Starting phenix.real_space_refine on Sun Aug 4 06:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6a_38983/08_2024/8y6a_38983.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 6214 2.51 5 N 1618 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9786 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 587, 4783 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560} Conformer: "B" Number of residues, atoms: 587, 4783 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 560} bond proxies already assigned to first conformer: 4902 Chain: "B" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Chain: "D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.03, per 1000 atoms: 0.82 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 - 3.50 Amino acid : False - 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: 4.40 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 802 " - pdb=" NE2 HIS A 374 " 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 36.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 53 removed outlier: 4.644A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.665A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.846A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.203A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.633A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.970A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.613A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.923A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.759A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.743A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.560A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.133A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.318A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.292A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.659A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.531A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.630A pdb=" N THR B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.450A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.865A pdb=" N SER C 194 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.865A pdb=" N SER C 194 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 191 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 183 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 4.073A pdb=" N TYR C 208 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.081A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.081A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 29 removed outlier: 12.432A pdb=" N CYS D 23 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 11.416A pdb=" N THR D 75 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ALA D 25 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N THR D 73 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N GLN D 27 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP D 71 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 139 removed outlier: 3.593A pdb=" N LEU D 175 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 178 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 153 through 154 396 hydrogen bonds defined for protein. 1081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.78 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: 99.58 - 106.47: 314 106.47 - 113.36: 5403 113.36 - 120.24: 3530 120.24 - 127.13: 4264 127.13 - 134.02: 135 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: 1.840 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 34.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- 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 10042 Z= 0.254 Angle : 0.731 7.454 13646 Z= 0.418 Chirality : 0.061 0.860 1505 Planarity : 0.008 0.167 1738 Dihedral : 15.694 106.313 3857 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.52 % Favored : 92.98 % Rotamer: Outliers : 0.48 % Allowed : 0.76 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1199 helix: -0.63 (0.25), residues: 409 sheet: -0.76 (0.37), residues: 199 loop : -1.88 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 459 HIS 0.007 0.001 HIS A 374 PHE 0.035 0.001 PHE A 464 TYR 0.021 0.002 TYR B 501 ARG 0.007 0.000 ARG B 454 *********************** 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 fitting. rotamer outliers: 5 poor density : 269 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.1196 (OUTLIER) cc_final: -0.0169 (mm110) REVERT: A 31 LYS cc_start: 0.5644 (OUTLIER) cc_final: 0.4484 (tptm) REVERT: A 111 ASP cc_start: 0.9017 (t70) cc_final: 0.8805 (p0) REVERT: A 117 ASN cc_start: 0.7759 (m-40) cc_final: 0.7535 (t0) REVERT: A 179 LEU cc_start: 0.8778 (mm) cc_final: 0.8378 (mm) REVERT: A 196 TYR cc_start: 0.7583 (m-80) cc_final: 0.7170 (m-10) REVERT: A 429 GLN cc_start: 0.8218 (mt0) cc_final: 0.7949 (pp30) REVERT: A 577 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7240 (pttt) REVERT: B 366 SER cc_start: 0.9254 (m) cc_final: 0.8996 (p) REVERT: C 80 TYR cc_start: 0.6027 (m-80) cc_final: 0.5343 (m-80) REVERT: D 162 SER cc_start: 0.7972 (t) cc_final: 0.7699 (m) outliers start: 5 outliers final: 2 residues processed: 272 average time/residue: 1.2514 time to fit residues: 363.6107 Evaluate side-chains 138 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 508 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 422 ASN B 474 GLN C 57 ASN C 62 GLN C 65 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 189 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10042 Z= 0.281 Angle : 0.845 14.059 13646 Z= 0.425 Chirality : 0.047 0.237 1505 Planarity : 0.005 0.047 1738 Dihedral : 10.450 76.871 1623 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.11 % Favored : 92.56 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1199 helix: -0.70 (0.24), residues: 410 sheet: -0.94 (0.37), residues: 204 loop : -1.86 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 168 HIS 0.009 0.002 HIS C 214 PHE 0.031 0.002 PHE A 523 TYR 0.030 0.002 TYR A 587 ARG 0.007 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.118 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: 0.0926 (OUTLIER) cc_final: -0.0596 (mm110) REVERT: A 31 LYS cc_start: 0.5489 (OUTLIER) cc_final: 0.4885 (tptm) REVERT: A 111 ASP cc_start: 0.9049 (t70) cc_final: 0.8831 (p0) REVERT: A 162 LEU cc_start: 0.9291 (tm) cc_final: 0.9000 (mt) REVERT: A 195 HIS cc_start: 0.7014 (t-90) cc_final: 0.6779 (t70) REVERT: A 248 LEU cc_start: 0.6767 (mt) cc_final: 0.6317 (tt) REVERT: A 376 MET cc_start: 0.8856 (mmt) cc_final: 0.8586 (mmt) REVERT: A 429 GLN cc_start: 0.8190 (mt0) cc_final: 0.7987 (pp30) REVERT: C 80 TYR cc_start: 0.5896 (m-80) cc_final: 0.5303 (m-80) REVERT: C 158 ASP cc_start: 0.8067 (t0) cc_final: 0.7655 (t0) REVERT: C 193 SER cc_start: 0.8884 (m) cc_final: 0.8589 (p) outliers start: 24 outliers final: 9 residues processed: 176 average time/residue: 1.0379 time to fit residues: 198.3238 Evaluate side-chains 134 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 508 ASN C 62 GLN C 65 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10042 Z= 0.251 Angle : 0.819 16.634 13646 Z= 0.407 Chirality : 0.046 0.240 1505 Planarity : 0.005 0.050 1738 Dihedral : 8.795 56.669 1620 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.81 % Rotamer: Outliers : 3.24 % Allowed : 16.76 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1199 helix: -0.57 (0.25), residues: 402 sheet: -1.05 (0.36), residues: 201 loop : -1.84 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 163 HIS 0.009 0.001 HIS C 214 PHE 0.023 0.002 PHE A 464 TYR 0.046 0.002 TYR A 202 ARG 0.009 0.001 ARG D 78 *********************** 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 169 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0803 (OUTLIER) cc_final: -0.0667 (mm110) REVERT: A 111 ASP cc_start: 0.9016 (t70) cc_final: 0.8784 (p0) REVERT: A 162 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8988 (mt) REVERT: A 248 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6183 (tt) REVERT: A 376 MET cc_start: 0.8821 (mmt) cc_final: 0.8456 (mmt) REVERT: B 421 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.3292 (p90) REVERT: C 64 PHE cc_start: 0.7327 (m-80) cc_final: 0.7099 (m-80) REVERT: C 80 TYR cc_start: 0.5933 (m-80) cc_final: 0.5304 (m-80) REVERT: C 158 ASP cc_start: 0.7953 (t0) cc_final: 0.7495 (t0) REVERT: C 193 SER cc_start: 0.8954 (m) cc_final: 0.8543 (p) REVERT: D 137 ASN cc_start: 0.7707 (t0) cc_final: 0.6636 (p0) outliers start: 34 outliers final: 10 residues processed: 152 average time/residue: 1.0208 time to fit residues: 169.4366 Evaluate side-chains 125 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 A residue 592 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.165 10042 Z= 0.422 Angle : 0.895 13.885 13646 Z= 0.450 Chirality : 0.049 0.332 1505 Planarity : 0.006 0.058 1738 Dihedral : 7.811 53.330 1616 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.03 % Favored : 90.72 % Rotamer: Outliers : 3.62 % Allowed : 18.29 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1199 helix: -0.72 (0.24), residues: 394 sheet: -1.15 (0.36), residues: 203 loop : -1.85 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 168 HIS 0.009 0.002 HIS A 401 PHE 0.031 0.002 PHE A 464 TYR 0.038 0.003 TYR A 381 ARG 0.014 0.001 ARG A 518 *********************** 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 169 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0682 (OUTLIER) cc_final: -0.1186 (mm110) REVERT: A 111 ASP cc_start: 0.8991 (t70) cc_final: 0.8769 (p0) REVERT: A 162 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8961 (mt) REVERT: A 248 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6121 (tt) REVERT: A 255 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.4054 (m-10) REVERT: A 297 MET cc_start: 0.6020 (mmp) cc_final: 0.5564 (mmp) REVERT: A 376 MET cc_start: 0.8892 (mmt) cc_final: 0.8505 (mmt) REVERT: B 421 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.3051 (p90) REVERT: C 158 ASP cc_start: 0.8024 (t0) cc_final: 0.7527 (t0) REVERT: C 193 SER cc_start: 0.8871 (m) cc_final: 0.8455 (p) REVERT: D 175 LEU cc_start: 0.9138 (tt) cc_final: 0.8928 (mt) outliers start: 38 outliers final: 16 residues processed: 157 average time/residue: 0.9136 time to fit residues: 157.8520 Evaluate side-chains 133 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 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 42 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10042 Z= 0.244 Angle : 0.824 16.726 13646 Z= 0.406 Chirality : 0.045 0.270 1505 Planarity : 0.005 0.054 1738 Dihedral : 6.637 48.653 1616 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 2.48 % Allowed : 20.48 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.23), residues: 1199 helix: -0.44 (0.25), residues: 395 sheet: -1.13 (0.34), residues: 211 loop : -1.70 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.023 0.002 PHE A 525 TYR 0.028 0.002 TYR C 27 ARG 0.012 0.001 ARG D 24 *********************** 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 142 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.309 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: A 24 GLN cc_start: 0.0585 (OUTLIER) cc_final: -0.1409 (mm110) REVERT: A 111 ASP cc_start: 0.9005 (t70) cc_final: 0.8756 (p0) REVERT: A 248 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6043 (tt) REVERT: A 255 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.3959 (m-10) REVERT: A 297 MET cc_start: 0.5746 (mmp) cc_final: 0.4733 (tpp) REVERT: A 376 MET cc_start: 0.8842 (mmt) cc_final: 0.8444 (mmt) REVERT: B 421 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.3171 (p90) REVERT: C 64 PHE cc_start: 0.7344 (m-80) cc_final: 0.7137 (m-80) REVERT: C 158 ASP cc_start: 0.8071 (t0) cc_final: 0.7435 (p0) REVERT: C 193 SER cc_start: 0.8920 (m) cc_final: 0.8552 (p) REVERT: D 137 ASN cc_start: 0.7841 (t0) cc_final: 0.6875 (p0) REVERT: D 175 LEU cc_start: 0.9123 (tt) cc_final: 0.8922 (mt) outliers start: 26 outliers final: 13 residues processed: 134 average time/residue: 0.9638 time to fit residues: 141.5918 Evaluate side-chains 122 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 255 TYR 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 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 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0040 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10042 Z= 0.271 Angle : 0.830 16.795 13646 Z= 0.408 Chirality : 0.045 0.288 1505 Planarity : 0.005 0.048 1738 Dihedral : 6.145 36.303 1616 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 2.76 % Allowed : 21.14 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1199 helix: -0.36 (0.25), residues: 396 sheet: -1.09 (0.35), residues: 213 loop : -1.62 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 163 HIS 0.006 0.001 HIS C 214 PHE 0.027 0.002 PHE D 209 TYR 0.036 0.002 TYR A 202 ARG 0.008 0.001 ARG D 78 *********************** 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 fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.212 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: 0.0823 (OUTLIER) cc_final: -0.1274 (mm110) REVERT: A 111 ASP cc_start: 0.8979 (t70) cc_final: 0.8736 (p0) REVERT: A 248 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6012 (tt) REVERT: A 297 MET cc_start: 0.5768 (mmp) cc_final: 0.4689 (tpp) REVERT: A 376 MET cc_start: 0.8851 (mmt) cc_final: 0.8447 (mmt) REVERT: B 421 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.3052 (p90) REVERT: C 80 TYR cc_start: 0.6030 (m-80) cc_final: 0.5393 (m-80) REVERT: C 158 ASP cc_start: 0.7976 (t0) cc_final: 0.7363 (p0) REVERT: C 193 SER cc_start: 0.8993 (m) cc_final: 0.8641 (p) REVERT: D 137 ASN cc_start: 0.7983 (t0) cc_final: 0.7060 (p0) REVERT: D 209 PHE cc_start: 0.7338 (t80) cc_final: 0.7116 (t80) outliers start: 29 outliers final: 18 residues processed: 138 average time/residue: 0.9535 time to fit residues: 144.5006 Evaluate side-chains 123 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 423 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 10042 Z= 0.342 Angle : 0.888 17.471 13646 Z= 0.439 Chirality : 0.047 0.300 1505 Planarity : 0.005 0.045 1738 Dihedral : 6.133 36.705 1616 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.03 % Favored : 91.72 % Rotamer: Outliers : 2.57 % Allowed : 22.48 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.23), residues: 1199 helix: -0.46 (0.25), residues: 391 sheet: -1.14 (0.35), residues: 220 loop : -1.65 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 163 HIS 0.007 0.001 HIS A 401 PHE 0.027 0.002 PHE A 464 TYR 0.025 0.002 TYR A 381 ARG 0.007 0.001 ARG A 518 *********************** 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 140 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0579 (OUTLIER) cc_final: -0.1340 (mm110) REVERT: A 111 ASP cc_start: 0.8964 (t70) cc_final: 0.8700 (p0) REVERT: A 376 MET cc_start: 0.8867 (mmt) cc_final: 0.8448 (mmt) REVERT: B 421 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.3023 (p90) REVERT: C 80 TYR cc_start: 0.6019 (m-80) cc_final: 0.5422 (m-80) REVERT: C 158 ASP cc_start: 0.7993 (t0) cc_final: 0.7385 (p0) REVERT: C 193 SER cc_start: 0.8966 (m) cc_final: 0.8563 (p) REVERT: D 137 ASN cc_start: 0.8052 (t0) cc_final: 0.7143 (p0) outliers start: 27 outliers final: 17 residues processed: 131 average time/residue: 0.9630 time to fit residues: 139.4418 Evaluate side-chains 123 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 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 C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 40.0000 chunk 100 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10042 Z= 0.237 Angle : 0.858 18.025 13646 Z= 0.417 Chirality : 0.045 0.223 1505 Planarity : 0.005 0.079 1738 Dihedral : 5.815 39.652 1616 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.77 % Favored : 92.98 % Rotamer: Outliers : 2.57 % Allowed : 22.67 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1199 helix: -0.26 (0.25), residues: 394 sheet: -1.01 (0.35), residues: 214 loop : -1.60 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.027 0.002 PHE A 525 TYR 0.025 0.002 TYR C 54 ARG 0.014 0.001 ARG A 518 *********************** 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 142 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.134 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: 0.0595 (OUTLIER) cc_final: -0.1261 (mm-40) REVERT: A 111 ASP cc_start: 0.8949 (t70) cc_final: 0.8679 (p0) REVERT: A 287 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: A 376 MET cc_start: 0.8814 (mmt) cc_final: 0.8537 (mmt) REVERT: B 421 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.3255 (p90) REVERT: C 80 TYR cc_start: 0.5857 (m-80) cc_final: 0.5317 (m-80) REVERT: C 158 ASP cc_start: 0.7977 (t0) cc_final: 0.7387 (p0) REVERT: C 193 SER cc_start: 0.8889 (m) cc_final: 0.8532 (p) REVERT: D 137 ASN cc_start: 0.8025 (t0) cc_final: 0.7123 (p0) REVERT: D 209 PHE cc_start: 0.7152 (t80) cc_final: 0.6919 (t80) outliers start: 27 outliers final: 17 residues processed: 134 average time/residue: 0.9261 time to fit residues: 136.5083 Evaluate side-chains 121 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10042 Z= 0.259 Angle : 0.850 19.031 13646 Z= 0.416 Chirality : 0.045 0.239 1505 Planarity : 0.005 0.093 1738 Dihedral : 5.774 40.566 1616 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.44 % Favored : 92.39 % Rotamer: Outliers : 2.00 % Allowed : 23.71 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1199 helix: -0.22 (0.25), residues: 395 sheet: -0.91 (0.35), residues: 215 loop : -1.60 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 163 HIS 0.005 0.001 HIS C 214 PHE 0.024 0.002 PHE A 525 TYR 0.024 0.002 TYR C 54 ARG 0.019 0.001 ARG A 518 *********************** 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 127 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0828 (OUTLIER) cc_final: -0.1003 (mm-40) REVERT: A 111 ASP cc_start: 0.8968 (t70) cc_final: 0.8686 (p0) REVERT: A 287 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: A 376 MET cc_start: 0.8834 (mmt) cc_final: 0.8463 (mmt) REVERT: B 421 TYR cc_start: 0.5760 (OUTLIER) cc_final: 0.3127 (p90) REVERT: C 80 TYR cc_start: 0.5894 (m-80) cc_final: 0.5307 (m-80) REVERT: C 158 ASP cc_start: 0.8013 (t0) cc_final: 0.7427 (p0) REVERT: C 193 SER cc_start: 0.8879 (m) cc_final: 0.8532 (p) REVERT: D 137 ASN cc_start: 0.8053 (t0) cc_final: 0.7135 (p0) REVERT: D 209 PHE cc_start: 0.7130 (t80) cc_final: 0.6848 (t80) outliers start: 21 outliers final: 15 residues processed: 123 average time/residue: 0.8944 time to fit residues: 121.1913 Evaluate side-chains 123 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 94 optimal weight: 0.0970 chunk 9 optimal weight: 0.0770 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10042 Z= 0.226 Angle : 0.863 17.524 13646 Z= 0.421 Chirality : 0.045 0.233 1505 Planarity : 0.005 0.095 1738 Dihedral : 5.759 43.939 1616 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.89 % Rotamer: Outliers : 1.62 % Allowed : 24.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1199 helix: -0.14 (0.26), residues: 396 sheet: -0.85 (0.35), residues: 216 loop : -1.57 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.002 PHE A 525 TYR 0.026 0.002 TYR A 516 ARG 0.021 0.001 ARG A 518 ********************** 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 130 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.0735 (OUTLIER) cc_final: -0.1046 (mm110) REVERT: A 100 LEU cc_start: 0.4600 (tp) cc_final: 0.4379 (tt) REVERT: A 111 ASP cc_start: 0.8980 (t70) cc_final: 0.8690 (p0) REVERT: A 159 ASN cc_start: 0.8140 (t0) cc_final: 0.7912 (p0) REVERT: A 255 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.3678 (m-10) REVERT: A 334 THR cc_start: 0.8689 (m) cc_final: 0.8473 (p) REVERT: A 376 MET cc_start: 0.8791 (mmt) cc_final: 0.8434 (mmt) REVERT: B 421 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.2994 (p90) REVERT: C 158 ASP cc_start: 0.8043 (t0) cc_final: 0.7483 (p0) REVERT: C 193 SER cc_start: 0.8975 (m) cc_final: 0.8667 (p) REVERT: D 137 ASN cc_start: 0.8034 (t0) cc_final: 0.7133 (p0) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.9599 time to fit residues: 133.3522 Evaluate side-chains 116 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 255 TYR 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 C residue 27 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.117978 restraints weight = 53828.413| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 5.76 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4230 r_free = 0.4230 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 = 0.4230 r_free = 0.4230 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10042 Z= 0.240 Angle : 0.866 16.782 13646 Z= 0.428 Chirality : 0.045 0.228 1505 Planarity : 0.005 0.051 1738 Dihedral : 5.729 43.374 1616 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 1.62 % Allowed : 24.38 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1199 helix: -0.20 (0.26), residues: 394 sheet: -0.81 (0.34), residues: 220 loop : -1.61 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.028 0.002 PHE A 525 TYR 0.022 0.002 TYR C 54 ARG 0.009 0.001 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.32 seconds wall clock time: 68 minutes 55.65 seconds (4135.65 seconds total)