Starting phenix.real_space_refine on Wed Sep 17 16:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y6a_38983/09_2025/8y6a_38983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y6a_38983/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y6a_38983/09_2025/8y6a_38983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y6a_38983/09_2025/8y6a_38983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y6a_38983/09_2025/8y6a_38983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y6a_38983/09_2025/8y6a_38983.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.34, per 1000 atoms: 0.34 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: 0.97 Conformation dependent library (CDL) restraints added in 446.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.36 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: 1.48 Time building geometry restraints manager: 1.28 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: 1.950 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- 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 : 14.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 454 TYR 0.021 0.002 TYR B 501 PHE 0.035 0.001 PHE A 464 TRP 0.018 0.002 TRP A 459 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00390 (10042) covalent geometry : angle 0.73115 (13646) SS BOND : bond 0.00451 ( 10) SS BOND : angle 2.08938 ( 20) hydrogen bonds : bond 0.20344 ( 371) hydrogen bonds : angle 8.81809 ( 1081) metal coordination : bond 0.02646 ( 2) link_ALPHA1-3 : bond 0.04529 ( 1) link_ALPHA1-3 : angle 4.31444 ( 3) link_BETA1-4 : bond 0.03722 ( 7) link_BETA1-4 : angle 7.23403 ( 21) link_NAG-ASN : bond 0.01068 ( 7) link_NAG-ASN : angle 4.92020 ( 21) *********************** 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 : 0.349 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: 0.1196 (OUTLIER) cc_final: -0.0179 (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: 0.8377 (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) REVERT: D 167 ASP cc_start: 0.8961 (t70) cc_final: 0.8696 (t0) outliers start: 5 outliers final: 2 residues processed: 272 average time/residue: 0.5997 time to fit residues: 173.8660 Evaluate side-chains 130 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 340 GLN A 508 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 422 ASN C 57 ASN C 62 GLN C 65 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 189 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.141659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.117698 restraints weight = 41997.286| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 5.00 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 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 = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10069 Z= 0.196 Angle : 0.858 13.397 13711 Z= 0.427 Chirality : 0.047 0.248 1505 Planarity : 0.005 0.045 1738 Dihedral : 10.554 78.476 1623 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.61 % Favored : 92.06 % Rotamer: Outliers : 2.38 % Allowed : 15.33 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.23), residues: 1199 helix: -0.73 (0.24), residues: 410 sheet: -0.93 (0.37), residues: 204 loop : -1.89 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.028 0.002 TYR A 587 PHE 0.029 0.002 PHE A 523 TRP 0.027 0.003 TRP C 168 HIS 0.009 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00443 (10042) covalent geometry : angle 0.83940 (13646) SS BOND : bond 0.00774 ( 10) SS BOND : angle 2.02841 ( 20) hydrogen bonds : bond 0.05543 ( 371) hydrogen bonds : angle 6.56614 ( 1081) metal coordination : bond 0.00118 ( 2) link_ALPHA1-3 : bond 0.01373 ( 1) link_ALPHA1-3 : angle 0.74161 ( 3) link_BETA1-4 : bond 0.00667 ( 7) link_BETA1-4 : angle 2.88490 ( 21) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 3.19513 ( 21) *********************** 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 185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.309 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: 0.0642 (OUTLIER) cc_final: -0.0655 (mm110) REVERT: A 31 LYS cc_start: 0.5118 (OUTLIER) cc_final: 0.4619 (tttp) REVERT: A 111 ASP cc_start: 0.9067 (t70) cc_final: 0.8840 (p0) REVERT: A 162 LEU cc_start: 0.9335 (tm) cc_final: 0.9002 (pp) REVERT: A 247 LYS cc_start: 0.6406 (mmtt) cc_final: 0.6176 (mmtp) REVERT: A 248 LEU cc_start: 0.6861 (mt) cc_final: 0.6376 (tt) REVERT: A 376 MET cc_start: 0.8873 (mmt) cc_final: 0.8568 (mmt) REVERT: A 429 GLN cc_start: 0.8222 (mt0) cc_final: 0.8016 (pp30) REVERT: B 386 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8954 (tptp) REVERT: C 65 GLN cc_start: 0.8576 (mm110) cc_final: 0.8329 (mm-40) REVERT: C 80 TYR cc_start: 0.6010 (m-80) cc_final: 0.5222 (m-80) REVERT: C 105 TRP cc_start: 0.8281 (m-10) cc_final: 0.7996 (m-10) REVERT: C 158 ASP cc_start: 0.8255 (t0) cc_final: 0.7866 (t0) REVERT: C 190 TYR cc_start: 0.8426 (m-80) cc_final: 0.8209 (m-80) REVERT: C 193 SER cc_start: 0.9162 (m) cc_final: 0.8695 (p) outliers start: 25 outliers final: 10 residues processed: 176 average time/residue: 0.5004 time to fit residues: 95.1971 Evaluate side-chains 136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE 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 9 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 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 = 0.4621 r_free = 0.4621 target = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.118360 restraints weight = 50800.993| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 6.46 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 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 = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.116 | | 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: 0.6531 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10069 Z= 0.164 Angle : 0.833 18.991 13711 Z= 0.407 Chirality : 0.046 0.215 1505 Planarity : 0.005 0.047 1738 Dihedral : 8.948 58.559 1620 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 3.05 % Allowed : 17.24 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.23), residues: 1199 helix: -0.57 (0.25), residues: 404 sheet: -0.94 (0.36), residues: 200 loop : -1.85 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 78 TYR 0.047 0.002 TYR A 202 PHE 0.025 0.002 PHE A 464 TRP 0.024 0.002 TRP A 163 HIS 0.009 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00357 (10042) covalent geometry : angle 0.81625 (13646) SS BOND : bond 0.01006 ( 10) SS BOND : angle 1.77915 ( 20) hydrogen bonds : bond 0.05052 ( 371) hydrogen bonds : angle 6.23874 ( 1081) metal coordination : bond 0.00131 ( 2) link_ALPHA1-3 : bond 0.01106 ( 1) link_ALPHA1-3 : angle 1.32315 ( 3) link_BETA1-4 : bond 0.00643 ( 7) link_BETA1-4 : angle 2.64725 ( 21) link_NAG-ASN : bond 0.01223 ( 7) link_NAG-ASN : angle 3.14607 ( 21) *********************** 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 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.359 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: 0.0535 (OUTLIER) cc_final: -0.0827 (mm110) REVERT: A 31 LYS cc_start: 0.5308 (OUTLIER) cc_final: 0.4756 (tttp) REVERT: A 111 ASP cc_start: 0.9105 (t70) cc_final: 0.8859 (p0) REVERT: A 195 HIS cc_start: 0.7338 (t-90) cc_final: 0.7137 (t70) REVERT: A 376 MET cc_start: 0.8829 (mmt) cc_final: 0.8425 (mmt) REVERT: A 429 GLN cc_start: 0.8546 (mt0) cc_final: 0.8184 (pp30) REVERT: B 335 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 386 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8988 (tptp) REVERT: B 421 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.2990 (p90) REVERT: C 64 PHE cc_start: 0.7910 (m-80) cc_final: 0.7555 (m-80) REVERT: C 65 GLN cc_start: 0.8705 (mm110) cc_final: 0.8392 (mm-40) REVERT: C 80 TYR cc_start: 0.6109 (m-80) cc_final: 0.5304 (m-80) REVERT: C 105 TRP cc_start: 0.8242 (m-10) cc_final: 0.8001 (m-10) REVERT: C 158 ASP cc_start: 0.8219 (t0) cc_final: 0.7787 (t0) REVERT: C 193 SER cc_start: 0.9233 (m) cc_final: 0.8823 (p) REVERT: D 137 ASN cc_start: 0.7807 (t0) cc_final: 0.6824 (p0) REVERT: D 175 LEU cc_start: 0.9170 (tt) cc_final: 0.8936 (mt) outliers start: 32 outliers final: 13 residues processed: 149 average time/residue: 0.4502 time to fit residues: 73.2450 Evaluate side-chains 125 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE 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 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 80 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.141764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.117804 restraints weight = 61274.415| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 7.53 r_work: 0.4048 rms_B_bonded: 7.09 restraints_weight: 2.0000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10069 Z= 0.155 Angle : 0.782 16.834 13711 Z= 0.385 Chirality : 0.045 0.261 1505 Planarity : 0.005 0.045 1738 Dihedral : 7.409 55.865 1620 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 2.86 % Allowed : 18.95 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.24), residues: 1199 helix: -0.28 (0.25), residues: 398 sheet: -1.00 (0.35), residues: 209 loop : -1.74 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.021 0.002 TYR B 365 PHE 0.025 0.002 PHE A 464 TRP 0.023 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00351 (10042) covalent geometry : angle 0.76126 (13646) SS BOND : bond 0.00609 ( 10) SS BOND : angle 2.56587 ( 20) hydrogen bonds : bond 0.04795 ( 371) hydrogen bonds : angle 5.91660 ( 1081) metal coordination : bond 0.00123 ( 2) link_ALPHA1-3 : bond 0.01616 ( 1) link_ALPHA1-3 : angle 1.20547 ( 3) link_BETA1-4 : bond 0.00631 ( 7) link_BETA1-4 : angle 2.52624 ( 21) link_NAG-ASN : bond 0.00699 ( 7) link_NAG-ASN : angle 3.08780 ( 21) *********************** 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 153 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.403 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: 0.0746 (OUTLIER) cc_final: -0.0879 (mm110) REVERT: A 111 ASP cc_start: 0.9151 (t70) cc_final: 0.8912 (p0) REVERT: A 162 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9048 (pp) REVERT: A 248 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6342 (tt) REVERT: A 297 MET cc_start: 0.5495 (mmp) cc_final: 0.4399 (tpp) REVERT: A 429 GLN cc_start: 0.8464 (mt0) cc_final: 0.8155 (pp30) REVERT: B 335 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 421 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.3537 (p90) REVERT: C 64 PHE cc_start: 0.7665 (m-80) cc_final: 0.7320 (m-80) REVERT: C 70 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6126 (mtt) REVERT: C 158 ASP cc_start: 0.8430 (t0) cc_final: 0.7833 (t0) REVERT: C 193 SER cc_start: 0.9220 (m) cc_final: 0.8757 (p) REVERT: D 24 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8224 (tpp80) REVERT: D 137 ASN cc_start: 0.7796 (t0) cc_final: 0.6884 (p0) REVERT: D 175 LEU cc_start: 0.9057 (tt) cc_final: 0.8852 (mt) outliers start: 30 outliers final: 11 residues processed: 143 average time/residue: 0.4706 time to fit residues: 73.4014 Evaluate side-chains 126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 324 THR 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 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.141483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.118078 restraints weight = 42734.078| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 5.00 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 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 = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10069 Z= 0.162 Angle : 0.785 16.921 13711 Z= 0.386 Chirality : 0.045 0.265 1505 Planarity : 0.005 0.045 1738 Dihedral : 6.434 57.793 1616 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 3.05 % Allowed : 18.95 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.24), residues: 1199 helix: -0.23 (0.25), residues: 395 sheet: -0.96 (0.36), residues: 203 loop : -1.69 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 518 TYR 0.027 0.002 TYR C 27 PHE 0.022 0.002 PHE A 464 TRP 0.028 0.002 TRP A 163 HIS 0.015 0.002 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00372 (10042) covalent geometry : angle 0.76946 (13646) SS BOND : bond 0.00648 ( 10) SS BOND : angle 2.39655 ( 20) hydrogen bonds : bond 0.04816 ( 371) hydrogen bonds : angle 5.81817 ( 1081) metal coordination : bond 0.00228 ( 2) link_ALPHA1-3 : bond 0.01216 ( 1) link_ALPHA1-3 : angle 0.87426 ( 3) link_BETA1-4 : bond 0.00628 ( 7) link_BETA1-4 : angle 2.30574 ( 21) link_NAG-ASN : bond 0.00667 ( 7) link_NAG-ASN : angle 2.66099 ( 21) *********************** 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 150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.334 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: 0.0533 (OUTLIER) cc_final: -0.1095 (mm-40) REVERT: A 148 LEU cc_start: 0.6597 (tm) cc_final: 0.6332 (tp) REVERT: A 162 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 248 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6252 (tt) REVERT: A 297 MET cc_start: 0.5670 (mmp) cc_final: 0.4577 (tpp) REVERT: A 376 MET cc_start: 0.8652 (mmt) cc_final: 0.8282 (mmt) REVERT: B 335 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 421 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.2852 (p90) REVERT: C 64 PHE cc_start: 0.7750 (m-80) cc_final: 0.7428 (m-80) REVERT: C 87 ARG cc_start: 0.8108 (mmp80) cc_final: 0.7907 (mmp-170) REVERT: C 158 ASP cc_start: 0.8272 (t0) cc_final: 0.7697 (t0) REVERT: C 193 SER cc_start: 0.9196 (m) cc_final: 0.8774 (p) REVERT: D 137 ASN cc_start: 0.7936 (t0) cc_final: 0.7054 (p0) outliers start: 32 outliers final: 12 residues processed: 141 average time/residue: 0.5129 time to fit residues: 78.0816 Evaluate side-chains 119 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 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 C residue 111 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 90 optimal weight: 50.0000 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 345 HIS C 43 GLN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.114696 restraints weight = 50765.533| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 6.52 r_work: 0.4002 rms_B_bonded: 6.46 restraints_weight: 2.0000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 10069 Z= 0.230 Angle : 0.866 18.212 13711 Z= 0.427 Chirality : 0.047 0.304 1505 Planarity : 0.005 0.045 1738 Dihedral : 6.352 58.046 1616 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.28 % Favored : 91.47 % Rotamer: Outliers : 3.14 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.24), residues: 1199 helix: -0.31 (0.25), residues: 399 sheet: -1.07 (0.34), residues: 217 loop : -1.73 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 211 TYR 0.028 0.002 TYR A 381 PHE 0.026 0.002 PHE A 464 TRP 0.030 0.003 TRP A 163 HIS 0.013 0.002 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00534 (10042) covalent geometry : angle 0.85311 (13646) SS BOND : bond 0.00932 ( 10) SS BOND : angle 2.40229 ( 20) hydrogen bonds : bond 0.05447 ( 371) hydrogen bonds : angle 5.87995 ( 1081) metal coordination : bond 0.00327 ( 2) link_ALPHA1-3 : bond 0.01131 ( 1) link_ALPHA1-3 : angle 1.01291 ( 3) link_BETA1-4 : bond 0.00549 ( 7) link_BETA1-4 : angle 2.15357 ( 21) link_NAG-ASN : bond 0.00667 ( 7) link_NAG-ASN : angle 2.60997 ( 21) *********************** 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 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.366 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: 0.0818 (OUTLIER) cc_final: -0.1319 (mm110) REVERT: A 248 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6083 (tt) REVERT: A 376 MET cc_start: 0.8995 (mmt) cc_final: 0.8726 (mmt) REVERT: B 386 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7521 (tptp) REVERT: B 421 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.3238 (p90) REVERT: C 43 GLN cc_start: 0.8914 (mt0) cc_final: 0.8661 (mt0) REVERT: C 64 PHE cc_start: 0.7864 (m-80) cc_final: 0.7572 (m-80) REVERT: C 158 ASP cc_start: 0.8406 (t0) cc_final: 0.7806 (t0) REVERT: C 193 SER cc_start: 0.9203 (m) cc_final: 0.8778 (p) REVERT: D 90 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7177 (tm-30) outliers start: 33 outliers final: 17 residues processed: 140 average time/residue: 0.4749 time to fit residues: 72.1615 Evaluate side-chains 129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 248 LEU 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 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 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 111 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 40 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 overall best weight: 0.3774 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.139953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.115632 restraints weight = 62770.909| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 7.11 r_work: 0.4050 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 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 = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10069 Z= 0.155 Angle : 0.839 17.771 13711 Z= 0.408 Chirality : 0.045 0.281 1505 Planarity : 0.005 0.074 1738 Dihedral : 6.115 58.313 1616 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.44 % Favored : 93.31 % Rotamer: Outliers : 2.29 % Allowed : 21.71 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1199 helix: -0.25 (0.25), residues: 397 sheet: -0.92 (0.35), residues: 213 loop : -1.57 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 518 TYR 0.028 0.002 TYR C 27 PHE 0.019 0.001 PHE A 464 TRP 0.036 0.002 TRP A 163 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00347 (10042) covalent geometry : angle 0.82761 (13646) SS BOND : bond 0.00954 ( 10) SS BOND : angle 2.20949 ( 20) hydrogen bonds : bond 0.04644 ( 371) hydrogen bonds : angle 5.69106 ( 1081) metal coordination : bond 0.00112 ( 2) link_ALPHA1-3 : bond 0.01481 ( 1) link_ALPHA1-3 : angle 1.13672 ( 3) link_BETA1-4 : bond 0.00538 ( 7) link_BETA1-4 : angle 2.05554 ( 21) link_NAG-ASN : bond 0.00503 ( 7) link_NAG-ASN : angle 2.36059 ( 21) *********************** 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 145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.386 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: 0.0641 (OUTLIER) cc_final: -0.1292 (mm-40) REVERT: A 162 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9172 (mt) REVERT: A 249 MET cc_start: 0.7117 (ptp) cc_final: 0.5908 (pp-130) REVERT: A 277 ASN cc_start: 0.7956 (m-40) cc_final: 0.7754 (m110) REVERT: A 291 ILE cc_start: 0.8495 (mm) cc_final: 0.8247 (pt) REVERT: A 376 MET cc_start: 0.8942 (mmt) cc_final: 0.8706 (mmt) REVERT: B 335 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8334 (mm) REVERT: B 421 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.3443 (p90) REVERT: C 43 GLN cc_start: 0.8847 (mt0) cc_final: 0.8642 (mt0) REVERT: C 64 PHE cc_start: 0.7587 (m-80) cc_final: 0.7292 (m-80) REVERT: C 158 ASP cc_start: 0.8328 (t0) cc_final: 0.7757 (t0) REVERT: C 193 SER cc_start: 0.9259 (m) cc_final: 0.8871 (p) REVERT: D 90 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7478 (tm130) REVERT: D 137 ASN cc_start: 0.8029 (t0) cc_final: 0.7025 (p0) outliers start: 24 outliers final: 12 residues processed: 139 average time/residue: 0.4849 time to fit residues: 73.3560 Evaluate side-chains 129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 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 D residue 90 GLN Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 62 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.140034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.115622 restraints weight = 56589.779| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 6.97 r_work: 0.4018 rms_B_bonded: 6.71 restraints_weight: 2.0000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 10069 Z= 0.193 Angle : 0.866 18.704 13711 Z= 0.423 Chirality : 0.046 0.268 1505 Planarity : 0.005 0.052 1738 Dihedral : 6.142 59.906 1616 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.61 % Favored : 92.14 % Rotamer: Outliers : 2.57 % Allowed : 22.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.24), residues: 1199 helix: -0.27 (0.25), residues: 397 sheet: -1.03 (0.35), residues: 218 loop : -1.60 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 85 TYR 0.021 0.002 TYR A 127 PHE 0.030 0.002 PHE D 209 TRP 0.036 0.003 TRP A 163 HIS 0.007 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00448 (10042) covalent geometry : angle 0.85497 (13646) SS BOND : bond 0.00667 ( 10) SS BOND : angle 2.18593 ( 20) hydrogen bonds : bond 0.05016 ( 371) hydrogen bonds : angle 5.71260 ( 1081) metal coordination : bond 0.00234 ( 2) link_ALPHA1-3 : bond 0.01270 ( 1) link_ALPHA1-3 : angle 1.17243 ( 3) link_BETA1-4 : bond 0.00544 ( 7) link_BETA1-4 : angle 1.97842 ( 21) link_NAG-ASN : bond 0.00570 ( 7) link_NAG-ASN : angle 2.35281 ( 21) *********************** 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 140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.400 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: 0.0661 (OUTLIER) cc_final: -0.1303 (mm-40) REVERT: A 161 ARG cc_start: 0.6689 (mtp85) cc_final: 0.6381 (mmm-85) REVERT: A 162 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9120 (pp) REVERT: A 376 MET cc_start: 0.8914 (mmt) cc_final: 0.8673 (mmt) REVERT: B 421 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.3402 (p90) REVERT: C 43 GLN cc_start: 0.8925 (mt0) cc_final: 0.8714 (mt0) REVERT: C 64 PHE cc_start: 0.7702 (m-80) cc_final: 0.7363 (m-80) REVERT: C 80 TYR cc_start: 0.6082 (m-80) cc_final: 0.5170 (m-80) REVERT: C 95 TYR cc_start: 0.6301 (m-10) cc_final: 0.5914 (m-10) REVERT: C 158 ASP cc_start: 0.8443 (t0) cc_final: 0.7893 (t0) REVERT: C 193 SER cc_start: 0.9184 (m) cc_final: 0.8741 (p) REVERT: D 90 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: D 137 ASN cc_start: 0.8166 (t0) cc_final: 0.7154 (p0) outliers start: 27 outliers final: 16 residues processed: 133 average time/residue: 0.4424 time to fit residues: 64.4588 Evaluate side-chains 126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 247 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 112 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.0010 chunk 44 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 62 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.142747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.118872 restraints weight = 53700.162| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 6.89 r_work: 0.4073 rms_B_bonded: 6.77 restraints_weight: 2.0000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10069 Z= 0.150 Angle : 0.853 18.227 13711 Z= 0.412 Chirality : 0.045 0.261 1505 Planarity : 0.005 0.078 1738 Dihedral : 5.942 51.649 1616 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 2.00 % Allowed : 23.33 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.24), residues: 1199 helix: -0.18 (0.25), residues: 399 sheet: -0.87 (0.35), residues: 215 loop : -1.59 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 518 TYR 0.021 0.002 TYR A 385 PHE 0.019 0.001 PHE A 464 TRP 0.041 0.002 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00337 (10042) covalent geometry : angle 0.84361 (13646) SS BOND : bond 0.00578 ( 10) SS BOND : angle 1.81335 ( 20) hydrogen bonds : bond 0.04540 ( 371) hydrogen bonds : angle 5.61953 ( 1081) metal coordination : bond 0.00149 ( 2) link_ALPHA1-3 : bond 0.01194 ( 1) link_ALPHA1-3 : angle 1.29559 ( 3) link_BETA1-4 : bond 0.00520 ( 7) link_BETA1-4 : angle 1.97462 ( 21) link_NAG-ASN : bond 0.00443 ( 7) link_NAG-ASN : angle 2.22978 ( 21) *********************** 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: 21 poor density : 116 time to evaluate : 0.311 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: 0.0564 (OUTLIER) cc_final: -0.1344 (mm-40) REVERT: A 162 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9142 (pp) REVERT: A 249 MET cc_start: 0.7128 (ptp) cc_final: 0.5903 (pp-130) REVERT: A 376 MET cc_start: 0.9108 (mmt) cc_final: 0.8787 (mmt) REVERT: B 335 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 421 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.3356 (p90) REVERT: C 64 PHE cc_start: 0.7549 (m-80) cc_final: 0.7167 (m-80) REVERT: C 80 TYR cc_start: 0.6040 (m-80) cc_final: 0.5228 (m-80) REVERT: C 95 TYR cc_start: 0.6216 (m-10) cc_final: 0.5681 (m-10) REVERT: C 158 ASP cc_start: 0.8481 (t0) cc_final: 0.7968 (t0) REVERT: C 193 SER cc_start: 0.9225 (m) cc_final: 0.8843 (p) REVERT: D 137 ASN cc_start: 0.8098 (t0) cc_final: 0.7151 (p0) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.4638 time to fit residues: 67.0731 Evaluate side-chains 125 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 D residue 115 VAL Chi-restraints excluded: chain D residue 169 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 52 optimal weight: 0.3980 chunk 109 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 62 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.138476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.113987 restraints weight = 42632.042| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 5.14 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 10069 Z= 0.244 Angle : 0.935 20.852 13711 Z= 0.455 Chirality : 0.048 0.270 1505 Planarity : 0.006 0.085 1738 Dihedral : 6.021 40.728 1616 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.95 % Favored : 90.80 % Rotamer: Outliers : 1.90 % Allowed : 24.00 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.24), residues: 1199 helix: -0.42 (0.25), residues: 398 sheet: -0.91 (0.35), residues: 221 loop : -1.63 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 518 TYR 0.032 0.003 TYR A 381 PHE 0.042 0.002 PHE D 209 TRP 0.038 0.003 TRP A 163 HIS 0.008 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00568 (10042) covalent geometry : angle 0.92468 (13646) SS BOND : bond 0.00709 ( 10) SS BOND : angle 2.13849 ( 20) hydrogen bonds : bond 0.05472 ( 371) hydrogen bonds : angle 5.80575 ( 1081) metal coordination : bond 0.00386 ( 2) link_ALPHA1-3 : bond 0.01052 ( 1) link_ALPHA1-3 : angle 1.35338 ( 3) link_BETA1-4 : bond 0.00546 ( 7) link_BETA1-4 : angle 1.93445 ( 21) link_NAG-ASN : bond 0.00638 ( 7) link_NAG-ASN : angle 2.52349 ( 21) ********************** 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 132 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.343 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: 0.0158 (OUTLIER) cc_final: -0.1684 (mm-40) REVERT: A 249 MET cc_start: 0.7006 (ptp) cc_final: 0.5770 (pp-130) REVERT: A 376 MET cc_start: 0.8743 (mmt) cc_final: 0.8341 (mmt) REVERT: B 421 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.2983 (p90) REVERT: C 64 PHE cc_start: 0.7882 (m-80) cc_final: 0.7617 (m-80) REVERT: C 80 TYR cc_start: 0.5978 (m-80) cc_final: 0.5208 (m-80) REVERT: C 95 TYR cc_start: 0.6247 (m-10) cc_final: 0.5980 (m-10) REVERT: C 158 ASP cc_start: 0.8386 (t0) cc_final: 0.7912 (t0) REVERT: C 193 SER cc_start: 0.9186 (m) cc_final: 0.8776 (p) outliers start: 20 outliers final: 10 residues processed: 127 average time/residue: 0.4906 time to fit residues: 67.7598 Evaluate side-chains 118 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 247 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS 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 D residue 169 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 52 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.0050 chunk 51 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 277 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 = 0.4637 r_free = 0.4637 target = 0.143017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.117851 restraints weight = 73451.589| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 8.19 r_work: 0.4035 rms_B_bonded: 7.76 restraints_weight: 2.0000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10069 Z= 0.150 Angle : 0.868 18.415 13711 Z= 0.417 Chirality : 0.046 0.314 1505 Planarity : 0.005 0.064 1738 Dihedral : 5.718 46.047 1616 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.02 % Favored : 92.81 % Rotamer: Outliers : 2.10 % Allowed : 24.19 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.24), residues: 1199 helix: -0.25 (0.25), residues: 395 sheet: -0.90 (0.34), residues: 225 loop : -1.54 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 518 TYR 0.033 0.002 TYR C 54 PHE 0.020 0.001 PHE A 464 TRP 0.042 0.002 TRP A 163 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00335 (10042) covalent geometry : angle 0.85922 (13646) SS BOND : bond 0.00590 ( 10) SS BOND : angle 1.86796 ( 20) hydrogen bonds : bond 0.04445 ( 371) hydrogen bonds : angle 5.60413 ( 1081) metal coordination : bond 0.00011 ( 2) link_ALPHA1-3 : bond 0.01050 ( 1) link_ALPHA1-3 : angle 1.42301 ( 3) link_BETA1-4 : bond 0.00533 ( 7) link_BETA1-4 : angle 1.98489 ( 21) link_NAG-ASN : bond 0.00438 ( 7) link_NAG-ASN : angle 2.17303 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5131.25 seconds wall clock time: 88 minutes 0.71 seconds (5280.71 seconds total)