Starting phenix.real_space_refine on Tue May 13 07:09:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6a_38983/05_2025/8y6a_38983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6a_38983/05_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_38983/05_2025/8y6a_38983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6a_38983/05_2025/8y6a_38983.map" model { file = "/net/cci-nas-00/data/ceres_data/8y6a_38983/05_2025/8y6a_38983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6a_38983/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.84, per 1000 atoms: 0.80 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: 2.50 Conformation dependent library (CDL) restraints added in 1.6 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: 1.00 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: 2.95 Time building geometry restraints manager: 2.89 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: 1.350 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.420 Find NCS groups from input model: 0.130 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- 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 : 1.206 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: 1.2102 time to fit residues: 352.3483 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 : 1.088 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.117276 restraints weight = 56379.675| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 5.94 r_work (final): 0.4212 ------------------------------------------------------------------------------- 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: 0.6553 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 : 1.190 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: 0.0605 (OUTLIER) cc_final: -0.0718 (mm110) REVERT: A 31 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4623 (tptm) REVERT: A 111 ASP cc_start: 0.9048 (t70) cc_final: 0.8828 (p0) REVERT: A 162 LEU cc_start: 0.9335 (tm) cc_final: 0.9014 (mt) REVERT: A 195 HIS cc_start: 0.7320 (t-90) cc_final: 0.7045 (t70) REVERT: A 196 TYR cc_start: 0.7376 (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: 0.8862 (mmt) cc_final: 0.8568 (mmt) REVERT: A 429 GLN cc_start: 0.8310 (mt0) cc_final: 0.8077 (pp30) REVERT: B 386 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8970 (tptp) REVERT: C 64 PHE cc_start: 0.7910 (m-80) cc_final: 0.7607 (m-80) REVERT: C 65 GLN cc_start: 0.8572 (mm110) cc_final: 0.8321 (mm-40) REVERT: C 80 TYR cc_start: 0.6100 (m-80) cc_final: 0.5324 (m-80) REVERT: C 105 TRP cc_start: 0.8262 (m-10) cc_final: 0.7954 (m-10) REVERT: C 158 ASP cc_start: 0.8348 (t0) cc_final: 0.7928 (t0) REVERT: C 190 TYR cc_start: 0.8367 (m-80) cc_final: 0.8150 (m-80) REVERT: C 193 SER cc_start: 0.9165 (m) cc_final: 0.8722 (p) outliers start: 24 outliers final: 9 residues processed: 176 average time/residue: 1.0448 time to fit residues: 199.7149 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 : 0.994 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 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: 7.9990 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 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 = 0.4619 r_free = 0.4619 target = 0.141592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.116629 restraints weight = 65686.019| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 7.17 r_work: 0.4056 rms_B_bonded: 6.91 restraints_weight: 2.0000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3497 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= 0.171 Angle : 0.832 15.884 13711 Z= 0.409 Chirality : 0.046 0.242 1505 Planarity : 0.005 0.051 1738 Dihedral : 8.697 54.749 1620 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 3.24 % Allowed : 16.67 % Favored : 80.10 % 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: -0.61 (0.24), residues: 402 sheet: -1.07 (0.36), residues: 201 loop : -1.83 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 163 HIS 0.009 0.001 HIS C 214 PHE 0.025 0.002 PHE A 464 TYR 0.046 0.002 TYR A 202 ARG 0.007 0.001 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 7) link_NAG-ASN : angle 3.13928 ( 21) link_BETA1-4 : bond 0.00495 ( 7) link_BETA1-4 : angle 2.84066 ( 21) link_ALPHA1-3 : bond 0.01299 ( 1) link_ALPHA1-3 : angle 1.31559 ( 3) hydrogen bonds : bond 0.05033 ( 371) hydrogen bonds : angle 6.31135 ( 1081) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00518 ( 10) SS BOND : angle 2.19428 ( 20) covalent geometry : bond 0.00384 (10042) covalent geometry : angle 0.81274 (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 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.977 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: 0.0969 (OUTLIER) cc_final: -0.0590 (mm-40) REVERT: A 31 LYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4731 (tttp) REVERT: A 111 ASP cc_start: 0.9114 (t70) cc_final: 0.8862 (p0) REVERT: A 162 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9061 (mt) REVERT: A 195 HIS cc_start: 0.7017 (t-90) cc_final: 0.6777 (t70) REVERT: A 196 TYR cc_start: 0.7512 (m-80) cc_final: 0.7267 (m-10) REVERT: A 248 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6351 (tt) REVERT: A 376 MET cc_start: 0.9143 (mmt) cc_final: 0.8870 (mmt) REVERT: A 429 GLN cc_start: 0.8345 (mt0) cc_final: 0.8126 (pp30) REVERT: B 335 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 386 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8967 (tptp) REVERT: B 421 TYR cc_start: 0.5795 (OUTLIER) cc_final: 0.3485 (p90) REVERT: C 27 TYR cc_start: 0.3239 (p90) cc_final: 0.2920 (p90) REVERT: C 64 PHE cc_start: 0.7777 (m-80) cc_final: 0.7404 (m-80) REVERT: C 65 GLN cc_start: 0.8735 (mm110) cc_final: 0.8454 (mm-40) REVERT: C 80 TYR cc_start: 0.6171 (m-80) cc_final: 0.5277 (m-80) REVERT: C 95 TYR cc_start: 0.6142 (m-10) cc_final: 0.5773 (m-10) REVERT: C 105 TRP cc_start: 0.8551 (m-10) cc_final: 0.8271 (m-10) REVERT: C 158 ASP cc_start: 0.8382 (t0) cc_final: 0.7882 (t0) REVERT: C 166 VAL cc_start: 0.9195 (t) cc_final: 0.8919 (p) REVERT: C 193 SER cc_start: 0.9217 (m) cc_final: 0.8566 (p) REVERT: D 137 ASN cc_start: 0.7702 (t0) cc_final: 0.6753 (p0) outliers start: 34 outliers final: 11 residues processed: 154 average time/residue: 1.0068 time to fit residues: 169.4878 Evaluate side-chains 130 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 335 LEU 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 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 101 GLN ** 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 = 0.4619 r_free = 0.4619 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.116289 restraints weight = 65349.116| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 7.48 r_work: 0.4021 rms_B_bonded: 7.14 restraints_weight: 2.0000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 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 = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3852 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= 0.171 Angle : 0.820 17.324 13711 Z= 0.401 Chirality : 0.046 0.282 1505 Planarity : 0.005 0.046 1738 Dihedral : 7.238 46.680 1620 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.86 % Favored : 91.89 % Rotamer: Outliers : 3.52 % Allowed : 18.19 % Favored : 78.29 % 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: -1.77 (0.23), residues: 1199 helix: -0.39 (0.25), residues: 398 sheet: -1.10 (0.35), residues: 210 loop : -1.73 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.026 0.002 PHE A 464 TYR 0.020 0.002 TYR B 365 ARG 0.005 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 7) link_NAG-ASN : angle 2.90926 ( 21) link_BETA1-4 : bond 0.00618 ( 7) link_BETA1-4 : angle 2.63193 ( 21) link_ALPHA1-3 : bond 0.01331 ( 1) link_ALPHA1-3 : angle 1.33013 ( 3) hydrogen bonds : bond 0.04955 ( 371) hydrogen bonds : angle 6.03767 ( 1081) metal coordination : bond 0.00178 ( 2) SS BOND : bond 0.00616 ( 10) SS BOND : angle 2.53673 ( 20) covalent geometry : bond 0.00389 (10042) covalent geometry : angle 0.80109 (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 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.996 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: 0.0912 (OUTLIER) cc_final: -0.0749 (mm-40) REVERT: A 31 LYS cc_start: 0.5186 (OUTLIER) cc_final: 0.4756 (tttp) REVERT: A 111 ASP cc_start: 0.9089 (t70) cc_final: 0.8861 (p0) REVERT: A 162 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9018 (mt) REVERT: A 195 HIS cc_start: 0.6940 (t-90) cc_final: 0.6697 (t70) REVERT: A 196 TYR cc_start: 0.7587 (m-80) cc_final: 0.7291 (m-10) REVERT: A 248 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6301 (tt) REVERT: A 255 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.4402 (m-10) REVERT: A 297 MET cc_start: 0.5568 (mmp) cc_final: 0.4482 (tpp) REVERT: A 429 GLN cc_start: 0.8429 (mt0) cc_final: 0.8140 (pp30) REVERT: B 421 TYR cc_start: 0.5855 (OUTLIER) cc_final: 0.3564 (p90) REVERT: C 64 PHE cc_start: 0.7773 (m-80) cc_final: 0.7362 (m-80) REVERT: C 80 TYR cc_start: 0.6203 (m-80) cc_final: 0.5348 (m-80) REVERT: C 95 TYR cc_start: 0.6128 (m-10) cc_final: 0.5924 (m-10) REVERT: C 105 TRP cc_start: 0.8586 (m-10) cc_final: 0.7940 (m-10) REVERT: C 158 ASP cc_start: 0.8408 (t0) cc_final: 0.7870 (t0) REVERT: C 193 SER cc_start: 0.9122 (m) cc_final: 0.8813 (p) REVERT: D 137 ASN cc_start: 0.7836 (t0) cc_final: 0.6907 (p0) outliers start: 37 outliers final: 17 residues processed: 151 average time/residue: 0.8620 time to fit residues: 142.8742 Evaluate side-chains 134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 603 PHE 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 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 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: 0.9980 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.0000 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- 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** 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 = 0.4635 r_free = 0.4635 target = 0.142707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.118219 restraints weight = 53784.663| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 5.87 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 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 = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10069 Z= 0.146 Angle : 0.793 17.495 13711 Z= 0.386 Chirality : 0.045 0.250 1505 Planarity : 0.005 0.049 1738 Dihedral : 6.266 44.477 1620 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.36 % Favored : 92.39 % Rotamer: Outliers : 2.57 % Allowed : 18.95 % Favored : 78.48 % 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: -1.57 (0.24), residues: 1199 helix: -0.17 (0.25), residues: 396 sheet: -1.02 (0.34), residues: 207 loop : -1.64 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.021 0.001 PHE A 464 TYR 0.026 0.002 TYR C 54 ARG 0.005 0.000 ARG D 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 2.64647 ( 21) link_BETA1-4 : bond 0.00533 ( 7) link_BETA1-4 : angle 2.41966 ( 21) link_ALPHA1-3 : bond 0.01426 ( 1) link_ALPHA1-3 : angle 1.54777 ( 3) hydrogen bonds : bond 0.04672 ( 371) hydrogen bonds : angle 5.85659 ( 1081) metal coordination : bond 0.00160 ( 2) SS BOND : bond 0.00518 ( 10) SS BOND : angle 2.38973 ( 20) covalent geometry : bond 0.00332 (10042) covalent geometry : angle 0.77637 (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 151 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.091 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: 0.0214 (OUTLIER) cc_final: -0.1215 (mm110) REVERT: A 162 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8940 (pp) REVERT: A 248 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6024 (tt) REVERT: A 297 MET cc_start: 0.5585 (mmp) cc_final: 0.4550 (tpp) REVERT: A 376 MET cc_start: 0.8746 (mmt) cc_final: 0.8398 (mmt) REVERT: A 429 GLN cc_start: 0.8333 (mt0) cc_final: 0.8090 (pp30) REVERT: B 335 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 421 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.2889 (p90) REVERT: C 80 TYR cc_start: 0.6090 (m-80) cc_final: 0.5330 (m-80) REVERT: C 158 ASP cc_start: 0.8326 (t0) cc_final: 0.7540 (p0) REVERT: C 193 SER cc_start: 0.9084 (m) cc_final: 0.8439 (p) REVERT: D 137 ASN cc_start: 0.7997 (t0) cc_final: 0.7136 (p0) outliers start: 27 outliers final: 11 residues processed: 141 average time/residue: 1.0299 time to fit residues: 158.0856 Evaluate side-chains 125 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 247 LYS 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 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 C residue 75 SER 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: 5.9990 chunk 115 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 chunk 89 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 overall best weight: 1.6790 ------------------------------------------------------------------------------- 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** C 62 GLN D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.140131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.115588 restraints weight = 57522.067| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 6.77 r_work: 0.4015 rms_B_bonded: 6.72 restraints_weight: 2.0000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 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 = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 10069 Z= 0.195 Angle : 0.834 16.618 13711 Z= 0.408 Chirality : 0.045 0.298 1505 Planarity : 0.005 0.048 1738 Dihedral : 6.041 50.555 1616 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.03 % Favored : 91.72 % Rotamer: Outliers : 2.86 % Allowed : 20.00 % Favored : 77.14 % 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: -1.56 (0.24), residues: 1199 helix: -0.25 (0.25), residues: 401 sheet: -0.99 (0.34), residues: 212 loop : -1.57 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 163 HIS 0.007 0.001 HIS A 401 PHE 0.024 0.002 PHE A 464 TYR 0.027 0.002 TYR C 27 ARG 0.012 0.001 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 2.47782 ( 21) link_BETA1-4 : bond 0.00504 ( 7) link_BETA1-4 : angle 2.22340 ( 21) link_ALPHA1-3 : bond 0.01363 ( 1) link_ALPHA1-3 : angle 1.69779 ( 3) hydrogen bonds : bond 0.05091 ( 371) hydrogen bonds : angle 5.77743 ( 1081) metal coordination : bond 0.00216 ( 2) SS BOND : bond 0.00706 ( 10) SS BOND : angle 2.42233 ( 20) covalent geometry : bond 0.00452 (10042) covalent geometry : angle 0.81987 (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 147 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.012 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: 0.1158 (OUTLIER) cc_final: -0.0845 (mm110) REVERT: A 196 TYR cc_start: 0.7429 (m-10) cc_final: 0.7212 (m-10) REVERT: A 376 MET cc_start: 0.9036 (mmt) cc_final: 0.8777 (mmt) REVERT: A 429 GLN cc_start: 0.8306 (mt0) cc_final: 0.8024 (pp30) REVERT: B 386 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7522 (tptp) REVERT: B 421 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.3402 (p90) REVERT: C 105 TRP cc_start: 0.8579 (m-10) cc_final: 0.8281 (m-10) REVERT: C 158 ASP cc_start: 0.8440 (t0) cc_final: 0.7860 (t0) REVERT: C 193 SER cc_start: 0.9158 (m) cc_final: 0.8678 (p) REVERT: D 137 ASN cc_start: 0.8141 (t0) cc_final: 0.7252 (p0) outliers start: 30 outliers final: 16 residues processed: 139 average time/residue: 0.9701 time to fit residues: 147.2243 Evaluate side-chains 129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 324 THR 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 385 THR Chi-restraints excluded: chain B residue 386 LYS 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 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: 0.6980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN C 62 GLN ** C 116 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 = 0.4566 r_free = 0.4566 target = 0.139161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.116190 restraints weight = 35181.712| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 4.48 r_work: 0.4120 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4120 r_free = 0.4120 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 = 0.4120 r_free = 0.4120 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10069 Z= 0.161 Angle : 0.838 17.275 13711 Z= 0.408 Chirality : 0.045 0.279 1505 Planarity : 0.005 0.051 1738 Dihedral : 5.940 50.452 1616 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 2.19 % Allowed : 20.95 % Favored : 76.86 % 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: -1.51 (0.24), residues: 1199 helix: -0.19 (0.25), residues: 397 sheet: -0.98 (0.35), residues: 215 loop : -1.55 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 163 HIS 0.005 0.001 HIS C 214 PHE 0.020 0.001 PHE A 464 TYR 0.020 0.002 TYR A 385 ARG 0.014 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 7) link_NAG-ASN : angle 2.31331 ( 21) link_BETA1-4 : bond 0.00533 ( 7) link_BETA1-4 : angle 2.15480 ( 21) link_ALPHA1-3 : bond 0.01784 ( 1) link_ALPHA1-3 : angle 1.91424 ( 3) hydrogen bonds : bond 0.04798 ( 371) hydrogen bonds : angle 5.72762 ( 1081) metal coordination : bond 0.00158 ( 2) SS BOND : bond 0.00888 ( 10) SS BOND : angle 2.09294 ( 20) covalent geometry : bond 0.00369 (10042) covalent geometry : angle 0.82651 (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 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.088 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: 0.1035 (OUTLIER) cc_final: -0.0780 (mm110) REVERT: A 287 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: A 376 MET cc_start: 0.8920 (mmt) cc_final: 0.8618 (mmt) REVERT: A 393 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6873 (mpt-90) REVERT: B 421 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.3309 (p90) REVERT: C 80 TYR cc_start: 0.6248 (m-80) cc_final: 0.5441 (m-80) REVERT: C 95 TYR cc_start: 0.6086 (m-10) cc_final: 0.5627 (m-10) REVERT: C 105 TRP cc_start: 0.8468 (m-10) cc_final: 0.7906 (m-10) REVERT: C 158 ASP cc_start: 0.8391 (t0) cc_final: 0.7815 (t0) REVERT: C 193 SER cc_start: 0.9288 (m) cc_final: 0.8835 (p) REVERT: D 90 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7405 (tm130) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 1.0606 time to fit residues: 163.3718 Evaluate side-chains 125 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 247 LYS 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 393 ARG 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 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 27 TYR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN C 62 GLN ** C 116 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 = 0.4602 r_free = 0.4602 target = 0.140813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.116223 restraints weight = 63436.353| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 7.24 r_work: 0.4017 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 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 = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10069 Z= 0.174 Angle : 0.860 18.146 13711 Z= 0.417 Chirality : 0.045 0.253 1505 Planarity : 0.005 0.056 1738 Dihedral : 6.036 59.937 1616 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.61 % Favored : 92.14 % Rotamer: Outliers : 2.86 % Allowed : 21.62 % Favored : 75.52 % 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: -1.53 (0.24), residues: 1199 helix: -0.26 (0.25), residues: 398 sheet: -0.99 (0.34), residues: 221 loop : -1.52 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 163 HIS 0.005 0.001 HIS C 214 PHE 0.033 0.002 PHE D 209 TYR 0.019 0.002 TYR A 385 ARG 0.015 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 7) link_NAG-ASN : angle 2.29743 ( 21) link_BETA1-4 : bond 0.00512 ( 7) link_BETA1-4 : angle 2.09625 ( 21) link_ALPHA1-3 : bond 0.01170 ( 1) link_ALPHA1-3 : angle 1.93179 ( 3) hydrogen bonds : bond 0.04853 ( 371) hydrogen bonds : angle 5.67248 ( 1081) metal coordination : bond 0.00217 ( 2) SS BOND : bond 0.00655 ( 10) SS BOND : angle 2.22993 ( 20) covalent geometry : bond 0.00404 (10042) covalent geometry : angle 0.84872 (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 143 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.126 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: 0.1083 (OUTLIER) cc_final: -0.0732 (mm110) REVERT: A 287 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: A 376 MET cc_start: 0.8917 (mmt) cc_final: 0.8712 (mmt) REVERT: A 393 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6937 (mpt-90) REVERT: B 390 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4586 (pt) REVERT: B 421 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.3404 (p90) REVERT: C 80 TYR cc_start: 0.6283 (m-80) cc_final: 0.5380 (m-80) REVERT: C 95 TYR cc_start: 0.6220 (m-10) cc_final: 0.5699 (m-10) REVERT: C 105 TRP cc_start: 0.8565 (m-10) cc_final: 0.7919 (m-10) REVERT: C 158 ASP cc_start: 0.8460 (t0) cc_final: 0.7865 (t0) REVERT: C 193 SER cc_start: 0.9205 (m) cc_final: 0.8739 (p) REVERT: D 24 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8146 (tmm-80) REVERT: D 90 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7212 (tm-30) outliers start: 30 outliers final: 14 residues processed: 136 average time/residue: 0.9496 time to fit residues: 141.3716 Evaluate side-chains 124 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 247 LYS 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 393 ARG 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 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 75 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 101 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.139788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.114229 restraints weight = 75969.720| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 7.65 r_work: 0.3990 rms_B_bonded: 7.26 restraints_weight: 2.0000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 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 = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 10069 Z= 0.196 Angle : 0.886 18.866 13711 Z= 0.432 Chirality : 0.046 0.256 1505 Planarity : 0.005 0.065 1738 Dihedral : 6.128 54.992 1616 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 2.48 % Allowed : 22.48 % Favored : 75.05 % 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: -1.63 (0.24), residues: 1199 helix: -0.44 (0.24), residues: 405 sheet: -0.85 (0.35), residues: 212 loop : -1.60 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 163 HIS 0.006 0.001 HIS A 401 PHE 0.023 0.002 PHE A 464 TYR 0.027 0.002 TYR C 54 ARG 0.023 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 7) link_NAG-ASN : angle 2.25203 ( 21) link_BETA1-4 : bond 0.00491 ( 7) link_BETA1-4 : angle 2.07174 ( 21) link_ALPHA1-3 : bond 0.01244 ( 1) link_ALPHA1-3 : angle 2.06467 ( 3) hydrogen bonds : bond 0.05058 ( 371) hydrogen bonds : angle 5.76604 ( 1081) metal coordination : bond 0.00280 ( 2) SS BOND : bond 0.00728 ( 10) SS BOND : angle 1.91153 ( 20) covalent geometry : bond 0.00454 (10042) covalent geometry : angle 0.87680 (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 137 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.096 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: 0.0961 (OUTLIER) cc_final: -0.0783 (mm110) REVERT: A 277 ASN cc_start: 0.8021 (m-40) cc_final: 0.7763 (m110) REVERT: A 287 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: A 393 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6879 (mpt-90) REVERT: B 421 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.3455 (p90) REVERT: B 513 LEU cc_start: 0.8996 (mm) cc_final: 0.8714 (mp) REVERT: C 80 TYR cc_start: 0.6160 (m-80) cc_final: 0.5279 (m-80) REVERT: C 95 TYR cc_start: 0.6264 (m-10) cc_final: 0.5791 (m-10) REVERT: C 105 TRP cc_start: 0.8637 (m-10) cc_final: 0.8010 (m-10) REVERT: C 158 ASP cc_start: 0.8507 (t0) cc_final: 0.7973 (t0) REVERT: C 193 SER cc_start: 0.9275 (m) cc_final: 0.8846 (p) REVERT: C 225 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7604 (p) REVERT: D 24 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8146 (tmm-80) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.9944 time to fit residues: 144.6835 Evaluate side-chains 127 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 185 VAL 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 393 ARG Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN 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 27 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** 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 = 0.4623 r_free = 0.4623 target = 0.141772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.118214 restraints weight = 50666.539| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 6.10 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.5021 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= 0.159 Angle : 0.877 18.010 13711 Z= 0.425 Chirality : 0.046 0.226 1505 Planarity : 0.005 0.098 1738 Dihedral : 5.927 43.043 1616 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.19 % Favored : 92.64 % Rotamer: Outliers : 2.10 % Allowed : 23.05 % Favored : 74.86 % 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: -1.58 (0.24), residues: 1199 helix: -0.35 (0.25), residues: 398 sheet: -0.93 (0.33), residues: 231 loop : -1.55 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 163 HIS 0.004 0.001 HIS C 214 PHE 0.043 0.002 PHE D 209 TYR 0.027 0.002 TYR C 54 ARG 0.023 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 2.13286 ( 21) link_BETA1-4 : bond 0.00517 ( 7) link_BETA1-4 : angle 2.04699 ( 21) link_ALPHA1-3 : bond 0.01235 ( 1) link_ALPHA1-3 : angle 2.11384 ( 3) hydrogen bonds : bond 0.04652 ( 371) hydrogen bonds : angle 5.67942 ( 1081) metal coordination : bond 0.00118 ( 2) SS BOND : bond 0.00620 ( 10) SS BOND : angle 1.78018 ( 20) covalent geometry : bond 0.00363 (10042) covalent geometry : angle 0.86846 (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 140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.113 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: 0.0534 (OUTLIER) cc_final: -0.0798 (mm110) REVERT: A 287 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: A 302 TRP cc_start: 0.7185 (m-10) cc_final: 0.6477 (m100) REVERT: A 393 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6667 (mpt-90) REVERT: B 421 TYR cc_start: 0.5465 (OUTLIER) cc_final: 0.2838 (p90) REVERT: C 43 GLN cc_start: 0.8743 (mt0) cc_final: 0.8163 (mp10) REVERT: C 80 TYR cc_start: 0.5928 (m-80) cc_final: 0.5142 (m-80) REVERT: C 95 TYR cc_start: 0.5908 (m-10) cc_final: 0.5483 (m-10) REVERT: C 105 TRP cc_start: 0.8269 (m-10) cc_final: 0.7787 (m-10) REVERT: C 158 ASP cc_start: 0.8353 (t0) cc_final: 0.7916 (t0) REVERT: C 193 SER cc_start: 0.9231 (m) cc_final: 0.8797 (p) outliers start: 22 outliers final: 13 residues processed: 137 average time/residue: 0.9908 time to fit residues: 147.9364 Evaluate side-chains 123 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 174 LYS 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 393 ARG 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 27 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 0.0270 chunk 26 optimal weight: 0.0000 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B A 42 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4633 r_free = 0.4633 target = 0.143082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.120117 restraints weight = 40837.047| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 4.87 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10069 Z= 0.152 Angle : 0.867 16.361 13711 Z= 0.425 Chirality : 0.046 0.258 1505 Planarity : 0.005 0.097 1738 Dihedral : 5.678 44.174 1616 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.47 % Rotamer: Outliers : 1.81 % Allowed : 24.00 % Favored : 74.19 % 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: -1.47 (0.24), residues: 1199 helix: -0.26 (0.25), residues: 399 sheet: -0.82 (0.34), residues: 226 loop : -1.52 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.020 0.001 PHE A 464 TYR 0.026 0.002 TYR C 54 ARG 0.027 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 7) link_NAG-ASN : angle 2.11489 ( 21) link_BETA1-4 : bond 0.00546 ( 7) link_BETA1-4 : angle 2.00989 ( 21) link_ALPHA1-3 : bond 0.01173 ( 1) link_ALPHA1-3 : angle 2.05001 ( 3) hydrogen bonds : bond 0.04494 ( 371) hydrogen bonds : angle 5.67396 ( 1081) metal coordination : bond 0.00147 ( 2) SS BOND : bond 0.00632 ( 10) SS BOND : angle 1.62519 ( 20) covalent geometry : bond 0.00342 (10042) covalent geometry : angle 0.85869 (13646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10267.76 seconds wall clock time: 176 minutes 49.67 seconds (10609.67 seconds total)