Starting phenix.real_space_refine on Thu Feb 15 11:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c96_7434/02_2024/6c96_7434.pdb" } resolution = 3.4 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= 0.007 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 S 76 5.16 5 Na 2 4.78 5 C 7960 2.51 5 N 1978 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 787": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12090 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "B" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 6002 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 20, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: 6.48, per 1000 atoms: 0.54 Number of scatterers: 12090 At special positions: 0 Unit cell: (131.61, 105.93, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Na 2 11.00 O 2074 8.00 N 1978 7.00 C 7960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1003 " - " ASN A 612 " " NAG B1003 " - " ASN B 612 " " NAG C 1 " - " ASN A 600 " " NAG D 1 " - " ASN B 600 " Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 2.3 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 75.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 66 through 84 removed outlier: 3.784A pdb=" N GLY A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 123 removed outlier: 3.510A pdb=" N TYR A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 removed outlier: 3.812A pdb=" N GLU A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 137 through 163 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.028A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 4.351A pdb=" N ILE A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.965A pdb=" N THR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.617A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 4.010A pdb=" N ARG A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 350 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 441 through 466 removed outlier: 3.883A pdb=" N GLN A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 450 " --> pdb=" O TYR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.801A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 588 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.533A pdb=" N ASN A 617 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 4.460A pdb=" N ILE A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.784A pdb=" N GLY B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.007A pdb=" N LEU B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.508A pdb=" N TYR B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 3.811A pdb=" N GLU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 137 through 163 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.772A pdb=" N MET B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 206 through 212 removed outlier: 4.029A pdb=" N LEU B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.548A pdb=" N SER B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 256 removed outlier: 4.352A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.964A pdb=" N THR B 279 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.616A pdb=" N MET B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 4.010A pdb=" N ARG B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.917A pdb=" N PHE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 350 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 441 through 466 removed outlier: 3.884A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 499 removed outlier: 3.625A pdb=" N VAL B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 505 Processing helix chain 'B' and resid 507 through 527 removed outlier: 3.673A pdb=" N PHE B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 550 removed outlier: 3.803A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 550 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 removed outlier: 3.645A pdb=" N ARG B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 588 Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.532A pdb=" N ASN B 617 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 614 through 618' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.790A pdb=" N ASN B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 removed outlier: 3.762A pdb=" N VAL B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 4.461A pdb=" N ILE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 698 removed outlier: 4.137A pdb=" N PHE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 removed outlier: 3.675A pdb=" N LEU B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 752 removed outlier: 3.826A pdb=" N VAL B 738 " --> pdb=" O THR B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 774 Processing helix chain 'B' and resid 777 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA4, first strand: chain 'B' and resid 610 through 613 773 hydrogen bonds defined for protein. 2241 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: 4.09 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3562 1.34 - 1.45: 2387 1.45 - 1.57: 6317 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 12402 Sorted by residual: bond pdb=" CB ASN A 222 " pdb=" CG ASN A 222 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.19e+00 bond pdb=" CB ASN B 222 " pdb=" CG ASN B 222 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.09e+00 bond pdb=" CG1 ILE A 236 " pdb=" CD1 ILE A 236 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.14e+00 bond pdb=" CG1 ILE B 236 " pdb=" CD1 ILE B 236 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 bond pdb=" C1 NAG A1003 " pdb=" O5 NAG A1003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 12397 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.12: 185 105.12 - 112.36: 6071 112.36 - 119.60: 4469 119.60 - 126.83: 5929 126.83 - 134.07: 138 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 112.83 107.38 5.45 9.90e-01 1.02e+00 3.04e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 112.83 107.39 5.44 9.90e-01 1.02e+00 3.02e+01 angle pdb=" CA THR B 619 " pdb=" CB THR B 619 " pdb=" CG2 THR B 619 " ideal model delta sigma weight residual 110.50 117.76 -7.26 1.70e+00 3.46e-01 1.82e+01 angle pdb=" CA THR A 619 " pdb=" CB THR A 619 " pdb=" CG2 THR A 619 " ideal model delta sigma weight residual 110.50 117.73 -7.23 1.70e+00 3.46e-01 1.81e+01 angle pdb=" CA ARG B 355 " pdb=" CB ARG B 355 " pdb=" CG ARG B 355 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.52e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 6862 15.13 - 30.25: 396 30.25 - 45.38: 102 45.38 - 60.51: 6 60.51 - 75.63: 4 Dihedral angle restraints: 7370 sinusoidal: 3066 harmonic: 4304 Sorted by residual: dihedral pdb=" CA THR B 645 " pdb=" C THR B 645 " pdb=" N VAL B 646 " pdb=" CA VAL B 646 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA THR A 645 " pdb=" C THR A 645 " pdb=" N VAL A 646 " pdb=" CA VAL A 646 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA SER A 128 " pdb=" C SER A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1172 0.050 - 0.101: 541 0.101 - 0.151: 150 0.151 - 0.201: 25 0.201 - 0.251: 10 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.32e+00 chirality pdb=" CA THR A 619 " pdb=" N THR A 619 " pdb=" C THR A 619 " pdb=" CB THR A 619 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR B 619 " pdb=" N THR B 619 " pdb=" C THR B 619 " pdb=" CB THR B 619 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1895 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 355 " 0.043 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 356 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 355 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO B 356 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 128 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 129 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.036 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3381 2.80 - 3.33: 11053 3.33 - 3.85: 18816 3.85 - 4.38: 21201 4.38 - 4.90: 36317 Nonbonded interactions: 90768 Sorted by model distance: nonbonded pdb=" OE1 GLU B 623 " pdb=" OH TYR B 627 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLU A 623 " pdb=" OH TYR A 627 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 480 " pdb=" O ALA A 519 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B 480 " pdb=" O ALA B 519 " model vdw 2.282 2.440 nonbonded pdb=" OD2 ASP A 326 " pdb=" NH1 ARG B 699 " model vdw 2.318 2.520 ... (remaining 90763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 795 or resid 1003)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=1.00 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: 2.880 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: 0.020 Extract box with map and model: 5.130 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 38.190 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.010 0.090 12402 Z= 0.595 Angle : 1.050 9.725 16792 Z= 0.564 Chirality : 0.061 0.251 1898 Planarity : 0.007 0.063 2066 Dihedral : 10.434 75.633 4582 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.30 % Allowed : 3.04 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.38 (0.17), residues: 1438 helix: -2.62 (0.11), residues: 1042 sheet: -2.73 (0.66), residues: 40 loop : -3.09 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 508 HIS 0.010 0.002 HIS B 141 PHE 0.028 0.003 PHE B 638 TYR 0.043 0.004 TYR A 110 ARG 0.011 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 313 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8257 (t0) cc_final: 0.7954 (t0) REVERT: A 111 MET cc_start: 0.8333 (tpp) cc_final: 0.8026 (tpp) REVERT: A 153 VAL cc_start: 0.9232 (t) cc_final: 0.9008 (t) REVERT: A 347 TYR cc_start: 0.8665 (t80) cc_final: 0.7821 (t80) REVERT: A 399 ASP cc_start: 0.7753 (m-30) cc_final: 0.7521 (m-30) REVERT: A 440 ASN cc_start: 0.8353 (t0) cc_final: 0.7703 (m110) REVERT: A 458 TRP cc_start: 0.8268 (t-100) cc_final: 0.7886 (t-100) REVERT: A 515 VAL cc_start: 0.9056 (t) cc_final: 0.8804 (m) REVERT: B 106 ASN cc_start: 0.8087 (t0) cc_final: 0.7669 (t0) REVERT: B 123 LEU cc_start: 0.8933 (tt) cc_final: 0.8672 (tt) REVERT: B 144 LEU cc_start: 0.8948 (mt) cc_final: 0.8640 (mt) REVERT: B 150 MET cc_start: 0.8133 (tpt) cc_final: 0.7850 (tpp) REVERT: B 224 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7761 (ptp-170) REVERT: B 226 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8742 (mt) REVERT: B 347 TYR cc_start: 0.8852 (t80) cc_final: 0.8580 (t80) REVERT: B 440 ASN cc_start: 0.8186 (t0) cc_final: 0.7476 (m110) REVERT: B 458 TRP cc_start: 0.8305 (t-100) cc_final: 0.7952 (t-100) REVERT: B 726 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8318 (tp30) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.2416 time to fit residues: 107.8884 Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 222 ASN A 314 ASN A 388 ASN A 509 ASN A 591 ASN A 636 ASN A 785 HIS B 222 ASN B 314 ASN B 388 ASN B 509 ASN B 636 ASN B 785 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12402 Z= 0.187 Angle : 0.639 8.803 16792 Z= 0.333 Chirality : 0.042 0.244 1898 Planarity : 0.005 0.044 2066 Dihedral : 5.221 51.273 1728 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.90 % Allowed : 10.79 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1438 helix: -0.29 (0.15), residues: 1056 sheet: -1.76 (0.60), residues: 60 loop : -2.65 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 650 HIS 0.010 0.001 HIS A 141 PHE 0.021 0.001 PHE A 89 TYR 0.020 0.002 TYR B 487 ARG 0.009 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 225 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.7700 (ttm) cc_final: 0.7395 (ttt) REVERT: A 111 MET cc_start: 0.8405 (tpp) cc_final: 0.8204 (tpp) REVERT: A 175 MET cc_start: 0.8473 (mmt) cc_final: 0.8187 (mmt) REVERT: A 347 TYR cc_start: 0.8507 (t80) cc_final: 0.7772 (t80) REVERT: A 399 ASP cc_start: 0.7729 (m-30) cc_final: 0.7440 (p0) REVERT: A 440 ASN cc_start: 0.8145 (t0) cc_final: 0.7422 (m110) REVERT: A 458 TRP cc_start: 0.8168 (t-100) cc_final: 0.7846 (t-100) REVERT: B 106 ASN cc_start: 0.7852 (t0) cc_final: 0.7535 (t0) REVERT: B 111 MET cc_start: 0.8698 (tpp) cc_final: 0.8254 (tpp) REVERT: B 112 MET cc_start: 0.8703 (tmm) cc_final: 0.8450 (tmm) REVERT: B 144 LEU cc_start: 0.8837 (mt) cc_final: 0.8543 (mt) REVERT: B 150 MET cc_start: 0.8065 (tpt) cc_final: 0.7760 (tpp) REVERT: B 155 GLU cc_start: 0.8131 (tt0) cc_final: 0.7931 (tt0) REVERT: B 440 ASN cc_start: 0.8097 (t0) cc_final: 0.7240 (m110) REVERT: B 445 GLN cc_start: 0.8935 (mt0) cc_final: 0.8626 (mp10) REVERT: B 458 TRP cc_start: 0.8205 (t-100) cc_final: 0.7797 (t-100) REVERT: B 490 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8008 (pp20) REVERT: B 726 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8425 (tp30) outliers start: 25 outliers final: 12 residues processed: 236 average time/residue: 0.1938 time to fit residues: 69.9453 Evaluate side-chains 186 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12402 Z= 0.237 Angle : 0.601 12.402 16792 Z= 0.312 Chirality : 0.041 0.162 1898 Planarity : 0.004 0.046 2066 Dihedral : 4.552 20.672 1726 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.74 % Allowed : 13.75 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.22), residues: 1438 helix: 0.51 (0.16), residues: 1062 sheet: -1.48 (0.60), residues: 64 loop : -2.62 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 508 HIS 0.008 0.001 HIS A 141 PHE 0.014 0.001 PHE B 686 TYR 0.016 0.002 TYR A 110 ARG 0.003 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 146 LEU cc_start: 0.8469 (mp) cc_final: 0.8186 (mp) REVERT: A 313 MET cc_start: 0.8456 (tpp) cc_final: 0.8201 (mmt) REVERT: A 347 TYR cc_start: 0.8533 (t80) cc_final: 0.7741 (t80) REVERT: A 399 ASP cc_start: 0.7827 (m-30) cc_final: 0.7574 (p0) REVERT: A 440 ASN cc_start: 0.8431 (t0) cc_final: 0.7568 (m110) REVERT: A 448 MET cc_start: 0.8700 (tpt) cc_final: 0.8479 (tpt) REVERT: A 458 TRP cc_start: 0.8162 (t-100) cc_final: 0.7927 (t-100) REVERT: A 748 MET cc_start: 0.4146 (ptp) cc_final: 0.3891 (ptp) REVERT: B 106 ASN cc_start: 0.7945 (t0) cc_final: 0.7630 (t0) REVERT: B 119 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8682 (tp) REVERT: B 175 MET cc_start: 0.8192 (mmt) cc_final: 0.7846 (mmt) REVERT: B 224 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7817 (ptp-170) REVERT: B 310 TYR cc_start: 0.8075 (t80) cc_final: 0.7867 (t80) REVERT: B 440 ASN cc_start: 0.8325 (t0) cc_final: 0.7383 (m110) REVERT: B 458 TRP cc_start: 0.8326 (t-100) cc_final: 0.7987 (t-100) REVERT: B 462 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8414 (tp30) outliers start: 36 outliers final: 21 residues processed: 214 average time/residue: 0.2069 time to fit residues: 67.1674 Evaluate side-chains 195 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 789 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12402 Z= 0.184 Angle : 0.569 11.153 16792 Z= 0.292 Chirality : 0.040 0.173 1898 Planarity : 0.004 0.038 2066 Dihedral : 4.301 19.963 1726 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.04 % Allowed : 15.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.23), residues: 1438 helix: 0.95 (0.16), residues: 1066 sheet: -1.40 (0.62), residues: 64 loop : -2.45 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 650 HIS 0.008 0.001 HIS A 141 PHE 0.012 0.001 PHE B 686 TYR 0.011 0.001 TYR A 110 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8654 (tpp) cc_final: 0.8300 (tpp) REVERT: A 119 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 175 MET cc_start: 0.8410 (mmt) cc_final: 0.7976 (mmt) REVERT: A 313 MET cc_start: 0.8335 (tpp) cc_final: 0.8071 (mmt) REVERT: A 399 ASP cc_start: 0.7823 (m-30) cc_final: 0.7570 (p0) REVERT: A 440 ASN cc_start: 0.8453 (t0) cc_final: 0.7522 (m110) REVERT: A 680 MET cc_start: 0.7263 (mmm) cc_final: 0.7053 (mmm) REVERT: B 111 MET cc_start: 0.8717 (tpp) cc_final: 0.8500 (tpp) REVERT: B 113 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 382 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 440 ASN cc_start: 0.8255 (t0) cc_final: 0.7331 (m110) REVERT: B 458 TRP cc_start: 0.8226 (t-100) cc_final: 0.7974 (t-100) REVERT: B 670 MET cc_start: 0.8332 (mtt) cc_final: 0.8027 (mtt) REVERT: B 695 MET cc_start: 0.8221 (mmt) cc_final: 0.7477 (mmm) outliers start: 40 outliers final: 16 residues processed: 212 average time/residue: 0.2100 time to fit residues: 68.1590 Evaluate side-chains 193 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12402 Z= 0.207 Angle : 0.565 10.916 16792 Z= 0.290 Chirality : 0.040 0.178 1898 Planarity : 0.004 0.040 2066 Dihedral : 4.177 19.381 1726 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.96 % Allowed : 15.43 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.23), residues: 1438 helix: 1.20 (0.16), residues: 1068 sheet: -1.16 (0.63), residues: 64 loop : -2.35 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 458 HIS 0.007 0.001 HIS A 141 PHE 0.016 0.001 PHE A 447 TYR 0.015 0.001 TYR A 487 ARG 0.003 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ASP cc_start: 0.7834 (m-30) cc_final: 0.7596 (p0) REVERT: A 440 ASN cc_start: 0.8323 (t0) cc_final: 0.7530 (m110) REVERT: A 448 MET cc_start: 0.8930 (tpt) cc_final: 0.8679 (mmt) REVERT: A 462 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 493 MET cc_start: 0.8559 (ttm) cc_final: 0.8349 (ttp) REVERT: A 670 MET cc_start: 0.8356 (mtt) cc_final: 0.8050 (mtt) REVERT: A 680 MET cc_start: 0.7257 (mmm) cc_final: 0.7022 (mmm) REVERT: B 111 MET cc_start: 0.8772 (tpp) cc_final: 0.8559 (tpp) REVERT: B 175 MET cc_start: 0.8166 (mmt) cc_final: 0.7806 (mmt) REVERT: B 310 TYR cc_start: 0.8160 (t80) cc_final: 0.7856 (t80) REVERT: B 382 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8244 (mp) REVERT: B 440 ASN cc_start: 0.8323 (t0) cc_final: 0.7396 (m110) REVERT: B 458 TRP cc_start: 0.8201 (t-100) cc_final: 0.7988 (t-100) REVERT: B 465 MET cc_start: 0.8466 (tpp) cc_final: 0.8255 (tpp) REVERT: B 540 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8437 (mtm-85) REVERT: B 670 MET cc_start: 0.8333 (mtt) cc_final: 0.8041 (mtt) REVERT: B 695 MET cc_start: 0.8271 (mmt) cc_final: 0.7612 (mmm) outliers start: 39 outliers final: 23 residues processed: 214 average time/residue: 0.2068 time to fit residues: 66.7038 Evaluate side-chains 191 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12402 Z= 0.176 Angle : 0.548 12.929 16792 Z= 0.279 Chirality : 0.039 0.175 1898 Planarity : 0.003 0.036 2066 Dihedral : 4.070 18.590 1726 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.36 % Allowed : 16.26 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.23), residues: 1438 helix: 1.32 (0.16), residues: 1080 sheet: -1.03 (0.63), residues: 64 loop : -2.35 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.007 0.001 HIS B 141 PHE 0.015 0.001 PHE B 447 TYR 0.013 0.001 TYR B 487 ARG 0.003 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8702 (tpp) cc_final: 0.8440 (tpp) REVERT: A 234 MET cc_start: 0.8165 (mmm) cc_final: 0.7907 (mmm) REVERT: A 399 ASP cc_start: 0.7782 (m-30) cc_final: 0.7530 (p0) REVERT: A 440 ASN cc_start: 0.8340 (t0) cc_final: 0.7524 (m110) REVERT: A 448 MET cc_start: 0.8958 (tpt) cc_final: 0.8635 (mmt) REVERT: A 462 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 520 PHE cc_start: 0.8197 (m-80) cc_final: 0.7947 (m-80) REVERT: A 670 MET cc_start: 0.8324 (mtt) cc_final: 0.8006 (mtt) REVERT: A 680 MET cc_start: 0.6812 (mmm) cc_final: 0.6556 (mmm) REVERT: B 111 MET cc_start: 0.8740 (tpp) cc_final: 0.8377 (tpp) REVERT: B 158 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8608 (mmm) REVERT: B 175 MET cc_start: 0.8146 (mmt) cc_final: 0.7758 (mmt) REVERT: B 310 TYR cc_start: 0.8181 (t80) cc_final: 0.7927 (t80) REVERT: B 382 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 440 ASN cc_start: 0.8228 (t0) cc_final: 0.7346 (m110) REVERT: B 462 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 465 MET cc_start: 0.8464 (tpp) cc_final: 0.8264 (tpp) REVERT: B 540 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8406 (mtm-85) REVERT: B 670 MET cc_start: 0.8269 (mtt) cc_final: 0.7911 (mtt) outliers start: 31 outliers final: 21 residues processed: 196 average time/residue: 0.2104 time to fit residues: 61.7811 Evaluate side-chains 189 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 540 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12402 Z= 0.303 Angle : 0.615 12.651 16792 Z= 0.314 Chirality : 0.042 0.212 1898 Planarity : 0.004 0.037 2066 Dihedral : 4.159 19.779 1726 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.04 % Allowed : 15.81 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.23), residues: 1438 helix: 1.27 (0.16), residues: 1078 sheet: -1.00 (0.63), residues: 64 loop : -2.33 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 458 HIS 0.007 0.001 HIS A 141 PHE 0.016 0.002 PHE B 447 TYR 0.016 0.002 TYR A 110 ARG 0.009 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8722 (tpp) cc_final: 0.8475 (tpp) REVERT: A 399 ASP cc_start: 0.7826 (m-30) cc_final: 0.7543 (p0) REVERT: A 440 ASN cc_start: 0.8395 (t0) cc_final: 0.7553 (m110) REVERT: A 462 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 111 MET cc_start: 0.8788 (tpp) cc_final: 0.8527 (tpp) REVERT: B 175 MET cc_start: 0.8291 (mmt) cc_final: 0.7870 (mmt) REVERT: B 382 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 440 ASN cc_start: 0.8310 (t0) cc_final: 0.7410 (m110) REVERT: B 462 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8253 (tm-30) outliers start: 40 outliers final: 31 residues processed: 199 average time/residue: 0.2081 time to fit residues: 62.9384 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 659 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12402 Z= 0.170 Angle : 0.564 12.445 16792 Z= 0.284 Chirality : 0.039 0.195 1898 Planarity : 0.003 0.035 2066 Dihedral : 4.034 18.129 1726 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.20 % Allowed : 16.72 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.23), residues: 1438 helix: 1.43 (0.16), residues: 1076 sheet: -0.87 (0.62), residues: 64 loop : -2.20 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 458 HIS 0.007 0.001 HIS B 141 PHE 0.013 0.001 PHE B 447 TYR 0.012 0.001 TYR B 310 ARG 0.005 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7164 (mp0) REVERT: A 175 MET cc_start: 0.8290 (mmt) cc_final: 0.7759 (mmt) REVERT: A 399 ASP cc_start: 0.7824 (m-30) cc_final: 0.7531 (p0) REVERT: A 440 ASN cc_start: 0.8386 (t0) cc_final: 0.7579 (m110) REVERT: A 448 MET cc_start: 0.8622 (mmt) cc_final: 0.8273 (mmt) REVERT: A 462 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 670 MET cc_start: 0.8309 (mtt) cc_final: 0.8009 (mtt) REVERT: A 680 MET cc_start: 0.6932 (mmm) cc_final: 0.6647 (mmm) REVERT: B 111 MET cc_start: 0.8745 (tpp) cc_final: 0.8391 (tpp) REVERT: B 158 MET cc_start: 0.8947 (mmp) cc_final: 0.8706 (mmm) REVERT: B 175 MET cc_start: 0.8247 (mmt) cc_final: 0.7874 (mmt) REVERT: B 382 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 440 ASN cc_start: 0.8300 (t0) cc_final: 0.7428 (m110) REVERT: B 462 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 490 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7967 (pp20) REVERT: B 540 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8325 (mtm-85) REVERT: B 670 MET cc_start: 0.8302 (mtt) cc_final: 0.7998 (mtt) outliers start: 29 outliers final: 22 residues processed: 199 average time/residue: 0.2070 time to fit residues: 61.8687 Evaluate side-chains 190 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12402 Z= 0.152 Angle : 0.566 12.120 16792 Z= 0.282 Chirality : 0.039 0.185 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.944 17.063 1726 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.66 % Allowed : 16.87 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.23), residues: 1438 helix: 1.47 (0.16), residues: 1078 sheet: -0.81 (0.61), residues: 64 loop : -2.25 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 650 HIS 0.009 0.001 HIS A 785 PHE 0.013 0.001 PHE B 447 TYR 0.014 0.001 TYR A 310 ARG 0.003 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7160 (mp0) REVERT: A 175 MET cc_start: 0.8191 (mmt) cc_final: 0.7687 (mmt) REVERT: A 234 MET cc_start: 0.8194 (mmm) cc_final: 0.7897 (mmm) REVERT: A 313 MET cc_start: 0.8276 (mmt) cc_final: 0.8053 (mmt) REVERT: A 349 LEU cc_start: 0.7996 (tp) cc_final: 0.7774 (tp) REVERT: A 399 ASP cc_start: 0.7822 (m-30) cc_final: 0.7544 (p0) REVERT: A 440 ASN cc_start: 0.8370 (t0) cc_final: 0.7603 (m110) REVERT: A 448 MET cc_start: 0.8560 (mmt) cc_final: 0.8275 (mmt) REVERT: A 462 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 520 PHE cc_start: 0.8147 (m-80) cc_final: 0.7915 (m-80) REVERT: A 670 MET cc_start: 0.8156 (mtt) cc_final: 0.7793 (mtt) REVERT: A 680 MET cc_start: 0.6747 (mmm) cc_final: 0.6464 (mmm) REVERT: A 719 GLU cc_start: 0.7929 (mp0) cc_final: 0.7682 (pm20) REVERT: B 111 MET cc_start: 0.8667 (tpp) cc_final: 0.8365 (tpp) REVERT: B 175 MET cc_start: 0.8191 (mmt) cc_final: 0.7893 (mmt) REVERT: B 224 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7449 (ttm-80) REVERT: B 382 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 440 ASN cc_start: 0.8348 (t0) cc_final: 0.7491 (m110) REVERT: B 462 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 540 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8252 (mtm-85) REVERT: B 680 MET cc_start: 0.6858 (mmm) cc_final: 0.6584 (mmm) outliers start: 35 outliers final: 26 residues processed: 200 average time/residue: 0.2070 time to fit residues: 62.5831 Evaluate side-chains 201 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12402 Z= 0.162 Angle : 0.574 12.239 16792 Z= 0.283 Chirality : 0.039 0.190 1898 Planarity : 0.003 0.035 2066 Dihedral : 3.891 16.996 1726 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.23), residues: 1438 helix: 1.50 (0.16), residues: 1078 sheet: -0.78 (0.61), residues: 64 loop : -2.22 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 650 HIS 0.010 0.001 HIS A 785 PHE 0.013 0.001 PHE B 447 TYR 0.013 0.001 TYR B 310 ARG 0.003 0.000 ARG B 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7170 (mp0) REVERT: A 175 MET cc_start: 0.8060 (mmt) cc_final: 0.7581 (mmt) REVERT: A 234 MET cc_start: 0.8205 (mmm) cc_final: 0.7918 (mmm) REVERT: A 349 LEU cc_start: 0.7942 (tp) cc_final: 0.7711 (tp) REVERT: A 440 ASN cc_start: 0.8392 (t0) cc_final: 0.7589 (m110) REVERT: A 448 MET cc_start: 0.8469 (mmt) cc_final: 0.8196 (mmt) REVERT: A 462 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 520 PHE cc_start: 0.8151 (m-80) cc_final: 0.7919 (m-80) REVERT: A 680 MET cc_start: 0.6833 (mmm) cc_final: 0.6555 (mmm) REVERT: A 719 GLU cc_start: 0.7909 (mp0) cc_final: 0.7658 (pm20) REVERT: B 111 MET cc_start: 0.8666 (tpp) cc_final: 0.8369 (tpp) REVERT: B 175 MET cc_start: 0.8156 (mmt) cc_final: 0.7879 (mmt) REVERT: B 224 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7517 (ttm-80) REVERT: B 234 MET cc_start: 0.8263 (mmm) cc_final: 0.8052 (mmm) REVERT: B 349 LEU cc_start: 0.8043 (tp) cc_final: 0.7815 (tp) REVERT: B 382 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 440 ASN cc_start: 0.8374 (t0) cc_final: 0.7500 (m110) REVERT: B 462 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 490 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 493 MET cc_start: 0.8805 (ttp) cc_final: 0.8567 (ptm) REVERT: B 540 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8366 (mtm-85) REVERT: B 680 MET cc_start: 0.6850 (mmm) cc_final: 0.6590 (mmm) outliers start: 31 outliers final: 24 residues processed: 203 average time/residue: 0.2152 time to fit residues: 66.0965 Evaluate side-chains 197 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 540 ARG Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097390 restraints weight = 23175.800| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.57 r_work: 0.3099 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12402 Z= 0.158 Angle : 0.593 14.424 16792 Z= 0.287 Chirality : 0.039 0.173 1898 Planarity : 0.003 0.034 2066 Dihedral : 3.849 16.609 1726 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.20 % Allowed : 17.78 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.23), residues: 1438 helix: 1.52 (0.16), residues: 1078 sheet: -1.03 (0.59), residues: 68 loop : -2.10 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 650 HIS 0.009 0.001 HIS A 785 PHE 0.013 0.001 PHE B 447 TYR 0.014 0.001 TYR B 310 ARG 0.006 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.01 seconds wall clock time: 46 minutes 46.12 seconds (2806.12 seconds total)