Starting phenix.real_space_refine on Fri Oct 11 20:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/10_2024/8xbs_38227.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.125 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 Zn 2 6.06 5 P 2 5.49 5 S 68 5.16 5 C 7018 2.51 5 N 1682 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10658 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.51, per 1000 atoms: 0.70 Number of scatterers: 10658 At special positions: 0 Unit cell: (92.0125, 87.6825, 128.817, 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) Zn 2 29.99 S 68 16.00 P 2 15.00 O 1886 8.00 N 1682 7.00 C 7018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 50.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.628A pdb=" N ILE A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.500A pdb=" N LEU A 431 " --> pdb=" O HIS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.869A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.762A pdb=" N ALA A 471 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.607A pdb=" N ILE A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 removed outlier: 3.704A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.987A pdb=" N GLN A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 Processing helix chain 'A' and resid 601 through 626 Processing helix chain 'A' and resid 628 through 652 removed outlier: 3.947A pdb=" N PHE A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 684 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 738 through 761 Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.889A pdb=" N ILE A 766 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.628A pdb=" N ILE B 68 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.500A pdb=" N LEU B 431 " --> pdb=" O HIS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.868A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.763A pdb=" N ALA B 471 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.607A pdb=" N ILE B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 removed outlier: 3.704A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 552 through 569 removed outlier: 3.987A pdb=" N GLN B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 596 Processing helix chain 'B' and resid 601 through 626 Processing helix chain 'B' and resid 628 through 652 removed outlier: 3.947A pdb=" N PHE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 660 through 684 Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 738 through 761 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.888A pdb=" N ILE B 766 " --> pdb=" O ASP B 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.180A pdb=" N LEU A 36 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG A 60 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 38 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU A 62 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.758A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 194 removed outlier: 3.619A pdb=" N ASN A 191 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A 302 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 193 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 300 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.180A pdb=" N LEU B 36 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG B 60 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 38 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU B 62 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.757A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 194 removed outlier: 3.619A pdb=" N ASN B 191 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE B 302 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 193 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS B 300 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 205 578 hydrogen bonds defined for protein. 1626 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: 3.61 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 1320 1.24 - 1.38: 2808 1.38 - 1.53: 5523 1.53 - 1.67: 1155 1.67 - 1.82: 102 Bond restraints: 10908 Sorted by residual: bond pdb=" CA ASP A 239 " pdb=" C ASP A 239 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.23e-02 6.61e+03 1.04e+02 bond pdb=" CA ASP B 239 " pdb=" C ASP B 239 " ideal model delta sigma weight residual 1.524 1.399 0.124 1.23e-02 6.61e+03 1.02e+02 bond pdb=" C TYR A 238 " pdb=" O TYR A 238 " ideal model delta sigma weight residual 1.232 1.094 0.138 1.38e-02 5.25e+03 1.00e+02 bond pdb=" C TYR B 238 " pdb=" O TYR B 238 " ideal model delta sigma weight residual 1.232 1.095 0.137 1.38e-02 5.25e+03 9.92e+01 bond pdb=" C ASP A 239 " pdb=" O ASP A 239 " ideal model delta sigma weight residual 1.234 1.118 0.116 1.34e-02 5.57e+03 7.51e+01 ... (remaining 10903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 14734 5.97 - 11.95: 56 11.95 - 17.92: 6 17.92 - 23.90: 8 23.90 - 29.87: 4 Bond angle restraints: 14808 Sorted by residual: angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.78 87.26 23.52 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.78 87.27 23.51 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta sigma weight residual 110.29 86.97 23.32 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta sigma weight residual 110.29 86.99 23.30 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C SER B 33 " pdb=" CA SER B 33 " pdb=" CB SER B 33 " ideal model delta sigma weight residual 110.10 86.16 23.94 1.90e+00 2.77e-01 1.59e+02 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.28: 6250 25.28 - 50.55: 554 50.55 - 75.83: 108 75.83 - 101.10: 34 101.10 - 126.38: 42 Dihedral angle restraints: 6988 sinusoidal: 3212 harmonic: 3776 Sorted by residual: dihedral pdb=" C ASP A 171 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C ASP B 171 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C SER B 244 " pdb=" N SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual -122.60 -92.61 -29.99 0 2.50e+00 1.60e-01 1.44e+02 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1740 0.226 - 0.451: 20 0.451 - 0.677: 4 0.677 - 0.903: 2 0.903 - 1.128: 4 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CA PHE A 296 " pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CB PHE A 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA PHE B 296 " pdb=" N PHE B 296 " pdb=" C PHE B 296 " pdb=" CB PHE B 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 1.43 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 1767 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " 0.291 2.00e-02 2.50e+03 2.55e-01 8.10e+02 pdb=" C7 NAG A 807 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " -0.459 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.291 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG B 807 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 327 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 328 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " 0.054 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 656 2.73 - 3.27: 9933 3.27 - 3.82: 17651 3.82 - 4.36: 22060 4.36 - 4.90: 36937 Nonbonded interactions: 87237 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 2.189 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 2.189 2.752 nonbonded pdb=" OH TYR B 677 " pdb=" OD2 ASP B 762 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 677 " pdb=" OD2 ASP A 762 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 612 " pdb=" OG SER B 616 " model vdw 2.284 3.040 ... (remaining 87232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.190 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.170 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.006 0.138 10908 Z= 0.399 Angle : 1.174 29.874 14808 Z= 0.668 Chirality : 0.083 1.128 1770 Planarity : 0.010 0.255 1760 Dihedral : 22.127 126.381 4506 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 20.77 % Favored : 76.06 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.24), residues: 1262 helix: 1.87 (0.22), residues: 552 sheet: 2.64 (0.31), residues: 252 loop : -0.93 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.014 0.002 PHE A 528 TYR 0.031 0.002 TYR B 238 ARG 0.012 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.231 Fit side-chains REVERT: A 129 GLN cc_start: 0.8271 (mp-120) cc_final: 0.7957 (mp10) REVERT: B 129 GLN cc_start: 0.8269 (mp-120) cc_final: 0.7949 (mp10) outliers start: 36 outliers final: 30 residues processed: 148 average time/residue: 1.1431 time to fit residues: 184.2343 Evaluate side-chains 146 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 685 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10908 Z= 0.302 Angle : 0.770 10.590 14808 Z= 0.373 Chirality : 0.051 0.333 1770 Planarity : 0.006 0.073 1760 Dihedral : 18.855 105.828 2218 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.87 % Allowed : 18.49 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.71 (0.24), residues: 1262 helix: 2.01 (0.22), residues: 542 sheet: 2.64 (0.32), residues: 250 loop : -0.85 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 567 HIS 0.006 0.001 HIS A 740 PHE 0.018 0.002 PHE A 528 TYR 0.024 0.002 TYR A 650 ARG 0.008 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 129 time to evaluate : 1.283 Fit side-chains REVERT: A 129 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: A 628 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.4659 (mm-30) REVERT: B 129 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: B 145 PHE cc_start: 0.8563 (m-80) cc_final: 0.8313 (m-80) REVERT: B 628 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4751 (mm-30) outliers start: 44 outliers final: 27 residues processed: 159 average time/residue: 1.1320 time to fit residues: 197.4180 Evaluate side-chains 155 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 628 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 556 GLN A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 556 GLN B 571 HIS ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10908 Z= 0.430 Angle : 0.811 10.022 14808 Z= 0.403 Chirality : 0.054 0.276 1770 Planarity : 0.006 0.077 1760 Dihedral : 16.770 110.254 2202 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.23 % Allowed : 17.34 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.35 (0.23), residues: 1262 helix: 1.56 (0.22), residues: 544 sheet: 2.55 (0.32), residues: 250 loop : -0.90 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.009 0.002 HIS B 740 PHE 0.021 0.003 PHE A 528 TYR 0.022 0.003 TYR B 673 ARG 0.007 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 1.125 Fit side-chains REVERT: A 129 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: A 145 PHE cc_start: 0.8574 (m-80) cc_final: 0.8365 (m-80) REVERT: A 521 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 691 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7701 (ttpp) REVERT: A 764 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 129 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 521 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 691 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7724 (ttpp) outliers start: 48 outliers final: 30 residues processed: 159 average time/residue: 0.7465 time to fit residues: 130.1626 Evaluate side-chains 157 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 33 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 571 HIS A 684 HIS B 205 ASN B 450 HIS B 571 HIS B 684 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10908 Z= 0.173 Angle : 0.616 9.790 14808 Z= 0.301 Chirality : 0.043 0.284 1770 Planarity : 0.004 0.062 1760 Dihedral : 14.530 103.308 2200 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.99 % Allowed : 18.57 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.94 (0.24), residues: 1262 helix: 2.27 (0.22), residues: 544 sheet: 2.62 (0.32), residues: 254 loop : -0.78 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.012 0.001 PHE A 279 TYR 0.023 0.001 TYR A 650 ARG 0.002 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.291 Fit side-chains REVERT: A 69 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 129 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: A 145 PHE cc_start: 0.8568 (m-80) cc_final: 0.8367 (m-80) REVERT: A 628 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4650 (tp30) REVERT: A 764 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 69 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 129 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7904 (mp10) outliers start: 34 outliers final: 19 residues processed: 152 average time/residue: 0.9686 time to fit residues: 160.8646 Evaluate side-chains 144 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 10908 Z= 0.545 Angle : 0.849 10.341 14808 Z= 0.426 Chirality : 0.057 0.307 1770 Planarity : 0.007 0.083 1760 Dihedral : 14.741 105.145 2196 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 3.70 % Allowed : 18.05 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.24), residues: 1262 helix: 1.50 (0.22), residues: 546 sheet: 2.55 (0.32), residues: 250 loop : -0.84 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 703 HIS 0.011 0.002 HIS B 740 PHE 0.023 0.003 PHE A 528 TYR 0.025 0.003 TYR B 673 ARG 0.011 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.278 Fit side-chains REVERT: A 129 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: A 521 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 628 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4820 (tp30) REVERT: A 641 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (mmp) REVERT: A 764 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7956 (p0) REVERT: B 129 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: B 521 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 641 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7685 (mmp) REVERT: B 764 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7982 (p0) outliers start: 42 outliers final: 28 residues processed: 149 average time/residue: 1.1175 time to fit residues: 181.0580 Evaluate side-chains 157 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: