Starting phenix.real_space_refine on Sun Dec 29 00:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl1_36386/12_2024/8jl1_36386.cif" } resolution = 2.8 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= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 6458 2.51 5 N 1364 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9384 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4189 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501} Chain breaks: 3 Chain: "B" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4189 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501} Chain breaks: 3 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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 447 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 36} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 447 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 36} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.08, per 1000 atoms: 0.75 Number of scatterers: 9384 At special positions: 0 Unit cell: (108.73, 87.15, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1516 8.00 N 1364 7.00 C 6458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " 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 " NAG-ASN " NAG A 802 " - " ASN A 94 " " NAG B 803 " - " ASN B 94 " " NAG C 1 " - " ASN A 142 " " NAG D 1 " - " ASN A 162 " " NAG E 1 " - " ASN B 142 " " NAG F 1 " - " ASN B 162 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.593A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.545A pdb=" N TYR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 296 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 3.538A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 437 removed outlier: 3.546A pdb=" N TRP A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.559A pdb=" N LYS A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.952A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 524 Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.549A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 Processing helix chain 'B' and resid 191 through 215 Processing helix chain 'B' and resid 268 through 287 removed outlier: 3.593A pdb=" N ASP B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.545A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.538A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 437 removed outlier: 3.546A pdb=" N TRP B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.559A pdb=" N LYS B 458 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.952A pdb=" N VAL B 488 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 524 Processing helix chain 'B' and resid 527 through 551 removed outlier: 3.550A pdb=" N ILE B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.935A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 168 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.841A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 8.936A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 168 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.840A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1403 1.32 - 1.45: 2457 1.45 - 1.57: 5642 1.57 - 1.69: 6 1.69 - 1.82: 54 Bond restraints: 9562 Sorted by residual: bond pdb=" CG LEU B 279 " pdb=" CD1 LEU B 279 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.10e+00 bond pdb=" CG LEU A 279 " pdb=" CD1 LEU A 279 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.08e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" CB PRO B 311 " pdb=" CG PRO B 311 " ideal model delta sigma weight residual 1.492 1.427 0.065 5.00e-02 4.00e+02 1.70e+00 ... (remaining 9557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12212 1.27 - 2.54: 422 2.54 - 3.81: 88 3.81 - 5.08: 22 5.08 - 6.35: 12 Bond angle restraints: 12756 Sorted by residual: angle pdb=" N MET B 282 " pdb=" CA MET B 282 " pdb=" CB MET B 282 " ideal model delta sigma weight residual 110.28 116.08 -5.80 1.55e+00 4.16e-01 1.40e+01 angle pdb=" N MET A 282 " pdb=" CA MET A 282 " pdb=" CB MET A 282 " ideal model delta sigma weight residual 110.28 116.08 -5.80 1.55e+00 4.16e-01 1.40e+01 angle pdb=" C LEU A 281 " pdb=" N MET A 282 " pdb=" CA MET A 282 " ideal model delta sigma weight residual 120.31 114.75 5.56 1.52e+00 4.33e-01 1.34e+01 angle pdb=" C LEU B 281 " pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta sigma weight residual 120.31 114.82 5.49 1.52e+00 4.33e-01 1.30e+01 angle pdb=" C MET A 282 " pdb=" CA MET A 282 " pdb=" CB MET A 282 " ideal model delta sigma weight residual 110.67 104.32 6.35 1.92e+00 2.71e-01 1.10e+01 ... (remaining 12751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 5073 15.47 - 30.94: 623 30.94 - 46.41: 158 46.41 - 61.88: 72 61.88 - 77.35: 12 Dihedral angle restraints: 5938 sinusoidal: 2896 harmonic: 3042 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 462 " pdb=" CB CYS B 462 " ideal model delta sinusoidal sigma weight residual 93.00 170.35 -77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 170.34 -77.34 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 151 " pdb=" SG CYS B 151 " pdb=" SG CYS B 179 " pdb=" CB CYS B 179 " ideal model delta sinusoidal sigma weight residual 93.00 138.30 -45.30 1 1.00e+01 1.00e-02 2.85e+01 ... (remaining 5935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 704 0.029 - 0.059: 490 0.059 - 0.088: 148 0.088 - 0.117: 69 0.117 - 0.147: 15 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 142 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 142 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" C PRO A 460 " pdb=" CB PRO A 460 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1423 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 420 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" CD GLN A 420 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN A 420 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN A 420 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 420 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" CD GLN B 420 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN B 420 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN B 420 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 192 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO B 193 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " -0.018 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1462 2.76 - 3.30: 7932 3.30 - 3.83: 14570 3.83 - 4.37: 18790 4.37 - 4.90: 32457 Nonbonded interactions: 75211 Sorted by model distance: nonbonded pdb=" OD1 ASN A 191 " pdb=" OH TYR A 294 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN B 191 " pdb=" OH TYR B 294 " model vdw 2.226 3.040 nonbonded pdb=" O ILE B 559 " pdb=" OG SER B 569 " model vdw 2.372 3.040 nonbonded pdb=" O ILE A 559 " pdb=" OG SER A 569 " model vdw 2.373 3.040 nonbonded pdb=" O LYS A 296 " pdb=" OG1 THR A 304 " model vdw 2.392 3.040 ... (remaining 75206 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' and (resid 75 through 663 or resid 805 through 806 or (resid 808 and \ (name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C0 \ 9 or name C10 or name C11 or name C12 or name C13 or name C14)) or resid 809 thr \ ough 811 or resid 818 or resid 823 through 825 or (resid 827 and (name C03 or na \ me C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 o \ r name C11 or name C12 or name C13 or name C14)) or resid 828 through 829 or res \ id 831 or resid 834 through 835)) selection = (chain 'B' and (resid 75 through 663 or resid 805 through 806 or resid 808 throu \ gh 811 or resid 818 or resid 823 through 825 or resid 827 through 829 or resid 8 \ 31 or resid 834 through 835)) } 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: 3.400 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 : 0.007 0.067 9562 Z= 0.427 Angle : 0.611 6.355 12756 Z= 0.313 Chirality : 0.044 0.147 1426 Planarity : 0.004 0.032 1446 Dihedral : 15.095 75.183 3972 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.25), residues: 1038 helix: 1.63 (0.22), residues: 498 sheet: 0.96 (0.43), residues: 122 loop : -0.35 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.010 0.001 HIS A 614 PHE 0.013 0.002 PHE A 322 TYR 0.020 0.002 TYR A 620 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.2868 time to fit residues: 107.9911 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9562 Z= 0.209 Angle : 0.495 6.250 12756 Z= 0.258 Chirality : 0.040 0.138 1426 Planarity : 0.004 0.035 1446 Dihedral : 12.474 59.284 2080 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.88 % Allowed : 7.99 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.26), residues: 1038 helix: 2.67 (0.22), residues: 496 sheet: 1.49 (0.42), residues: 114 loop : -0.27 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 PHE 0.014 0.001 PHE A 322 TYR 0.012 0.001 TYR B 570 ARG 0.005 0.001 ARG B 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.163 Fit side-chains REVERT: A 416 SER cc_start: 0.8772 (p) cc_final: 0.8519 (m) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 1.0560 time to fit residues: 80.5496 Evaluate side-chains 61 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 0.0000 chunk 75 optimal weight: 0.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9562 Z= 0.179 Angle : 0.470 6.257 12756 Z= 0.241 Chirality : 0.040 0.143 1426 Planarity : 0.003 0.034 1446 Dihedral : 11.557 55.714 2080 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.88 % Allowed : 9.74 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1038 helix: 3.08 (0.22), residues: 498 sheet: 1.07 (0.40), residues: 130 loop : -0.09 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.014 0.001 PHE B 322 TYR 0.011 0.001 TYR B 570 ARG 0.002 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.011 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.9450 time to fit residues: 62.8179 Evaluate side-chains 56 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9562 Z= 0.147 Angle : 0.441 6.313 12756 Z= 0.226 Chirality : 0.039 0.139 1426 Planarity : 0.003 0.034 1446 Dihedral : 10.596 58.572 2080 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.31 % Allowed : 10.39 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.26), residues: 1038 helix: 3.34 (0.22), residues: 498 sheet: 1.12 (0.40), residues: 130 loop : -0.04 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 PHE 0.013 0.001 PHE B 322 TYR 0.011 0.001 TYR B 570 ARG 0.001 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.111 Fit side-chains REVERT: A 148 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7541 (ptmt) REVERT: A 614 HIS cc_start: 0.9272 (OUTLIER) cc_final: 0.8945 (p-80) REVERT: A 630 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8080 (t0) REVERT: B 148 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7519 (ptmt) REVERT: B 614 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8946 (p-80) REVERT: B 630 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8081 (t0) outliers start: 12 outliers final: 2 residues processed: 66 average time/residue: 0.9493 time to fit residues: 69.6859 Evaluate side-chains 65 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 9562 Z= 0.469 Angle : 0.589 6.466 12756 Z= 0.300 Chirality : 0.046 0.157 1426 Planarity : 0.004 0.034 1446 Dihedral : 12.229 57.546 2080 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.19 % Allowed : 10.39 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1038 helix: 2.72 (0.21), residues: 498 sheet: 0.98 (0.40), residues: 130 loop : -0.08 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.008 0.002 HIS A 614 PHE 0.018 0.002 PHE A 322 TYR 0.016 0.002 TYR B 496 ARG 0.003 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.972 Fit side-chains REVERT: A 148 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7501 (ptmt) REVERT: A 325 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7897 (tpp) REVERT: A 337 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.7284 (ttm110) REVERT: A 614 HIS cc_start: 0.9371 (OUTLIER) cc_final: 0.9085 (p-80) REVERT: B 148 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7481 (ptmt) REVERT: B 325 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: B 337 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7286 (ttm110) REVERT: B 556 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: B 614 HIS cc_start: 0.9368 (OUTLIER) cc_final: 0.9083 (p-80) outliers start: 20 outliers final: 10 residues processed: 68 average time/residue: 1.1715 time to fit residues: 86.6490 Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9562 Z= 0.174 Angle : 0.455 6.372 12756 Z= 0.234 Chirality : 0.039 0.150 1426 Planarity : 0.003 0.032 1446 Dihedral : 10.925 58.515 2080 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.97 % Allowed : 10.94 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.26), residues: 1038 helix: 3.17 (0.21), residues: 498 sheet: 1.00 (0.40), residues: 130 loop : -0.11 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS A 614 PHE 0.013 0.001 PHE A 322 TYR 0.013 0.001 TYR A 570 ARG 0.001 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 1.022 Fit side-chains REVERT: A 148 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7473 (ptmt) REVERT: A 325 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7880 (tpp) REVERT: A 614 HIS cc_start: 0.9295 (OUTLIER) cc_final: 0.8972 (p-80) REVERT: A 630 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8185 (t0) REVERT: B 148 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7493 (ptmt) REVERT: B 325 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7885 (tpp) REVERT: B 614 HIS cc_start: 0.9294 (OUTLIER) cc_final: 0.8976 (p-80) REVERT: B 630 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8187 (t0) outliers start: 18 outliers final: 8 residues processed: 62 average time/residue: 0.9640 time to fit residues: 66.3415 Evaluate side-chains 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 358 ASN B 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9562 Z= 0.321 Angle : 0.511 6.436 12756 Z= 0.262 Chirality : 0.042 0.153 1426 Planarity : 0.004 0.031 1446 Dihedral : 11.401 56.578 2080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 11.27 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.26), residues: 1038 helix: 2.90 (0.21), residues: 500 sheet: 0.98 (0.40), residues: 130 loop : -0.07 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.006 0.001 HIS A 614 PHE 0.016 0.001 PHE B 322 TYR 0.013 0.002 TYR B 570 ARG 0.002 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.965 Fit side-chains REVERT: A 148 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7478 (ptmt) REVERT: A 325 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: A 556 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: A 614 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.9045 (p-80) REVERT: B 148 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7496 (ptmt) REVERT: B 325 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7925 (tpp) REVERT: B 614 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.9045 (p-80) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 1.0746 time to fit residues: 73.1112 Evaluate side-chains 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.005 0.055 9562 Z= 0.322 Angle : 0.515 6.398 12756 Z= 0.264 Chirality : 0.042 0.154 1426 Planarity : 0.004 0.033 1446 Dihedral : 11.652 59.840 2080 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.08 % Allowed : 11.71 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.26), residues: 1038 helix: 2.86 (0.21), residues: 500 sheet: 0.94 (0.40), residues: 130 loop : -0.13 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.006 0.001 HIS A 614 PHE 0.016 0.001 PHE B 322 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.023 Fit side-chains REVERT: A 87 HIS cc_start: 0.7999 (m-70) cc_final: 0.7484 (m90) REVERT: A 148 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7432 (ptmt) REVERT: A 325 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7924 (tpp) REVERT: A 556 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 614 HIS cc_start: 0.9344 (OUTLIER) cc_final: 0.9053 (p-80) REVERT: B 148 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7466 (ptmt) REVERT: B 325 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: B 614 HIS cc_start: 0.9344 (OUTLIER) cc_final: 0.9060 (p-80) outliers start: 19 outliers final: 10 residues processed: 64 average time/residue: 1.0169 time to fit residues: 71.6595 Evaluate side-chains 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 88 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.8525 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9562 Z= 0.176 Angle : 0.452 6.410 12756 Z= 0.233 Chirality : 0.039 0.149 1426 Planarity : 0.003 0.032 1446 Dihedral : 10.741 59.466 2080 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.75 % Allowed : 12.14 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.26), residues: 1038 helix: 3.16 (0.21), residues: 500 sheet: 0.99 (0.40), residues: 130 loop : -0.11 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.003 0.001 HIS A 614 PHE 0.013 0.001 PHE B 322 TYR 0.013 0.001 TYR B 570 ARG 0.001 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.049 Fit side-chains REVERT: A 148 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7478 (ptmt) REVERT: A 325 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 614 HIS cc_start: 0.9301 (OUTLIER) cc_final: 0.8978 (p-80) REVERT: A 630 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8161 (t0) REVERT: B 148 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7463 (ptmt) REVERT: B 325 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7900 (tpp) REVERT: B 614 HIS cc_start: 0.9301 (OUTLIER) cc_final: 0.8979 (p-80) outliers start: 16 outliers final: 6 residues processed: 61 average time/residue: 1.1537 time to fit residues: 76.8999 Evaluate side-chains 65 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.0040 chunk 25 optimal weight: 0.0040 overall best weight: 0.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 358 ASN B 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9562 Z= 0.118 Angle : 0.423 6.449 12756 Z= 0.218 Chirality : 0.038 0.143 1426 Planarity : 0.003 0.037 1446 Dihedral : 9.603 62.171 2080 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.20 % Allowed : 13.24 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.26), residues: 1038 helix: 3.45 (0.21), residues: 498 sheet: 0.99 (0.40), residues: 130 loop : -0.10 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 647 HIS 0.002 0.000 HIS B 614 PHE 0.015 0.001 PHE A 315 TYR 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 1.075 Fit side-chains REVERT: A 148 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7502 (ptmt) REVERT: A 325 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: A 614 HIS cc_start: 0.9274 (OUTLIER) cc_final: 0.8907 (p-80) REVERT: B 148 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7495 (ptmt) REVERT: B 325 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: B 614 HIS cc_start: 0.9274 (OUTLIER) cc_final: 0.8907 (p-80) outliers start: 11 outliers final: 3 residues processed: 57 average time/residue: 1.0417 time to fit residues: 65.6732 Evaluate side-chains 59 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 358 ASN B 358 ASN B 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.100461 restraints weight = 10160.041| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.80 r_work: 0.2847 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9562 Z= 0.303 Angle : 0.502 6.463 12756 Z= 0.258 Chirality : 0.042 0.150 1426 Planarity : 0.004 0.031 1446 Dihedral : 10.583 58.356 2080 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.20 % Allowed : 13.24 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.26), residues: 1038 helix: 3.05 (0.21), residues: 500 sheet: 1.02 (0.40), residues: 130 loop : -0.09 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS A 614 PHE 0.016 0.001 PHE B 322 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.21 seconds wall clock time: 47 minutes 25.43 seconds (2845.43 seconds total)