Starting phenix.real_space_refine on Thu Apr 11 18:10:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/04_2024/8tag_41134_trim.pdb" } resolution = 3.2 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= 0.007 sd= 0.097 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A ASP 774": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11240 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12189 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.30, per 1000 atoms: 0.44 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.918, 87.256, 120.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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 Atom "HETATM23469 O5 NAG A 903 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG B 901 " - " ASN B 362 " Time building additional restraints: 17.82 Conformation dependent library (CDL) restraints added in 2.5 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 63.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.797A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 326 removed outlier: 3.985A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.797A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.597A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 539 removed outlier: 4.009A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.652A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 625 through 638 removed outlier: 4.678A pdb=" N TRP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.527A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.056A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.125A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.990A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 removed outlier: 3.540A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.844A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 removed outlier: 3.605A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 188 through 195 removed outlier: 5.627A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.810A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.957A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.789A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 removed outlier: 3.598A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.928A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.262A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.810A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.908A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.278A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.060A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.807A pdb=" N VAL A 124 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 77 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 785 removed outlier: 3.556A pdb=" N CYS A 807 " --> pdb=" O PHE A 784 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.551A pdb=" N VAL B 124 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU B 78 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR B 242 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 3.802A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.765A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 782 through 785 694 hydrogen bonds defined for protein. 2040 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: 8.77 Time building geometry restraints manager: 18.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 290 1.23 - 1.43: 5062 1.43 - 1.63: 6784 1.63 - 1.83: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C ASP B 339 " pdb=" N PRO B 340 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.63e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 73.15 - 85.33: 24 85.33 - 97.51: 0 97.51 - 109.70: 16602 109.70 - 121.88: 22649 121.88 - 134.06: 3673 Bond angle restraints: 42948 Sorted by residual: angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 73.40 36.60 3.00e+00 1.11e-01 1.49e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.15 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.38 35.62 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.58 35.42 3.00e+00 1.11e-01 1.39e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 10195 17.52 - 35.05: 908 35.05 - 52.57: 228 52.57 - 70.09: 60 70.09 - 87.61: 31 Dihedral angle restraints: 11422 sinusoidal: 6018 harmonic: 5404 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -166.42 80.42 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -136.14 50.14 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.781: 1819 0.781 - 1.561: 1 1.561 - 2.342: 0 2.342 - 3.123: 0 3.123 - 3.904: 1 Chirality restraints: 1821 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 1.50 -3.90 2.00e-01 2.50e+01 3.81e+02 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.03e+01 chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1818 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 362 " -0.081 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" CG ASN B 362 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 362 " -0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 362 " 0.346 2.00e-02 2.50e+03 pdb=" C1 NAG B 901 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 540 " -0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO B 541 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 541 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 541 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 618 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 618 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 618 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A 619 " -0.013 2.00e-02 2.50e+03 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 145 1.96 - 2.62: 28470 2.62 - 3.28: 70344 3.28 - 3.94: 86455 3.94 - 4.60: 135851 Nonbonded interactions: 321265 Sorted by model distance: nonbonded pdb="HD21 ASN A 778 " pdb=" O5 NAG A 903 " model vdw 1.304 1.850 nonbonded pdb=" OD1 ASP A 286 " pdb="HH12 ARG A 289 " model vdw 1.390 1.850 nonbonded pdb=" OD1 ASN A 525 " pdb="HE22 GLN A 559 " model vdw 1.520 1.850 nonbonded pdb="HH11 ARG B 69 " pdb=" OE1 GLN B 111 " model vdw 1.527 1.850 nonbonded pdb=" OE1 GLN A 506 " pdb=" H GLN A 506 " model vdw 1.586 1.850 ... (remaining 321260 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 59 through 361 or (resid 362 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 363 through 868 or resid 901 through 902 or \ resid 904)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 784 or ( \ resid 785 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 786 t \ hrough 857 or (resid 858 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 859 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 860 through 868 or res \ id 902 through 903 or resid 905)) } 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: 1.120 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: 0.330 Extract box with map and model: 4.870 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 73.250 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 0.042 12236 Z= 0.283 Angle : 0.629 12.164 16607 Z= 0.347 Chirality : 0.109 3.904 1821 Planarity : 0.005 0.076 2064 Dihedral : 14.053 86.586 4503 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.07 % 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: 0.76 (0.22), residues: 1426 helix: 1.73 (0.17), residues: 821 sheet: -1.83 (0.79), residues: 40 loop : -1.19 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 132 HIS 0.004 0.001 HIS B 275 PHE 0.017 0.002 PHE A 560 TYR 0.030 0.001 TYR A 668 ARG 0.005 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.6560 (mtmt) cc_final: 0.6224 (ttpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.5749 time to fit residues: 120.9026 Evaluate side-chains 121 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12236 Z= 0.192 Angle : 0.532 7.195 16607 Z= 0.289 Chirality : 0.045 0.412 1821 Planarity : 0.005 0.059 2064 Dihedral : 5.480 52.286 1722 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.48 % Allowed : 3.73 % Favored : 95.79 % Cbeta Deviations : 0.07 % 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: 0.87 (0.22), residues: 1426 helix: 1.87 (0.17), residues: 823 sheet: -1.49 (0.73), residues: 48 loop : -1.27 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 650 HIS 0.003 0.001 HIS B 830 PHE 0.012 0.001 PHE A 560 TYR 0.020 0.001 TYR A 668 ARG 0.007 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.766 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 145 LYS cc_start: 0.6650 (mtmt) cc_final: 0.6054 (ttpt) REVERT: A 631 MET cc_start: 0.5024 (mpp) cc_final: 0.4550 (mmm) outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.5335 time to fit residues: 101.2662 Evaluate side-chains 129 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12236 Z= 0.154 Angle : 0.490 7.316 16607 Z= 0.265 Chirality : 0.044 0.413 1821 Planarity : 0.004 0.050 2064 Dihedral : 4.956 50.745 1722 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.63 % Allowed : 5.32 % Favored : 94.05 % Cbeta Deviations : 0.07 % 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: 1.12 (0.22), residues: 1426 helix: 2.09 (0.17), residues: 824 sheet: -1.30 (0.73), residues: 48 loop : -1.20 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.002 0.001 HIS B 830 PHE 0.010 0.001 PHE A 560 TYR 0.016 0.001 TYR A 528 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.6656 (mtmt) cc_final: 0.6067 (ttpt) REVERT: A 631 MET cc_start: 0.4851 (mpp) cc_final: 0.4543 (mmm) outliers start: 8 outliers final: 7 residues processed: 138 average time/residue: 0.5446 time to fit residues: 107.8827 Evaluate side-chains 131 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12236 Z= 0.201 Angle : 0.500 7.435 16607 Z= 0.273 Chirality : 0.045 0.414 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.852 50.019 1722 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 6.27 % Favored : 92.86 % Cbeta Deviations : 0.07 % 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: 1.07 (0.22), residues: 1426 helix: 2.07 (0.17), residues: 823 sheet: -1.77 (0.66), residues: 58 loop : -1.19 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 273 HIS 0.004 0.001 HIS B 830 PHE 0.012 0.001 PHE B 560 TYR 0.015 0.001 TYR A 668 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.751 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 604 GLU cc_start: 0.7529 (pp20) cc_final: 0.7268 (pt0) outliers start: 11 outliers final: 8 residues processed: 142 average time/residue: 0.5848 time to fit residues: 119.6439 Evaluate side-chains 136 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12236 Z= 0.248 Angle : 0.517 7.545 16607 Z= 0.283 Chirality : 0.045 0.416 1821 Planarity : 0.005 0.053 2064 Dihedral : 5.056 57.380 1722 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 0.95 % Allowed : 7.30 % Favored : 91.75 % Cbeta Deviations : 0.07 % 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 (0.22), residues: 1426 helix: 1.99 (0.17), residues: 823 sheet: -1.88 (0.66), residues: 58 loop : -1.22 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 273 HIS 0.003 0.001 HIS B 830 PHE 0.013 0.001 PHE B 300 TYR 0.018 0.001 TYR A 668 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.6476 (t80) cc_final: 0.6027 (t80) outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.5622 time to fit residues: 109.2178 Evaluate side-chains 138 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 0.0270 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12236 Z= 0.157 Angle : 0.477 7.474 16607 Z= 0.259 Chirality : 0.044 0.412 1821 Planarity : 0.004 0.050 2064 Dihedral : 4.832 57.543 1722 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 0.95 % Allowed : 7.86 % Favored : 91.19 % Cbeta Deviations : 0.07 % 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: 1.25 (0.22), residues: 1426 helix: 2.23 (0.17), residues: 824 sheet: -1.66 (0.66), residues: 58 loop : -1.15 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 PHE 0.022 0.001 PHE A 461 TYR 0.013 0.001 TYR A 668 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.6470 (t80) cc_final: 0.6032 (t80) REVERT: A 790 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6497 (tttp) REVERT: A 859 ASP cc_start: 0.1054 (OUTLIER) cc_final: 0.0800 (t0) REVERT: B 294 GLU cc_start: 0.7283 (mp0) cc_final: 0.6971 (tt0) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.5575 time to fit residues: 112.4314 Evaluate side-chains 134 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12236 Z= 0.337 Angle : 0.548 7.623 16607 Z= 0.303 Chirality : 0.046 0.417 1821 Planarity : 0.005 0.053 2064 Dihedral : 5.035 51.390 1722 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.03 % Allowed : 8.65 % Favored : 90.32 % Cbeta Deviations : 0.07 % 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: 0.78 (0.22), residues: 1426 helix: 1.86 (0.17), residues: 817 sheet: -1.91 (0.65), residues: 58 loop : -1.31 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.004 0.001 HIS B 830 PHE 0.017 0.002 PHE B 675 TYR 0.019 0.002 TYR A 668 ARG 0.005 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.729 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 203 PHE cc_start: 0.6471 (t80) cc_final: 0.5986 (t80) REVERT: A 859 ASP cc_start: 0.1141 (OUTLIER) cc_final: 0.0649 (t0) outliers start: 13 outliers final: 10 residues processed: 140 average time/residue: 0.5820 time to fit residues: 116.6671 Evaluate side-chains 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12236 Z= 0.235 Angle : 0.509 7.562 16607 Z= 0.279 Chirality : 0.045 0.416 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.881 52.342 1722 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 1.19 % Allowed : 8.89 % Favored : 89.92 % Cbeta Deviations : 0.07 % 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 (0.22), residues: 1426 helix: 1.95 (0.17), residues: 817 sheet: -1.87 (0.65), residues: 58 loop : -1.29 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.003 0.001 HIS B 830 PHE 0.019 0.001 PHE A 461 TYR 0.014 0.001 TYR A 668 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.807 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: symmetry clash REVERT: A 258 GLU cc_start: 0.4555 (mp0) cc_final: 0.4099 (pm20) REVERT: A 790 LYS cc_start: 0.7153 (mmmt) cc_final: 0.6701 (tttp) REVERT: A 859 ASP cc_start: 0.1065 (OUTLIER) cc_final: 0.0557 (t0) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.6047 time to fit residues: 124.4605 Evaluate side-chains 140 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP 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: 7.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12236 Z= 0.152 Angle : 0.476 7.412 16607 Z= 0.258 Chirality : 0.044 0.412 1821 Planarity : 0.004 0.052 2064 Dihedral : 4.536 51.038 1722 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 9.05 % Favored : 90.08 % Cbeta Deviations : 0.07 % 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: 1.19 (0.22), residues: 1426 helix: 2.22 (0.17), residues: 819 sheet: -1.69 (0.65), residues: 58 loop : -1.21 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.000 HIS B 830 PHE 0.012 0.001 PHE A 538 TYR 0.013 0.001 TYR A 668 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 ASP cc_start: 0.0967 (OUTLIER) cc_final: 0.0552 (t0) outliers start: 11 outliers final: 9 residues processed: 143 average time/residue: 0.5704 time to fit residues: 116.8063 Evaluate side-chains 137 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12236 Z= 0.204 Angle : 0.494 7.463 16607 Z= 0.269 Chirality : 0.045 0.414 1821 Planarity : 0.005 0.075 2064 Dihedral : 4.528 51.067 1722 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.71 % Allowed : 9.52 % Favored : 89.76 % Cbeta Deviations : 0.07 % 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: 1.16 (0.22), residues: 1426 helix: 2.18 (0.17), residues: 819 sheet: -1.71 (0.65), residues: 58 loop : -1.20 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 PHE 0.012 0.001 PHE A 538 TYR 0.015 0.001 TYR A 668 ARG 0.003 0.000 ARG A 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 ASP cc_start: 0.0974 (OUTLIER) cc_final: 0.0634 (t0) outliers start: 9 outliers final: 8 residues processed: 138 average time/residue: 0.5625 time to fit residues: 110.9102 Evaluate side-chains 136 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.197447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137495 restraints weight = 38361.971| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.57 r_work: 0.3351 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12236 Z= 0.341 Angle : 0.558 7.639 16607 Z= 0.310 Chirality : 0.047 0.420 1821 Planarity : 0.005 0.070 2064 Dihedral : 5.035 53.651 1722 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.95 % Allowed : 9.60 % Favored : 89.44 % Cbeta Deviations : 0.07 % 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: 0.74 (0.22), residues: 1426 helix: 1.80 (0.17), residues: 818 sheet: -1.85 (0.65), residues: 58 loop : -1.31 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.003 0.001 HIS A 108 PHE 0.020 0.002 PHE A 461 TYR 0.017 0.002 TYR A 668 ARG 0.004 0.000 ARG B 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.31 seconds wall clock time: 86 minutes 59.30 seconds (5219.30 seconds total)