Starting phenix.real_space_refine on Mon Jul 28 00:02:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6a_38983/07_2025/8y6a_38983.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 Zn 1 6.06 5 S 47 5.16 5 C 6214 2.51 5 N 1618 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9786 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 587, 4783 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560} Conformer: "B" Number of residues, atoms: 587, 4783 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560} bond proxies already assigned to first conformer: 4902 Chain: "B" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Chain: "D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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 Time building chain proxies: 8.37, per 1000 atoms: 0.86 Number of scatterers: 9786 At special positions: 0 Unit cell: (80.75, 96.05, 145.35, 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) Zn 1 29.99 S 47 16.00 O 1906 8.00 N 1618 7.00 C 6214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.02 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 801 " - " ASN A 103 " " NAG A 803 " - " ASN A 546 " " NAG B 601 " - " ASN B 354 " " NAG E 1 " - " ASN A 53 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN A 322 " " NAG H 1 " - " ASN B 343 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 374 " 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 36.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 53 removed outlier: 4.644A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.665A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.846A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.203A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.633A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.970A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.613A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.923A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.759A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.743A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.560A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.133A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.318A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.292A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.659A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.531A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.630A pdb=" N THR B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.450A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.865A pdb=" N SER C 194 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.865A pdb=" N SER C 194 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 191 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 183 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 4.073A pdb=" N TYR C 208 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.081A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.081A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 29 removed outlier: 12.432A pdb=" N CYS D 23 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 11.416A pdb=" N THR D 75 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ALA D 25 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N THR D 73 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N GLN D 27 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP D 71 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 139 removed outlier: 3.593A pdb=" N LEU D 175 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 178 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 153 through 154 396 hydrogen bonds defined for protein. 1081 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: 3.09 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2095 1.33 - 1.45: 2493 1.45 - 1.57: 5383 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 10042 Sorted by residual: bond pdb=" N ASN A 33 " pdb=" CA ASN A 33 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.28e-02 6.10e+03 8.21e+00 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.53e+00 bond pdb=" N TYR C 159 " pdb=" CA TYR C 159 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.41e+00 bond pdb=" N GLN A 24 " pdb=" CA GLN A 24 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.31e+00 bond pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.16e-02 7.43e+03 6.30e+00 ... (remaining 10037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 12928 1.49 - 2.98: 570 2.98 - 4.47: 122 4.47 - 5.96: 21 5.96 - 7.45: 5 Bond angle restraints: 13646 Sorted by residual: angle pdb=" CA PHE A 588 " pdb=" C PHE A 588 " pdb=" O PHE A 588 " ideal model delta sigma weight residual 122.63 116.65 5.98 1.29e+00 6.01e-01 2.15e+01 angle pdb=" O PHE B 342 " pdb=" C PHE B 342 " pdb=" N ASN B 343 " ideal model delta sigma weight residual 122.09 126.46 -4.37 1.08e+00 8.57e-01 1.64e+01 angle pdb=" N PHE A 588 " pdb=" CA PHE A 588 " pdb=" C PHE A 588 " ideal model delta sigma weight residual 109.62 103.59 6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" CA CYS A 498 " pdb=" C CYS A 498 " pdb=" O CYS A 498 " ideal model delta sigma weight residual 121.38 117.21 4.17 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N LYS A 31 " pdb=" CA LYS A 31 " pdb=" C LYS A 31 " ideal model delta sigma weight residual 111.07 107.32 3.75 1.07e+00 8.73e-01 1.23e+01 ... (remaining 13641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 5671 21.26 - 42.53: 370 42.53 - 63.79: 52 63.79 - 85.05: 32 85.05 - 106.31: 14 Dihedral angle restraints: 6139 sinusoidal: 2623 harmonic: 3516 Sorted by residual: dihedral pdb=" CA ALA A 501 " pdb=" C ALA A 501 " pdb=" N SER A 502 " pdb=" CA SER A 502 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -35.96 -50.04 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -135.62 49.62 1 1.00e+01 1.00e-02 3.38e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 1493 0.172 - 0.344: 8 0.344 - 0.516: 0 0.516 - 0.688: 2 0.688 - 0.860: 2 Chirality restraints: 1505 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.98e+01 chirality pdb=" C1 MAN E 4 " pdb=" O3 BMA E 3 " pdb=" C2 MAN E 4 " pdb=" O5 MAN E 4 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.27e+01 ... (remaining 1502 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.194 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" C7 NAG E 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.279 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.152 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" C7 NAG H 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.204 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.148 2.00e-02 2.50e+03 1.22e-01 1.87e+02 pdb=" C7 NAG B 601 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.196 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.020 2.00e-02 2.50e+03 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1094 2.75 - 3.29: 9830 3.29 - 3.82: 16559 3.82 - 4.36: 19254 4.36 - 4.90: 32540 Nonbonded interactions: 79277 Sorted by model distance: nonbonded pdb=" OD1 ASN D 137 " pdb=" N ASN D 138 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 802 " model vdw 2.213 2.230 nonbonded pdb=" CG PRO C 163 " pdb=" NE2 HIS C 214 " model vdw 2.215 3.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG B 346 " pdb=" OD2 ASP B 450 " model vdw 2.229 3.120 ... (remaining 79272 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 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 0.075 10069 Z= 0.228 Angle : 0.812 20.396 13711 Z= 0.434 Chirality : 0.061 0.860 1505 Planarity : 0.008 0.167 1738 Dihedral : 15.694 106.313 3857 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.52 % Favored : 92.98 % Rotamer: Outliers : 0.48 % Allowed : 0.76 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1199 helix: -0.63 (0.25), residues: 409 sheet: -0.76 (0.37), residues: 199 loop : -1.88 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 459 HIS 0.007 0.001 HIS A 374 PHE 0.035 0.001 PHE A 464 TYR 0.021 0.002 TYR B 501 ARG 0.007 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01068 ( 7) link_NAG-ASN : angle 4.92020 ( 21) link_BETA1-4 : bond 0.03722 ( 7) link_BETA1-4 : angle 7.23403 ( 21) link_ALPHA1-3 : bond 0.04529 ( 1) link_ALPHA1-3 : angle 4.31444 ( 3) hydrogen bonds : bond 0.20344 ( 371) hydrogen bonds : angle 8.81809 ( 1081) metal coordination : bond 0.02646 ( 2) SS BOND : bond 0.00451 ( 10) SS BOND : angle 2.08938 ( 20) covalent geometry : bond 0.00390 (10042) covalent geometry : angle 0.73115 (13646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.1196 (OUTLIER) cc_final: -0.0169 (mm110) REVERT: A 31 LYS cc_start: 0.5644 (OUTLIER) cc_final: 0.4484 (tptm) REVERT: A 111 ASP cc_start: 0.9017 (t70) cc_final: 0.8805 (p0) REVERT: A 117 ASN cc_start: 0.7759 (m-40) cc_final: 0.7535 (t0) REVERT: A 179 LEU cc_start: 0.8778 (mm) cc_final: 0.8378 (mm) REVERT: A 196 TYR cc_start: 0.7583 (m-80) cc_final: 0.7170 (m-10) REVERT: A 429 GLN cc_start: 0.8218 (mt0) cc_final: 0.7949 (pp30) REVERT: A 577 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7240 (pttt) REVERT: B 366 SER cc_start: 0.9254 (m) cc_final: 0.8996 (p) REVERT: C 80 TYR cc_start: 0.6027 (m-80) cc_final: 0.5343 (m-80) REVERT: D 162 SER cc_start: 0.7972 (t) cc_final: 0.7699 (m) outliers start: 5 outliers final: 2 residues processed: 272 average time/residue: 1.3385 time to fit residues: 388.7498 Evaluate side-chains 138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 508 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 422 ASN B 474 GLN C 57 ASN C 62 GLN C 65 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 189 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.142247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.117273 restraints weight = 56379.697| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 5.94 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4207 r_free = 0.4207 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10069 Z= 0.188 Angle : 0.863 14.059 13711 Z= 0.429 Chirality : 0.047 0.237 1505 Planarity : 0.005 0.047 1738 Dihedral : 10.450 76.871 1623 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.11 % Favored : 92.56 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1199 helix: -0.70 (0.24), residues: 410 sheet: -0.94 (0.37), residues: 204 loop : -1.86 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 168 HIS 0.009 0.002 HIS C 214 PHE 0.031 0.002 PHE A 523 TYR 0.030 0.002 TYR A 587 ARG 0.007 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 7) link_NAG-ASN : angle 3.14926 ( 21) link_BETA1-4 : bond 0.00896 ( 7) link_BETA1-4 : angle 2.88697 ( 21) link_ALPHA1-3 : bond 0.01503 ( 1) link_ALPHA1-3 : angle 0.74883 ( 3) hydrogen bonds : bond 0.05316 ( 371) hydrogen bonds : angle 6.53608 ( 1081) metal coordination : bond 0.00125 ( 2) SS BOND : bond 0.00820 ( 10) SS BOND : angle 1.93497 ( 20) covalent geometry : bond 0.00428 (10042) covalent geometry : angle 0.84529 (13646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0601 (OUTLIER) cc_final: -0.0722 (mm110) REVERT: A 31 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4618 (tptm) REVERT: A 111 ASP cc_start: 0.9051 (t70) cc_final: 0.8829 (p0) REVERT: A 162 LEU cc_start: 0.9338 (tm) cc_final: 0.9017 (mt) REVERT: A 195 HIS cc_start: 0.7321 (t-90) cc_final: 0.7046 (t70) REVERT: A 196 TYR cc_start: 0.7377 (m-80) cc_final: 0.7167 (m-10) REVERT: A 248 LEU cc_start: 0.6799 (mt) cc_final: 0.6360 (tt) REVERT: A 376 MET cc_start: 0.8865 (mmt) cc_final: 0.8571 (mmt) REVERT: A 429 GLN cc_start: 0.8322 (mt0) cc_final: 0.8080 (pp30) REVERT: B 386 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8971 (tptp) REVERT: C 64 PHE cc_start: 0.7917 (m-80) cc_final: 0.7614 (m-80) REVERT: C 65 GLN cc_start: 0.8583 (mm110) cc_final: 0.8328 (mm-40) REVERT: C 80 TYR cc_start: 0.6096 (m-80) cc_final: 0.5322 (m-80) REVERT: C 105 TRP cc_start: 0.8262 (m-10) cc_final: 0.7954 (m-10) REVERT: C 158 ASP cc_start: 0.8340 (t0) cc_final: 0.7919 (t0) REVERT: C 190 TYR cc_start: 0.8358 (m-80) cc_final: 0.8144 (m-80) REVERT: C 193 SER cc_start: 0.9163 (m) cc_final: 0.8721 (p) outliers start: 24 outliers final: 9 residues processed: 176 average time/residue: 1.0343 time to fit residues: 197.4511 Evaluate side-chains 135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.138457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.113211 restraints weight = 65668.582| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 7.24 r_work: 0.3974 rms_B_bonded: 7.05 restraints_weight: 2.0000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 10069 Z= 0.242 Angle : 0.890 15.469 13711 Z= 0.441 Chirality : 0.048 0.244 1505 Planarity : 0.006 0.051 1738 Dihedral : 8.843 53.036 1620 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.94 % Favored : 91.72 % Rotamer: Outliers : 3.81 % Allowed : 16.76 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.23), residues: 1199 helix: -0.83 (0.24), residues: 398 sheet: -1.09 (0.36), residues: 201 loop : -1.87 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 168 HIS 0.009 0.002 HIS C 214 PHE 0.031 0.002 PHE A 464 TYR 0.037 0.003 TYR A 202 ARG 0.006 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 7) link_NAG-ASN : angle 3.30014 ( 21) link_BETA1-4 : bond 0.00593 ( 7) link_BETA1-4 : angle 2.81138 ( 21) link_ALPHA1-3 : bond 0.01194 ( 1) link_ALPHA1-3 : angle 1.32753 ( 3) hydrogen bonds : bond 0.05709 ( 371) hydrogen bonds : angle 6.49618 ( 1081) metal coordination : bond 0.00343 ( 2) SS BOND : bond 0.00562 ( 10) SS BOND : angle 2.69865 ( 20) covalent geometry : bond 0.00554 (10042) covalent geometry : angle 0.86960 (13646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0871 (OUTLIER) cc_final: -0.0853 (mm-40) REVERT: A 31 LYS cc_start: 0.5424 (OUTLIER) cc_final: 0.5132 (tttp) REVERT: A 111 ASP cc_start: 0.9129 (t70) cc_final: 0.8872 (p0) REVERT: A 162 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 195 HIS cc_start: 0.7038 (t-90) cc_final: 0.6825 (t70) REVERT: A 196 TYR cc_start: 0.7548 (m-80) cc_final: 0.7332 (m-10) REVERT: A 248 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6358 (tt) REVERT: A 376 MET cc_start: 0.9181 (mmt) cc_final: 0.8840 (mmt) REVERT: A 429 GLN cc_start: 0.8357 (mt0) cc_final: 0.8065 (pp30) REVERT: B 386 LYS cc_start: 0.9226 (mtmt) cc_final: 0.9006 (tptp) REVERT: B 421 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.3326 (p90) REVERT: C 65 GLN cc_start: 0.8814 (mm110) cc_final: 0.8522 (mm-40) REVERT: C 80 TYR cc_start: 0.6294 (m-80) cc_final: 0.5370 (m-80) REVERT: C 95 TYR cc_start: 0.6274 (m-10) cc_final: 0.6046 (m-10) REVERT: C 105 TRP cc_start: 0.8704 (m-10) cc_final: 0.8420 (m-10) REVERT: C 158 ASP cc_start: 0.8402 (t0) cc_final: 0.7905 (t0) REVERT: C 193 SER cc_start: 0.9230 (m) cc_final: 0.8605 (p) REVERT: C 210 CYS cc_start: 0.7556 (p) cc_final: 0.6927 (p) outliers start: 40 outliers final: 11 residues processed: 161 average time/residue: 1.3653 time to fit residues: 240.8414 Evaluate side-chains 136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.115933 restraints weight = 65173.100| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 7.55 r_work: 0.4015 rms_B_bonded: 7.17 restraints_weight: 2.0000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10069 Z= 0.161 Angle : 0.831 16.405 13711 Z= 0.406 Chirality : 0.046 0.262 1505 Planarity : 0.005 0.046 1738 Dihedral : 7.629 52.637 1620 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.19 % Favored : 92.56 % Rotamer: Outliers : 3.14 % Allowed : 19.05 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1199 helix: -0.49 (0.25), residues: 397 sheet: -1.08 (0.35), residues: 204 loop : -1.71 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.025 0.002 PHE A 464 TYR 0.022 0.002 TYR A 385 ARG 0.004 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 7) link_NAG-ASN : angle 2.89512 ( 21) link_BETA1-4 : bond 0.00617 ( 7) link_BETA1-4 : angle 2.52408 ( 21) link_ALPHA1-3 : bond 0.01432 ( 1) link_ALPHA1-3 : angle 1.27605 ( 3) hydrogen bonds : bond 0.04899 ( 371) hydrogen bonds : angle 6.09865 ( 1081) metal coordination : bond 0.00118 ( 2) SS BOND : bond 0.00486 ( 10) SS BOND : angle 2.49335 ( 20) covalent geometry : bond 0.00366 (10042) covalent geometry : angle 0.81295 (13646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0858 (OUTLIER) cc_final: -0.1104 (mm110) REVERT: A 31 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4755 (tttp) REVERT: A 111 ASP cc_start: 0.9118 (t70) cc_final: 0.8855 (p0) REVERT: A 162 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9011 (mt) REVERT: A 195 HIS cc_start: 0.6945 (t-90) cc_final: 0.6729 (t70) REVERT: A 196 TYR cc_start: 0.7537 (m-80) cc_final: 0.7279 (m-10) REVERT: A 248 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6281 (tt) REVERT: A 255 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.4299 (m-10) REVERT: A 297 MET cc_start: 0.5636 (mmp) cc_final: 0.4606 (tpp) REVERT: A 376 MET cc_start: 0.9144 (mmt) cc_final: 0.8903 (mmt) REVERT: A 429 GLN cc_start: 0.8359 (mt0) cc_final: 0.8140 (pp30) REVERT: B 335 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 421 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.3505 (p90) REVERT: C 64 PHE cc_start: 0.7760 (m-80) cc_final: 0.7443 (m-80) REVERT: C 73 ASP cc_start: 0.8678 (t0) cc_final: 0.8469 (t0) REVERT: C 80 TYR cc_start: 0.6206 (m-80) cc_final: 0.5355 (m-80) REVERT: C 95 TYR cc_start: 0.6144 (m-10) cc_final: 0.5798 (m-10) REVERT: C 105 TRP cc_start: 0.8644 (m-10) cc_final: 0.7961 (m-10) REVERT: C 158 ASP cc_start: 0.8411 (t0) cc_final: 0.7881 (t0) REVERT: C 166 VAL cc_start: 0.9154 (t) cc_final: 0.8850 (p) REVERT: C 193 SER cc_start: 0.9144 (m) cc_final: 0.8878 (p) REVERT: D 137 ASN cc_start: 0.7871 (t0) cc_final: 0.6983 (p0) outliers start: 33 outliers final: 13 residues processed: 151 average time/residue: 0.9120 time to fit residues: 151.2885 Evaluate side-chains 132 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN D 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.137645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.113193 restraints weight = 53609.562| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 6.23 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 10069 Z= 0.249 Angle : 0.885 15.913 13711 Z= 0.439 Chirality : 0.048 0.283 1505 Planarity : 0.005 0.049 1738 Dihedral : 6.956 55.345 1620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.20 % Favored : 90.55 % Rotamer: Outliers : 3.62 % Allowed : 19.90 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1199 helix: -0.60 (0.25), residues: 393 sheet: -1.28 (0.34), residues: 217 loop : -1.74 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 168 HIS 0.009 0.002 HIS A 401 PHE 0.030 0.002 PHE A 464 TYR 0.031 0.003 TYR A 381 ARG 0.006 0.001 ARG D 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 7) link_NAG-ASN : angle 2.76636 ( 21) link_BETA1-4 : bond 0.00615 ( 7) link_BETA1-4 : angle 2.33112 ( 21) link_ALPHA1-3 : bond 0.01520 ( 1) link_ALPHA1-3 : angle 0.95890 ( 3) hydrogen bonds : bond 0.05701 ( 371) hydrogen bonds : angle 6.11321 ( 1081) metal coordination : bond 0.00402 ( 2) SS BOND : bond 0.00647 ( 10) SS BOND : angle 2.62425 ( 20) covalent geometry : bond 0.00574 (10042) covalent geometry : angle 0.86980 (13646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0302 (OUTLIER) cc_final: -0.1491 (mm-40) REVERT: A 31 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.5024 (tptp) REVERT: A 111 ASP cc_start: 0.8936 (t70) cc_final: 0.8693 (p0) REVERT: A 162 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8965 (mt) REVERT: A 195 HIS cc_start: 0.6875 (t-90) cc_final: 0.6675 (t70) REVERT: A 196 TYR cc_start: 0.7513 (m-80) cc_final: 0.7254 (m-10) REVERT: A 248 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6075 (tt) REVERT: A 255 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.4062 (m-10) REVERT: A 287 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: A 376 MET cc_start: 0.8925 (mmt) cc_final: 0.8566 (mmt) REVERT: A 429 GLN cc_start: 0.8461 (mt0) cc_final: 0.8127 (pp30) REVERT: B 421 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.2788 (p90) REVERT: C 64 PHE cc_start: 0.7991 (m-80) cc_final: 0.7727 (m-80) REVERT: C 73 ASP cc_start: 0.8586 (t0) cc_final: 0.8335 (t0) REVERT: C 80 TYR cc_start: 0.6359 (m-80) cc_final: 0.5488 (m-80) REVERT: C 95 TYR cc_start: 0.6039 (m-10) cc_final: 0.5725 (m-10) REVERT: C 105 TRP cc_start: 0.8144 (m-10) cc_final: 0.7885 (m-10) REVERT: C 158 ASP cc_start: 0.8324 (t0) cc_final: 0.7774 (t0) REVERT: C 193 SER cc_start: 0.9114 (m) cc_final: 0.8451 (p) REVERT: D 137 ASN cc_start: 0.8188 (t0) cc_final: 0.7218 (p0) outliers start: 38 outliers final: 15 residues processed: 148 average time/residue: 0.9738 time to fit residues: 157.7789 Evaluate side-chains 135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 116 ASN ** 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 = 0.4578 r_free = 0.4578 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.114605 restraints weight = 57505.648| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 6.58 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10069 Z= 0.178 Angle : 0.851 17.348 13711 Z= 0.413 Chirality : 0.045 0.286 1505 Planarity : 0.005 0.047 1738 Dihedral : 6.583 59.353 1620 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.02 % Favored : 92.73 % Rotamer: Outliers : 3.71 % Allowed : 20.67 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.23), residues: 1199 helix: -0.47 (0.25), residues: 397 sheet: -1.20 (0.35), residues: 214 loop : -1.66 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.023 0.002 PHE A 464 TYR 0.023 0.002 TYR C 54 ARG 0.007 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 7) link_NAG-ASN : angle 2.56683 ( 21) link_BETA1-4 : bond 0.00658 ( 7) link_BETA1-4 : angle 2.20023 ( 21) link_ALPHA1-3 : bond 0.01112 ( 1) link_ALPHA1-3 : angle 0.83066 ( 3) hydrogen bonds : bond 0.05079 ( 371) hydrogen bonds : angle 5.96032 ( 1081) metal coordination : bond 0.00150 ( 2) SS BOND : bond 0.00566 ( 10) SS BOND : angle 2.33220 ( 20) covalent geometry : bond 0.00409 (10042) covalent geometry : angle 0.83766 (13646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0442 (OUTLIER) cc_final: -0.1490 (mm110) REVERT: A 31 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.5099 (tptp) REVERT: A 111 ASP cc_start: 0.8943 (t70) cc_final: 0.8688 (p0) REVERT: A 162 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9008 (mt) REVERT: A 195 HIS cc_start: 0.6947 (t-90) cc_final: 0.6728 (t70) REVERT: A 196 TYR cc_start: 0.7522 (m-80) cc_final: 0.7237 (m-10) REVERT: A 248 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6051 (tt) REVERT: A 255 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.4133 (m-10) REVERT: A 287 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: A 297 MET cc_start: 0.5524 (mmp) cc_final: 0.4442 (tpp) REVERT: A 376 MET cc_start: 0.8919 (mmt) cc_final: 0.8610 (mmt) REVERT: A 429 GLN cc_start: 0.8471 (mt0) cc_final: 0.8185 (pp30) REVERT: B 421 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.2758 (p90) REVERT: C 64 PHE cc_start: 0.7986 (m-80) cc_final: 0.7672 (m-80) REVERT: C 73 ASP cc_start: 0.8686 (t0) cc_final: 0.8416 (t0) REVERT: C 80 TYR cc_start: 0.6218 (m-80) cc_final: 0.5358 (m-80) REVERT: C 95 TYR cc_start: 0.5997 (m-10) cc_final: 0.5653 (m-10) REVERT: C 105 TRP cc_start: 0.8297 (m-10) cc_final: 0.8063 (m-10) REVERT: C 158 ASP cc_start: 0.8343 (t0) cc_final: 0.7792 (t0) REVERT: C 193 SER cc_start: 0.9066 (m) cc_final: 0.8836 (p) REVERT: D 137 ASN cc_start: 0.8200 (t0) cc_final: 0.7265 (p0) outliers start: 39 outliers final: 17 residues processed: 149 average time/residue: 0.9973 time to fit residues: 162.0876 Evaluate side-chains 138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 111 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 116 ASN ** 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 = 0.4599 r_free = 0.4599 target = 0.141207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.118608 restraints weight = 34926.030| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 5.15 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10069 Z= 0.156 Angle : 0.829 17.167 13711 Z= 0.403 Chirality : 0.045 0.269 1505 Planarity : 0.005 0.047 1738 Dihedral : 6.165 57.607 1620 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Rotamer: Outliers : 2.57 % Allowed : 22.19 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1199 helix: -0.27 (0.25), residues: 396 sheet: -1.04 (0.34), residues: 221 loop : -1.62 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 163 HIS 0.005 0.001 HIS C 214 PHE 0.023 0.002 PHE D 209 TYR 0.028 0.002 TYR C 27 ARG 0.009 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 7) link_NAG-ASN : angle 2.38101 ( 21) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 2.09076 ( 21) link_ALPHA1-3 : bond 0.01353 ( 1) link_ALPHA1-3 : angle 1.03195 ( 3) hydrogen bonds : bond 0.04799 ( 371) hydrogen bonds : angle 5.76360 ( 1081) metal coordination : bond 0.00108 ( 2) SS BOND : bond 0.00826 ( 10) SS BOND : angle 2.19619 ( 20) covalent geometry : bond 0.00352 (10042) covalent geometry : angle 0.81687 (13646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0162 (OUTLIER) cc_final: -0.1485 (mm110) REVERT: A 111 ASP cc_start: 0.8851 (t70) cc_final: 0.8630 (p0) REVERT: A 162 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8975 (mt) REVERT: A 195 HIS cc_start: 0.6795 (t-90) cc_final: 0.6588 (t70) REVERT: A 196 TYR cc_start: 0.7416 (m-80) cc_final: 0.7167 (m-10) REVERT: A 248 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5930 (tt) REVERT: A 255 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.4317 (m-10) REVERT: A 376 MET cc_start: 0.8900 (mmt) cc_final: 0.8652 (mmt) REVERT: A 429 GLN cc_start: 0.8283 (mt0) cc_final: 0.8080 (pp30) REVERT: B 421 TYR cc_start: 0.5627 (OUTLIER) cc_final: 0.2889 (p90) REVERT: C 43 GLN cc_start: 0.8648 (mt0) cc_final: 0.8130 (pt0) REVERT: C 64 PHE cc_start: 0.7929 (m-80) cc_final: 0.7598 (m-80) REVERT: C 73 ASP cc_start: 0.8717 (t0) cc_final: 0.8448 (t0) REVERT: C 80 TYR cc_start: 0.6158 (m-80) cc_final: 0.5284 (m-80) REVERT: C 95 TYR cc_start: 0.6022 (m-10) cc_final: 0.5768 (m-10) REVERT: C 105 TRP cc_start: 0.8257 (m-10) cc_final: 0.7979 (m-10) REVERT: C 158 ASP cc_start: 0.8282 (t0) cc_final: 0.7564 (p0) REVERT: C 193 SER cc_start: 0.9088 (m) cc_final: 0.8684 (p) REVERT: D 137 ASN cc_start: 0.8155 (t0) cc_final: 0.7222 (p0) outliers start: 27 outliers final: 15 residues processed: 147 average time/residue: 0.9889 time to fit residues: 158.5206 Evaluate side-chains 133 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 116 ASN ** 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 = 0.4550 r_free = 0.4550 target = 0.138641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.114209 restraints weight = 63333.554| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 6.66 r_work: 0.4043 rms_B_bonded: 6.61 restraints_weight: 2.0000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10069 Z= 0.162 Angle : 0.845 17.450 13711 Z= 0.413 Chirality : 0.045 0.252 1505 Planarity : 0.005 0.055 1738 Dihedral : 5.777 37.203 1616 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.19 % Favored : 92.56 % Rotamer: Outliers : 2.19 % Allowed : 23.33 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.24), residues: 1199 helix: -0.18 (0.25), residues: 398 sheet: -0.96 (0.35), residues: 215 loop : -1.64 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 163 HIS 0.004 0.001 HIS C 214 PHE 0.021 0.001 PHE A 464 TYR 0.025 0.002 TYR C 54 ARG 0.013 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 7) link_NAG-ASN : angle 2.31726 ( 21) link_BETA1-4 : bond 0.00541 ( 7) link_BETA1-4 : angle 2.00462 ( 21) link_ALPHA1-3 : bond 0.01268 ( 1) link_ALPHA1-3 : angle 1.18160 ( 3) hydrogen bonds : bond 0.04852 ( 371) hydrogen bonds : angle 5.71358 ( 1081) metal coordination : bond 0.00164 ( 2) SS BOND : bond 0.00775 ( 10) SS BOND : angle 1.96131 ( 20) covalent geometry : bond 0.00369 (10042) covalent geometry : angle 0.83502 (13646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0846 (OUTLIER) cc_final: -0.0970 (mm-40) REVERT: A 111 ASP cc_start: 0.9002 (t70) cc_final: 0.8730 (p0) REVERT: A 162 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8991 (mt) REVERT: A 195 HIS cc_start: 0.6768 (t-90) cc_final: 0.6555 (t70) REVERT: A 196 TYR cc_start: 0.7409 (m-80) cc_final: 0.7166 (m-10) REVERT: A 255 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.4593 (m-10) REVERT: A 429 GLN cc_start: 0.8296 (mt0) cc_final: 0.8065 (pp30) REVERT: B 421 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.3376 (p90) REVERT: C 43 GLN cc_start: 0.8783 (mt0) cc_final: 0.8253 (mp10) REVERT: C 64 PHE cc_start: 0.7710 (m-80) cc_final: 0.7407 (m-80) REVERT: C 73 ASP cc_start: 0.8809 (t0) cc_final: 0.8510 (t0) REVERT: C 80 TYR cc_start: 0.6224 (m-80) cc_final: 0.5375 (m-80) REVERT: C 95 TYR cc_start: 0.6335 (m-10) cc_final: 0.5962 (m-10) REVERT: C 105 TRP cc_start: 0.8531 (m-10) cc_final: 0.8200 (m-10) REVERT: C 158 ASP cc_start: 0.8346 (t0) cc_final: 0.7563 (p0) REVERT: C 193 SER cc_start: 0.9158 (m) cc_final: 0.8755 (p) REVERT: D 90 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: D 137 ASN cc_start: 0.8169 (t0) cc_final: 0.7239 (p0) REVERT: D 209 PHE cc_start: 0.7135 (t80) cc_final: 0.6845 (t80) outliers start: 23 outliers final: 13 residues processed: 139 average time/residue: 1.0199 time to fit residues: 154.7337 Evaluate side-chains 130 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.0010 chunk 111 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN A 277 ASN C 62 GLN ** D 158 ASN ** 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 = 0.4613 r_free = 0.4613 target = 0.141691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.116023 restraints weight = 76070.413| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 7.16 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10069 Z= 0.155 Angle : 0.844 17.595 13711 Z= 0.410 Chirality : 0.045 0.252 1505 Planarity : 0.005 0.077 1738 Dihedral : 5.663 41.268 1616 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.53 % Favored : 92.31 % Rotamer: Outliers : 2.29 % Allowed : 23.90 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1199 helix: -0.13 (0.25), residues: 399 sheet: -0.94 (0.34), residues: 222 loop : -1.58 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.001 PHE A 464 TYR 0.026 0.002 TYR C 27 ARG 0.021 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 2.10080 ( 21) link_BETA1-4 : bond 0.00510 ( 7) link_BETA1-4 : angle 1.94370 ( 21) link_ALPHA1-3 : bond 0.01166 ( 1) link_ALPHA1-3 : angle 1.27600 ( 3) hydrogen bonds : bond 0.04737 ( 371) hydrogen bonds : angle 5.65968 ( 1081) metal coordination : bond 0.00157 ( 2) SS BOND : bond 0.00601 ( 10) SS BOND : angle 1.93050 ( 20) covalent geometry : bond 0.00352 (10042) covalent geometry : angle 0.83552 (13646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0404 (OUTLIER) cc_final: -0.1097 (mm-40) REVERT: A 111 ASP cc_start: 0.8931 (t70) cc_final: 0.8668 (p0) REVERT: A 162 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8989 (pp) REVERT: A 195 HIS cc_start: 0.6945 (t-90) cc_final: 0.6715 (t70) REVERT: A 196 TYR cc_start: 0.7387 (m-80) cc_final: 0.7123 (m-10) REVERT: A 376 MET cc_start: 0.8835 (mmt) cc_final: 0.8595 (mmt) REVERT: A 429 GLN cc_start: 0.8386 (mt0) cc_final: 0.8134 (pp30) REVERT: B 335 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8289 (tm) REVERT: B 421 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.2671 (p90) REVERT: C 43 GLN cc_start: 0.8851 (mt0) cc_final: 0.8330 (mp10) REVERT: C 64 PHE cc_start: 0.7859 (m-80) cc_final: 0.7574 (m-80) REVERT: C 73 ASP cc_start: 0.8700 (t0) cc_final: 0.8423 (t0) REVERT: C 80 TYR cc_start: 0.6137 (m-80) cc_final: 0.5268 (m-80) REVERT: C 95 TYR cc_start: 0.6174 (m-10) cc_final: 0.5835 (m-10) REVERT: C 105 TRP cc_start: 0.8263 (m-10) cc_final: 0.7963 (m-10) REVERT: C 122 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8583 (tm) REVERT: C 158 ASP cc_start: 0.8418 (t0) cc_final: 0.7630 (p0) REVERT: C 193 SER cc_start: 0.9127 (m) cc_final: 0.8707 (p) REVERT: D 137 ASN cc_start: 0.8168 (t0) cc_final: 0.7290 (p0) REVERT: D 209 PHE cc_start: 0.7245 (t80) cc_final: 0.6988 (t80) outliers start: 24 outliers final: 12 residues processed: 135 average time/residue: 1.0134 time to fit residues: 150.0147 Evaluate side-chains 129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.0030 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** 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 = 0.4640 r_free = 0.4640 target = 0.142748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.118479 restraints weight = 50907.643| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 5.69 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4238 r_free = 0.4238 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4238 r_free = 0.4238 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10069 Z= 0.150 Angle : 0.864 19.894 13711 Z= 0.417 Chirality : 0.045 0.268 1505 Planarity : 0.005 0.102 1738 Dihedral : 5.609 43.179 1616 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.02 % Favored : 92.81 % Rotamer: Outliers : 2.00 % Allowed : 24.95 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1199 helix: -0.05 (0.26), residues: 398 sheet: -0.94 (0.35), residues: 218 loop : -1.55 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.001 PHE A 464 TYR 0.025 0.002 TYR C 54 ARG 0.025 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 2.06194 ( 21) link_BETA1-4 : bond 0.00553 ( 7) link_BETA1-4 : angle 1.92002 ( 21) link_ALPHA1-3 : bond 0.01090 ( 1) link_ALPHA1-3 : angle 1.34856 ( 3) hydrogen bonds : bond 0.04589 ( 371) hydrogen bonds : angle 5.63493 ( 1081) metal coordination : bond 0.00122 ( 2) SS BOND : bond 0.00589 ( 10) SS BOND : angle 1.76417 ( 20) covalent geometry : bond 0.00338 (10042) covalent geometry : angle 0.85588 (13646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0447 (OUTLIER) cc_final: -0.1039 (mm-40) REVERT: A 111 ASP cc_start: 0.8888 (t70) cc_final: 0.8634 (p0) REVERT: A 162 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9056 (mt) REVERT: A 195 HIS cc_start: 0.6915 (t-90) cc_final: 0.6695 (t70) REVERT: A 196 TYR cc_start: 0.7298 (m-80) cc_final: 0.7039 (m-10) REVERT: A 334 THR cc_start: 0.8672 (m) cc_final: 0.8465 (p) REVERT: A 376 MET cc_start: 0.8713 (mmt) cc_final: 0.8330 (mmt) REVERT: B 335 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8253 (tm) REVERT: B 421 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.2601 (p90) REVERT: C 43 GLN cc_start: 0.8764 (mt0) cc_final: 0.8209 (mp10) REVERT: C 64 PHE cc_start: 0.7674 (m-80) cc_final: 0.7361 (m-80) REVERT: C 73 ASP cc_start: 0.8669 (t0) cc_final: 0.8404 (t0) REVERT: C 80 TYR cc_start: 0.6181 (m-80) cc_final: 0.5312 (m-80) REVERT: C 95 TYR cc_start: 0.6091 (m-10) cc_final: 0.5807 (m-10) REVERT: C 105 TRP cc_start: 0.8212 (m-10) cc_final: 0.7847 (m-10) REVERT: C 122 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8563 (tm) REVERT: C 158 ASP cc_start: 0.8363 (t0) cc_final: 0.7592 (p0) REVERT: C 193 SER cc_start: 0.9059 (m) cc_final: 0.8647 (p) REVERT: C 225 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7632 (p) REVERT: D 90 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: D 137 ASN cc_start: 0.8179 (t0) cc_final: 0.7287 (p0) REVERT: D 209 PHE cc_start: 0.7016 (t80) cc_final: 0.6734 (t80) outliers start: 21 outliers final: 9 residues processed: 141 average time/residue: 0.9422 time to fit residues: 145.5909 Evaluate side-chains 127 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** 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 = 0.4608 r_free = 0.4608 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.117652 restraints weight = 41013.807| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 4.96 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10069 Z= 0.175 Angle : 0.880 16.882 13711 Z= 0.427 Chirality : 0.046 0.228 1505 Planarity : 0.006 0.123 1738 Dihedral : 5.666 42.412 1616 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.97 % Rotamer: Outliers : 1.90 % Allowed : 25.33 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1199 helix: -0.04 (0.26), residues: 395 sheet: -0.91 (0.35), residues: 218 loop : -1.50 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.021 0.001 PHE A 464 TYR 0.023 0.002 TYR A 127 ARG 0.030 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 7) link_NAG-ASN : angle 2.01333 ( 21) link_BETA1-4 : bond 0.00539 ( 7) link_BETA1-4 : angle 1.90400 ( 21) link_ALPHA1-3 : bond 0.01099 ( 1) link_ALPHA1-3 : angle 1.38430 ( 3) hydrogen bonds : bond 0.04905 ( 371) hydrogen bonds : angle 5.63098 ( 1081) metal coordination : bond 0.00196 ( 2) SS BOND : bond 0.00608 ( 10) SS BOND : angle 1.92078 ( 20) covalent geometry : bond 0.00403 (10042) covalent geometry : angle 0.87223 (13646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10614.24 seconds wall clock time: 187 minutes 30.04 seconds (11250.04 seconds total)