-40) cc_final: 0.7803 (p0) REVERT: A 167 MET cc_start: 0.8517 (mtt) cc_final: 0.8232 (mtt) REVERT: A 184 LEU cc_start: 0.8797 (mp) cc_final: 0.8417 (mp) REVERT: A 505 TYR cc_start: 0.6074 (OUTLIER) cc_final: 0.4660 (p90) REVERT: C 1473 TRP cc_start: 0.7611 (p90) cc_final: 0.7272 (p90) REVERT: C 1620 TYR cc_start: 0.7794 (t80) cc_final: 0.7592 (t80) REVERT: C 1704 ASP cc_start: 0.8149 (p0) cc_final: 0.7780 (p0) REVERT: B 761 LEU cc_start: 0.8660 (tp) cc_final: 0.8318 (mp) REVERT: B 1360 PHE cc_start: 0.2794 (t80) cc_final: 0.2457 (t80) REVERT: B 1420 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.5712 (t80) REVERT: D 162 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8061 (ttt-90) REVERT: D 208 TYR cc_start: 0.7182 (p90) cc_final: 0.6863 (p90) REVERT: D 227 MET cc_start: 0.7034 (mmm) cc_final: 0.6230 (mmm) REVERT: D 260 ASP cc_start: 0.6685 (t70) cc_final: 0.6286 (t0) REVERT: D 306 MET cc_start: 0.8079 (tpp) cc_final: 0.7438 (tmm) REVERT: D 360 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7041 (mp0) REVERT: D 386 LYS cc_start: 0.8302 (tmmt) cc_final: 0.7903 (tttp) REVERT: D 408 ILE cc_start: 0.8530 (mp) cc_final: 0.8195 (mt) REVERT: D 684 PHE cc_start: 0.5281 (p90) cc_final: 0.4987 (p90) REVERT: D 721 LEU cc_start: 0.5568 (tp) cc_final: 0.5172 (mm) REVERT: D 735 LYS cc_start: 0.4135 (OUTLIER) cc_final: 0.2214 (pptt) outliers start: 89 outliers final: 53 residues processed: 264 average time/residue: 0.1066 time to fit residues: 44.1736 Evaluate side-chains 236 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 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 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1587 VAL Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1688 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN 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 901 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 167 optimal weight: 0.0770 chunk 181 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN C1550 GLN C1723 GLN B 848 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 611 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.138408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106690 restraints weight = 57026.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107108 restraints weight = 29477.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108192 restraints weight = 24949.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108667 restraints weight = 17590.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110267 restraints weight = 15673.834| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15613 Z= 0.124 Angle : 0.658 12.230 21182 Z= 0.319 Chirality : 0.045 0.291 2343 Planarity : 0.004 0.040 2763 Dihedral : 5.338 56.040 2188 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.75 % Allowed : 22.56 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.73 (0.19), residues: 1933 helix: 0.34 (0.33), residues: 256 sheet: -0.13 (0.21), residues: 645 loop : -0.89 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 578 TYR 0.016 0.001 TYR A 272 PHE 0.018 0.001 PHE B1360 TRP 0.020 0.001 TRP D 364 HIS 0.005 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00292 (15589) covalent geometry : angle 0.65037 (21131) SS BOND : bond 0.00377 ( 21) SS BOND : angle 2.07630 ( 42) hydrogen bonds : bond 0.03222 ( 461) hydrogen bonds : angle 5.92281 ( 1218) link_NAG-ASN : bond 0.00369 ( 3) link_NAG-ASN : angle 2.62328 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8663 (mt) cc_final: 0.8117 (mt) REVERT: A 66 VAL cc_start: 0.8816 (t) cc_final: 0.8564 (p) REVERT: A 107 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 116 TRP cc_start: 0.6928 (t60) cc_final: 0.6661 (t60) REVERT: A 131 ASN cc_start: 0.8133 (m-40) cc_final: 0.7711 (p0) REVERT: A 272 TYR cc_start: 0.8000 (p90) cc_final: 0.7201 (p90) REVERT: A 307 ASN cc_start: 0.7687 (t0) cc_final: 0.7465 (t0) REVERT: A 360 TRP cc_start: 0.6874 (OUTLIER) cc_final: 0.6293 (t60) REVERT: A 505 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.4449 (p90) REVERT: C 1473 TRP cc_start: 0.7570 (p90) cc_final: 0.7292 (p90) REVERT: C 1704 ASP cc_start: 0.8014 (p0) cc_final: 0.7689 (p0) REVERT: C 1716 ARG cc_start: 0.8348 (ppt170) cc_final: 0.8136 (ppt170) REVERT: C 1735 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8617 (tm-30) REVERT: B 761 LEU cc_start: 0.8601 (tp) cc_final: 0.8257 (mp) REVERT: B 934 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7548 (tm-30) REVERT: B 1420 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5573 (t80) REVERT: D 162 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.8079 (ttt-90) REVERT: D 208 TYR cc_start: 0.7157 (p90) cc_final: 0.6740 (p90) REVERT: D 260 ASP cc_start: 0.6496 (t70) cc_final: 0.6097 (t0) REVERT: D 306 MET cc_start: 0.7890 (tpp) cc_final: 0.7208 (tmm) REVERT: D 359 MET cc_start: 0.6274 (tpt) cc_final: 0.5379 (tpt) REVERT: D 360 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6971 (mp0) REVERT: D 386 LYS cc_start: 0.8233 (tmmt) cc_final: 0.7934 (tttp) REVERT: D 441 ASP cc_start: 0.7638 (p0) cc_final: 0.7373 (p0) REVERT: D 443 LYS cc_start: 0.8467 (tppt) cc_final: 0.8042 (tptt) REVERT: D 670 GLU cc_start: 0.6590 (pm20) cc_final: 0.4795 (mm-30) REVERT: D 684 PHE cc_start: 0.5253 (p90) cc_final: 0.4947 (p90) REVERT: D 721 LEU cc_start: 0.5399 (tp) cc_final: 0.5070 (mm) REVERT: D 735 LYS cc_start: 0.4194 (OUTLIER) cc_final: 0.2327 (pptt) outliers start: 63 outliers final: 37 residues processed: 250 average time/residue: 0.1132 time to fit residues: 43.7636 Evaluate side-chains 223 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 101 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 240 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.138925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.106391 restraints weight = 67143.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107943 restraints weight = 37568.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109527 restraints weight = 26394.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110263 restraints weight = 18606.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112362 restraints weight = 16198.510| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15613 Z= 0.120 Angle : 0.641 11.387 21182 Z= 0.309 Chirality : 0.045 0.240 2343 Planarity : 0.005 0.148 2763 Dihedral : 5.204 56.048 2187 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.69 % Allowed : 22.80 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.68 (0.19), residues: 1933 helix: 0.52 (0.33), residues: 255 sheet: -0.12 (0.21), residues: 643 loop : -0.87 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 593 TYR 0.019 0.001 TYR A 548 PHE 0.023 0.001 PHE D 224 TRP 0.018 0.001 TRP D 364 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00284 (15589) covalent geometry : angle 0.63645 (21131) SS BOND : bond 0.00373 ( 21) SS BOND : angle 1.40932 ( 42) hydrogen bonds : bond 0.03080 ( 461) hydrogen bonds : angle 5.71064 ( 1218) link_NAG-ASN : bond 0.00393 ( 3) link_NAG-ASN : angle 2.45077 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8739 (t) cc_final: 0.8480 (p) REVERT: A 107 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 116 TRP cc_start: 0.6948 (t60) cc_final: 0.6703 (t60) REVERT: A 131 ASN cc_start: 0.8176 (m-40) cc_final: 0.7756 (p0) REVERT: A 360 TRP cc_start: 0.6876 (OUTLIER) cc_final: 0.6273 (t60) REVERT: A 505 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.4392 (p90) REVERT: A 509 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8945 (mt) REVERT: C 1473 TRP cc_start: 0.7534 (p90) cc_final: 0.7128 (p90) REVERT: C 1704 ASP cc_start: 0.8059 (p0) cc_final: 0.7727 (p0) REVERT: C 1735 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8609 (tm-30) REVERT: B 761 LEU cc_start: 0.8580 (tp) cc_final: 0.8212 (mp) REVERT: B 934 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7537 (tm-30) REVERT: B 1420 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5568 (t80) REVERT: D 162 ARG cc_start: 0.8576 (ttp-170) cc_final: 0.8063 (ttt-90) REVERT: D 208 TYR cc_start: 0.7241 (p90) cc_final: 0.6821 (p90) REVERT: D 260 ASP cc_start: 0.6471 (t70) cc_final: 0.6096 (t0) REVERT: D 306 MET cc_start: 0.7832 (tpp) cc_final: 0.7166 (tmm) REVERT: D 359 MET cc_start: 0.6258 (tpt) cc_final: 0.5308 (tpt) REVERT: D 360 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6950 (mp0) REVERT: D 386 LYS cc_start: 0.8287 (tmmt) cc_final: 0.8006 (tttp) REVERT: D 441 ASP cc_start: 0.7637 (p0) cc_final: 0.7385 (p0) REVERT: D 443 LYS cc_start: 0.8573 (tppt) cc_final: 0.8216 (tptt) REVERT: D 648 MET cc_start: 0.5319 (ttm) cc_final: 0.4972 (tpp) REVERT: D 670 GLU cc_start: 0.6642 (pm20) cc_final: 0.4847 (mm-30) REVERT: D 721 LEU cc_start: 0.5544 (tp) cc_final: 0.5111 (mm) REVERT: D 735 LYS cc_start: 0.4197 (OUTLIER) cc_final: 0.2329 (pptt) outliers start: 62 outliers final: 41 residues processed: 236 average time/residue: 0.1086 time to fit residues: 40.1310 Evaluate side-chains 221 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1719 ARG Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 181 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 122 optimal weight: 0.0670 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 HIS ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103511 restraints weight = 59841.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105314 restraints weight = 33692.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105750 restraints weight = 28758.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107585 restraints weight = 18771.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107939 restraints weight = 15523.364| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15613 Z= 0.195 Angle : 0.675 11.231 21182 Z= 0.329 Chirality : 0.046 0.327 2343 Planarity : 0.005 0.109 2763 Dihedral : 5.410 57.288 2187 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.64 % Allowed : 21.73 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.80 (0.19), residues: 1933 helix: 0.41 (0.33), residues: 261 sheet: -0.19 (0.20), residues: 645 loop : -0.97 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 48 TYR 0.016 0.002 TYR C1619 PHE 0.017 0.002 PHE A 231 TRP 0.016 0.002 TRP D 364 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00460 (15589) covalent geometry : angle 0.67110 (21131) SS BOND : bond 0.00293 ( 21) SS BOND : angle 1.30297 ( 42) hydrogen bonds : bond 0.03315 ( 461) hydrogen bonds : angle 5.81977 ( 1218) link_NAG-ASN : bond 0.00206 ( 3) link_NAG-ASN : angle 2.41656 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8778 (t) cc_final: 0.8520 (p) REVERT: A 116 TRP cc_start: 0.7041 (t60) cc_final: 0.6785 (t60) REVERT: A 131 ASN cc_start: 0.8222 (m-40) cc_final: 0.7880 (p0) REVERT: A 272 TYR cc_start: 0.8176 (p90) cc_final: 0.7398 (p90) REVERT: A 505 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.4595 (p90) REVERT: A 509 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8909 (mt) REVERT: C 1473 TRP cc_start: 0.7704 (p90) cc_final: 0.7037 (p90) REVERT: C 1704 ASP cc_start: 0.8100 (p0) cc_final: 0.7712 (p0) REVERT: C 1735 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8610 (tm-30) REVERT: B 761 LEU cc_start: 0.8603 (tp) cc_final: 0.8264 (mp) REVERT: B 848 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: B 1420 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5653 (t80) REVERT: D 162 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8172 (ttt-90) REVERT: D 208 TYR cc_start: 0.7525 (p90) cc_final: 0.7259 (p90) REVERT: D 227 MET cc_start: 0.7015 (mmm) cc_final: 0.6708 (tpp) REVERT: D 260 ASP cc_start: 0.6599 (t70) cc_final: 0.6233 (t0) REVERT: D 316 MET cc_start: 0.8851 (tmm) cc_final: 0.8603 (tmm) REVERT: D 386 LYS cc_start: 0.8285 (tmmt) cc_final: 0.7987 (tttp) REVERT: D 441 ASP cc_start: 0.7753 (p0) cc_final: 0.7137 (p0) REVERT: D 461 THR cc_start: 0.8675 (t) cc_final: 0.8400 (p) REVERT: D 648 MET cc_start: 0.5380 (ttm) cc_final: 0.5042 (tpp) REVERT: D 684 PHE cc_start: 0.5189 (p90) cc_final: 0.4898 (p90) REVERT: D 721 LEU cc_start: 0.5515 (tp) cc_final: 0.5004 (mm) REVERT: D 735 LYS cc_start: 0.4363 (OUTLIER) cc_final: 0.2426 (pptt) outliers start: 78 outliers final: 56 residues processed: 238 average time/residue: 0.1115 time to fit residues: 41.8660 Evaluate side-chains 232 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1712 MET Chi-restraints excluded: chain C residue 1718 CYS Chi-restraints excluded: chain C residue 1719 ARG Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 24 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 611 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 = 0.4036 r_free = 0.4036 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.102888 restraints weight = 73118.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104392 restraints weight = 42254.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105293 restraints weight = 32585.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106788 restraints weight = 20648.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107811 restraints weight = 17341.001| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 15613 Z= 0.213 Angle : 0.696 10.849 21182 Z= 0.340 Chirality : 0.046 0.404 2343 Planarity : 0.004 0.076 2763 Dihedral : 5.512 58.037 2187 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.52 % Allowed : 22.02 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.92 (0.19), residues: 1933 helix: 0.45 (0.33), residues: 260 sheet: -0.32 (0.20), residues: 650 loop : -1.05 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 48 TYR 0.018 0.002 TYR C1619 PHE 0.016 0.002 PHE A 219 TRP 0.017 0.002 TRP D 518 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00500 (15589) covalent geometry : angle 0.69190 (21131) SS BOND : bond 0.00314 ( 21) SS BOND : angle 1.52895 ( 42) hydrogen bonds : bond 0.03393 ( 461) hydrogen bonds : angle 5.91479 ( 1218) link_NAG-ASN : bond 0.00211 ( 3) link_NAG-ASN : angle 2.48411 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 175 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8812 (t) cc_final: 0.8562 (p) REVERT: A 131 ASN cc_start: 0.8228 (m-40) cc_final: 0.7975 (p0) REVERT: A 180 ASN cc_start: 0.7738 (p0) cc_final: 0.7356 (p0) REVERT: A 184 LEU cc_start: 0.8761 (mp) cc_final: 0.8520 (mp) REVERT: A 505 TYR cc_start: 0.6357 (OUTLIER) cc_final: 0.4822 (p90) REVERT: A 509 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8942 (mt) REVERT: C 1704 ASP cc_start: 0.8127 (p0) cc_final: 0.7748 (p0) REVERT: C 1735 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 761 LEU cc_start: 0.8630 (tp) cc_final: 0.8344 (mp) REVERT: B 848 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: B 1420 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5694 (t80) REVERT: D 162 ARG cc_start: 0.8536 (ttp-170) cc_final: 0.8164 (ttt-90) REVERT: D 208 TYR cc_start: 0.7724 (p90) cc_final: 0.7404 (p90) REVERT: D 260 ASP cc_start: 0.6512 (t70) cc_final: 0.5923 (t0) REVERT: D 280 MET cc_start: 0.6650 (tmm) cc_final: 0.6360 (tmm) REVERT: D 306 MET cc_start: 0.8097 (tpp) cc_final: 0.7542 (tmm) REVERT: D 316 MET cc_start: 0.8887 (tmm) cc_final: 0.8630 (tmm) REVERT: D 648 MET cc_start: 0.5485 (ttm) cc_final: 0.5117 (tpp) REVERT: D 684 PHE cc_start: 0.5232 (p90) cc_final: 0.4924 (p90) REVERT: D 721 LEU cc_start: 0.5480 (tp) cc_final: 0.4936 (mm) REVERT: D 735 LYS cc_start: 0.4337 (OUTLIER) cc_final: 0.2402 (pptt) outliers start: 76 outliers final: 55 residues processed: 233 average time/residue: 0.1125 time to fit residues: 41.3472 Evaluate side-chains 229 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1712 MET Chi-restraints excluded: chain C residue 1719 ARG Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 24 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 0.0050 chunk 158 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1662 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104533 restraints weight = 64780.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105604 restraints weight = 37085.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106709 restraints weight = 29305.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107820 restraints weight = 19165.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109308 restraints weight = 16591.802| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15613 Z= 0.147 Angle : 0.670 11.023 21182 Z= 0.322 Chirality : 0.046 0.377 2343 Planarity : 0.004 0.074 2763 Dihedral : 5.354 57.452 2187 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.35 % Allowed : 22.68 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.87 (0.19), residues: 1933 helix: 0.54 (0.33), residues: 260 sheet: -0.30 (0.21), residues: 633 loop : -1.01 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1633 TYR 0.017 0.001 TYR C1619 PHE 0.022 0.001 PHE A 654 TRP 0.016 0.001 TRP D 518 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00348 (15589) covalent geometry : angle 0.66572 (21131) SS BOND : bond 0.00255 ( 21) SS BOND : angle 1.41041 ( 42) hydrogen bonds : bond 0.03116 ( 461) hydrogen bonds : angle 5.76637 ( 1218) link_NAG-ASN : bond 0.00331 ( 3) link_NAG-ASN : angle 2.38171 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8798 (t) cc_final: 0.8571 (p) REVERT: A 270 TYR cc_start: 0.8242 (m-80) cc_final: 0.7921 (m-80) REVERT: A 272 TYR cc_start: 0.8189 (p90) cc_final: 0.7327 (p90) REVERT: A 307 ASN cc_start: 0.7844 (t0) cc_final: 0.7513 (t0) REVERT: A 360 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6210 (t60) REVERT: A 505 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.4734 (p90) REVERT: A 509 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8888 (mt) REVERT: C 1473 TRP cc_start: 0.7759 (p90) cc_final: 0.6844 (p90) REVERT: C 1539 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: C 1704 ASP cc_start: 0.8098 (p0) cc_final: 0.7727 (p0) REVERT: C 1735 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 761 LEU cc_start: 0.8590 (tp) cc_final: 0.8314 (mp) REVERT: B 848 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: B 1420 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5735 (t80) REVERT: D 24 CYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5207 (m) REVERT: D 83 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8455 (m) REVERT: D 162 ARG cc_start: 0.8499 (ttp-170) cc_final: 0.8112 (ttt-90) REVERT: D 208 TYR cc_start: 0.7608 (p90) cc_final: 0.7242 (p90) REVERT: D 260 ASP cc_start: 0.6399 (t70) cc_final: 0.5807 (t0) REVERT: D 306 MET cc_start: 0.8018 (tpp) cc_final: 0.7425 (tmm) REVERT: D 316 MET cc_start: 0.8859 (tmm) cc_final: 0.8615 (tmm) REVERT: D 408 ILE cc_start: 0.8511 (mp) cc_final: 0.8149 (mt) REVERT: D 648 MET cc_start: 0.5574 (ttm) cc_final: 0.5182 (tpp) REVERT: D 684 PHE cc_start: 0.5234 (p90) cc_final: 0.4928 (p90) REVERT: D 721 LEU cc_start: 0.5517 (tp) cc_final: 0.4958 (mm) REVERT: D 735 LYS cc_start: 0.4220 (OUTLIER) cc_final: 0.2355 (pptt) outliers start: 73 outliers final: 59 residues processed: 236 average time/residue: 0.1129 time to fit residues: 41.6682 Evaluate side-chains 238 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1539 GLU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1662 ASN Chi-restraints excluded: chain C residue 1712 MET Chi-restraints excluded: chain C residue 1718 CYS Chi-restraints excluded: chain C residue 1719 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 24 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 735 LYS Chi-restraints excluded: chain D residue 766 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 186 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.137051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105148 restraints weight = 63581.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106058 restraints weight = 37422.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.107830 restraints weight = 26794.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108180 restraints weight = 19572.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110367 restraints weight = 16898.753| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15613 Z= 0.132 Angle : 0.663 12.117 21182 Z= 0.317 Chirality : 0.046 0.402 2343 Planarity : 0.004 0.065 2763 Dihedral : 5.256 57.850 2187 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.99 % Allowed : 23.10 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.84 (0.19), residues: 1933 helix: 0.58 (0.33), residues: 261 sheet: -0.28 (0.21), residues: 635 loop : -1.00 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 48 TYR 0.019 0.001 TYR C1619 PHE 0.012 0.001 PHE B1360 TRP 0.016 0.001 TRP D 518 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00317 (15589) covalent geometry : angle 0.66090 (21131) SS BOND : bond 0.00231 ( 21) SS BOND : angle 1.04090 ( 42) hydrogen bonds : bond 0.02988 ( 461) hydrogen bonds : angle 5.64779 ( 1218) link_NAG-ASN : bond 0.00377 ( 3) link_NAG-ASN : angle 2.31933 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8792 (t) cc_final: 0.8576 (p) REVERT: A 76 LEU cc_start: 0.8041 (mm) cc_final: 0.7692 (mm) REVERT: A 131 ASN cc_start: 0.7876 (m-40) cc_final: 0.7281 (p0) REVERT: A 270 TYR cc_start: 0.8236 (m-80) cc_final: 0.7926 (m-80) REVERT: A 272 TYR cc_start: 0.8118 (p90) cc_final: 0.7345 (p90) REVERT: A 307 ASN cc_start: 0.7856 (t0) cc_final: 0.7532 (t0) REVERT: A 360 TRP cc_start: 0.6925 (OUTLIER) cc_final: 0.6214 (t60) REVERT: A 505 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.4771 (p90) REVERT: A 509 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8869 (mt) REVERT: C 1473 TRP cc_start: 0.7756 (p90) cc_final: 0.6799 (p90) REVERT: C 1539 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: C 1704 ASP cc_start: 0.8065 (p0) cc_final: 0.7751 (p0) REVERT: C 1735 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 761 LEU cc_start: 0.8552 (tp) cc_final: 0.8283 (mp) REVERT: B 848 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: B 1420 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.5622 (t80) REVERT: D 24 CYS cc_start: 0.5656 (OUTLIER) cc_final: 0.5450 (m) REVERT: D 83 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8447 (m) REVERT: D 162 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8094 (ttt-90) REVERT: D 208 TYR cc_start: 0.7576 (p90) cc_final: 0.7187 (p90) REVERT: D 260 ASP cc_start: 0.6454 (t70) cc_final: 0.5884 (t0) REVERT: D 284 ILE cc_start: 0.7607 (tt) cc_final: 0.7400 (tt) REVERT: D 306 MET cc_start: 0.8056 (tpp) cc_final: 0.7489 (tmm) REVERT: D 316 MET cc_start: 0.8861 (tmm) cc_final: 0.8629 (tmm) REVERT: D 408 ILE cc_start: 0.8498 (mp) cc_final: 0.8151 (mt) REVERT: D 648 MET cc_start: 0.5616 (ttm) cc_final: 0.5264 (tpp) REVERT: D 684 PHE cc_start: 0.5133 (p90) cc_final: 0.4837 (p90) REVERT: D 721 LEU cc_start: 0.5465 (tp) cc_final: 0.4945 (mm) REVERT: D 735 LYS cc_start: 0.4227 (OUTLIER) cc_final: 0.2406 (pptt) outliers start: 67 outliers final: 49 residues processed: 231 average time/residue: 0.1158 time to fit residues: 42.4225 Evaluate side-chains 232 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1539 GLU Chi-restraints excluded: chain C residue 1549 VAL Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1712 MET Chi-restraints excluded: chain C residue 1718 CYS Chi-restraints excluded: chain C residue 1719 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 24 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 735 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 71 GLN D 331 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.138125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106701 restraints weight = 38266.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108404 restraints weight = 24191.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109011 restraints weight = 19272.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109417 restraints weight = 14806.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109632 restraints weight = 13698.367| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15613 Z= 0.116 Angle : 0.661 11.107 21182 Z= 0.314 Chirality : 0.045 0.404 2343 Planarity : 0.004 0.060 2763 Dihedral : 4.970 55.368 2185 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.39 % Allowed : 23.81 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.77 (0.19), residues: 1933 helix: 0.64 (0.33), residues: 261 sheet: -0.21 (0.21), residues: 636 loop : -0.98 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 48 TYR 0.019 0.001 TYR C1619 PHE 0.015 0.001 PHE D 533 TRP 0.015 0.001 TRP D 518 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00274 (15589) covalent geometry : angle 0.65829 (21131) SS BOND : bond 0.00285 ( 21) SS BOND : angle 1.20479 ( 42) hydrogen bonds : bond 0.02907 ( 461) hydrogen bonds : angle 5.54108 ( 1218) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 2.25802 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3866 Ramachandran restraints generated. 1933 Oldfield, 0 Emsley, 1933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8002 (mm) cc_final: 0.7682 (mm) REVERT: A 131 ASN cc_start: 0.7898 (m-40) cc_final: 0.7324 (p0) REVERT: A 177 MET cc_start: 0.8223 (ptm) cc_final: 0.7887 (ptm) REVERT: A 193 MET cc_start: 0.8074 (mmt) cc_final: 0.7810 (mmt) REVERT: A 270 TYR cc_start: 0.8025 (m-80) cc_final: 0.7694 (m-80) REVERT: A 272 TYR cc_start: 0.8088 (p90) cc_final: 0.7299 (p90) REVERT: A 307 ASN cc_start: 0.7812 (t0) cc_final: 0.7556 (t0) REVERT: A 360 TRP cc_start: 0.6835 (OUTLIER) cc_final: 0.6177 (t60) REVERT: A 505 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4803 (p90) REVERT: A 548 TYR cc_start: 0.8241 (m-80) cc_final: 0.7943 (m-10) REVERT: A 654 PHE cc_start: 0.8343 (t80) cc_final: 0.8103 (t80) REVERT: C 1473 TRP cc_start: 0.7622 (p90) cc_final: 0.6795 (p90) REVERT: C 1539 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6919 (mm-30) REVERT: C 1704 ASP cc_start: 0.8018 (p0) cc_final: 0.7675 (p0) REVERT: C 1735 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 761 LEU cc_start: 0.8524 (tp) cc_final: 0.8232 (mp) REVERT: B 1420 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5607 (t80) REVERT: D 83 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 162 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8092 (ttt-90) REVERT: D 208 TYR cc_start: 0.7518 (p90) cc_final: 0.7104 (p90) REVERT: D 260 ASP cc_start: 0.6446 (t70) cc_final: 0.5897 (t0) REVERT: D 306 MET cc_start: 0.7967 (tpp) cc_final: 0.7440 (tmm) REVERT: D 316 MET cc_start: 0.8861 (tmm) cc_final: 0.8634 (tmm) REVERT: D 408 ILE cc_start: 0.8473 (mp) cc_final: 0.8105 (mt) REVERT: D 648 MET cc_start: 0.5705 (ttm) cc_final: 0.5434 (tpp) REVERT: D 684 PHE cc_start: 0.5062 (p90) cc_final: 0.4799 (p90) REVERT: D 721 LEU cc_start: 0.5284 (tp) cc_final: 0.4826 (mm) REVERT: D 735 LYS cc_start: 0.4306 (OUTLIER) cc_final: 0.2439 (pptt) outliers start: 57 outliers final: 43 residues processed: 223 average time/residue: 0.1080 time to fit residues: 38.4481 Evaluate side-chains 224 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain C residue 1480 LEU Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1539 GLU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1627 PHE Chi-restraints excluded: chain C residue 1718 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 873 GLU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1373 ASN Chi-restraints excluded: chain B residue 1374 SER Chi-restraints excluded: chain B residue 1420 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain D residue 735 LYS Chi-restraints excluded: chain D residue 766 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 118 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105932 restraints weight = 78428.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107914 restraints weight = 43671.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109188 restraints weight = 29993.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110493 restraints weight = 19341.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112308 restraints weight = 16149.570| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15613 Z= 0.135 Angle : 0.675 11.234 21182 Z= 0.320 Chirality : 0.046 0.416 2343 Planarity : 0.004 0.050 2763 Dihedral : 4.988 55.449 2185 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.39 % Allowed : 24.11 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.76 (0.19), residues: 1933 helix: 0.54 (0.33), residues: 261 sheet: -0.20 (0.21), residues: 636 loop : -0.94 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1633 TYR 0.019 0.001 TYR C1619 PHE 0.016 0.001 PHE D 533 TRP 0.015 0.001 TRP D 518 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00324 (15589) covalent geometry : angle 0.67255 (21131) SS BOND : bond 0.00258 ( 21) SS BOND : angle 0.93340 ( 42) hydrogen bonds : bond 0.03046 ( 461) hydrogen bonds : angle 5.58356 ( 1218) link_NAG-ASN : bond 0.00366 ( 3) link_NAG-ASN : angle 2.23654 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.20 seconds wall clock time: 48 minutes 30.30 seconds (2910.30 seconds total)