Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 15:57:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/10_2023/8tag_41134_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/10_2023/8tag_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_41134/10_2023/8tag_41134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/10_2023/8tag_41134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/10_2023/8tag_41134_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tag_41134/10_2023/8tag_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-1.21rc1-5097/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 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 chiralities: 3 Time building chain proxies: 10.24, 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: 18.09 Conformation dependent library (CDL) restraints added in 1.9 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: 1.45 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: 8.22 Time building geometry restraints manager: 18.81 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: 8733 17.52 - 35.05: 814 35.05 - 52.57: 123 52.57 - 70.09: 19 70.09 - 87.61: 31 Dihedral angle restraints: 9720 sinusoidal: 4316 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 9717 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: 0.780 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: 0.340 Extract box with map and model: 4.840 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 72.230 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.470 ------------------------------------------------------------------------------- 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 : 13.859 86.586 4377 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 *********************** 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 : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.5501 time to fit residues: 114.3806 Evaluate side-chains 121 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6240 ------------------------------------------------------------------------------- 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: 10.0000 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12236 Z= 0.234 Angle : 0.548 7.240 16607 Z= 0.298 Chirality : 0.045 0.412 1821 Planarity : 0.005 0.060 2064 Dihedral : 4.124 19.801 1596 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 0.48 % Allowed : 4.05 % Favored : 95.48 % 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: 0.77 (0.22), residues: 1426 helix: 1.78 (0.17), residues: 824 sheet: -1.53 (0.74), residues: 48 loop : -1.30 (0.26), residues: 554 *********************** 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 : 1.830 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 outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.5295 time to fit residues: 100.4235 Evaluate side-chains 128 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2453 time to fit residues: 4.6192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 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: 0.9980 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 785 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12236 Z= 0.175 Angle : 0.502 7.381 16607 Z= 0.272 Chirality : 0.044 0.414 1821 Planarity : 0.004 0.050 2064 Dihedral : 3.941 18.669 1596 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.56 % Allowed : 5.40 % 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: 1.04 (0.22), residues: 1426 helix: 2.03 (0.17), residues: 824 sheet: -1.40 (0.73), residues: 48 loop : -1.25 (0.26), residues: 554 *********************** 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 136 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.951 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 outliers start: 7 outliers final: 3 residues processed: 134 average time/residue: 0.5647 time to fit residues: 107.8146 Evaluate side-chains 126 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.753 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2992 time to fit residues: 3.9287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7708 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12236 Z= 0.172 Angle : 0.493 7.391 16607 Z= 0.267 Chirality : 0.044 0.413 1821 Planarity : 0.004 0.049 2064 Dihedral : 3.879 18.156 1596 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 0.63 % Allowed : 6.59 % Favored : 92.78 % 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: 1.14 (0.22), residues: 1426 helix: 2.11 (0.17), residues: 824 sheet: -1.26 (0.72), residues: 48 loop : -1.22 (0.26), residues: 554 *********************** 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 139 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.795 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 outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.5929 time to fit residues: 114.0977 Evaluate side-chains 133 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.886 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.4489 time to fit residues: 7.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12236 Z= 0.262 Angle : 0.526 7.533 16607 Z= 0.289 Chirality : 0.045 0.415 1821 Planarity : 0.004 0.053 2064 Dihedral : 3.984 18.473 1596 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 7.78 % Favored : 91.83 % 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: 0.91 (0.22), residues: 1426 helix: 1.96 (0.17), residues: 824 sheet: -1.92 (0.73), residues: 48 loop : -1.31 (0.25), residues: 554 *********************** 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 137 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.694 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 outliers start: 5 outliers final: 4 residues processed: 137 average time/residue: 0.5752 time to fit residues: 111.7746 Evaluate side-chains 133 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2873 time to fit residues: 4.5104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12236 Z= 0.291 Angle : 0.541 7.621 16607 Z= 0.297 Chirality : 0.046 0.418 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.082 19.150 1596 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 0.56 % Allowed : 8.57 % Favored : 90.87 % 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: 0.75 (0.22), residues: 1426 helix: 1.79 (0.17), residues: 825 sheet: -1.96 (0.72), residues: 48 loop : -1.33 (0.26), residues: 553 *********************** 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 135 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 133 average time/residue: 0.5780 time to fit residues: 108.5081 Evaluate side-chains 131 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.775 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3114 time to fit residues: 3.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.198 Angle : 0.505 7.533 16607 Z= 0.275 Chirality : 0.045 0.413 1821 Planarity : 0.004 0.052 2064 Dihedral : 3.958 19.572 1596 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 0.32 % Allowed : 9.29 % Favored : 90.40 % 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: 0.93 (0.22), residues: 1426 helix: 1.99 (0.17), residues: 819 sheet: -1.86 (0.71), residues: 48 loop : -1.31 (0.26), residues: 559 *********************** 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 132 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 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 outliers start: 4 outliers final: 2 residues processed: 131 average time/residue: 0.5949 time to fit residues: 109.8074 Evaluate side-chains 128 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.697 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.6172 time to fit residues: 3.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12236 Z= 0.228 Angle : 0.512 7.553 16607 Z= 0.279 Chirality : 0.045 0.415 1821 Planarity : 0.004 0.052 2064 Dihedral : 3.942 19.464 1596 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 0.56 % Allowed : 9.05 % Favored : 90.40 % 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: 0.91 (0.22), residues: 1426 helix: 1.98 (0.17), residues: 819 sheet: -1.80 (0.72), residues: 48 loop : -1.32 (0.26), residues: 559 *********************** 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 133 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 131 average time/residue: 0.5800 time to fit residues: 107.6403 Evaluate side-chains 129 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.751 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2872 time to fit residues: 5.4770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.2062 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= 0.145 Angle : 0.482 7.472 16607 Z= 0.259 Chirality : 0.044 0.412 1821 Planarity : 0.004 0.050 2064 Dihedral : 3.814 19.134 1596 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 0.16 % Allowed : 9.44 % Favored : 90.40 % 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: 1.22 (0.22), residues: 1426 helix: 2.22 (0.17), residues: 819 sheet: -1.11 (0.72), residues: 48 loop : -1.24 (0.26), residues: 559 *********************** 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 130 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 130 average time/residue: 0.5751 time to fit residues: 106.3508 Evaluate side-chains 126 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.776 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4156 time to fit residues: 2.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.2174 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= 0.143 Angle : 0.478 7.484 16607 Z= 0.256 Chirality : 0.044 0.410 1821 Planarity : 0.004 0.051 2064 Dihedral : 3.724 19.397 1596 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.16 % Allowed : 9.68 % Favored : 90.16 % 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: 1.33 (0.22), residues: 1426 helix: 2.34 (0.17), residues: 820 sheet: -1.49 (0.67), residues: 58 loop : -1.20 (0.26), residues: 548 ********************** 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 132 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 2.060 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 outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.6043 time to fit residues: 112.8181 Evaluate side-chains 124 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.902 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4348 time to fit residues: 3.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 chunk 117 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138341 restraints weight = 38233.751| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.54 r_work: 0.3400 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2188 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= 0.231 Angle : 0.510 7.599 16607 Z= 0.277 Chirality : 0.045 0.415 1821 Planarity : 0.005 0.074 2064 Dihedral : 3.832 19.513 1596 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.07 % Favored : 95.86 % Rotamer: Outliers : 0.08 % Allowed : 9.84 % 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: 1.13 (0.22), residues: 1426 helix: 2.17 (0.17), residues: 819 sheet: -1.58 (0.73), residues: 48 loop : -1.27 (0.25), residues: 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.00 seconds wall clock time: 86 minutes 22.88 seconds (5182.88 seconds total)