Starting phenix.real_space_refine on Sat Aug 23 03:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl1_36386/08_2025/8jl1_36386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl1_36386/08_2025/8jl1_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_36386/08_2025/8jl1_36386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl1_36386/08_2025/8jl1_36386.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl1_36386/08_2025/8jl1_36386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl1_36386/08_2025/8jl1_36386.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.67, per 1000 atoms: 0.28 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: 1.05 Conformation dependent library (CDL) restraints added in 330.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.46 Time building geometry restraints manager: 1.31 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: 0.01 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: 5.340 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- 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 9578 Z= 0.262 Angle : 0.619 6.355 12798 Z= 0.316 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 379 TYR 0.020 0.002 TYR A 620 PHE 0.013 0.002 PHE A 322 TRP 0.013 0.001 TRP B 647 HIS 0.010 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 9562) covalent geometry : angle 0.61140 (12756) SS BOND : bond 0.00163 ( 6) SS BOND : angle 2.48520 ( 12) hydrogen bonds : bond 0.15142 ( 478) hydrogen bonds : angle 5.56503 ( 1356) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 1.12536 ( 12) link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 1.58170 ( 18) *********************** 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 : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6418 time to fit residues: 53.5852 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101932 restraints weight = 10366.963| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.77 r_work: 0.2926 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9578 Z= 0.147 Angle : 0.512 6.243 12798 Z= 0.264 Chirality : 0.041 0.145 1426 Planarity : 0.004 0.034 1446 Dihedral : 12.650 59.274 2080 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.88 % Allowed : 8.42 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.26), residues: 1038 helix: 2.59 (0.22), residues: 496 sheet: 1.43 (0.43), residues: 110 loop : -0.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 337 TYR 0.011 0.001 TYR B 570 PHE 0.015 0.001 PHE A 322 TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9562) covalent geometry : angle 0.50646 (12756) SS BOND : bond 0.00192 ( 6) SS BOND : angle 1.28113 ( 12) hydrogen bonds : bond 0.05209 ( 478) hydrogen bonds : angle 4.07351 ( 1356) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 1.23959 ( 12) link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 1.61443 ( 18) *********************** 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 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.343 Fit side-chains REVERT: A 416 SER cc_start: 0.8705 (p) cc_final: 0.8484 (m) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.4746 time to fit residues: 36.4250 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102204 restraints weight = 10383.070| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.75 r_work: 0.2909 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9578 Z= 0.141 Angle : 0.496 6.264 12798 Z= 0.252 Chirality : 0.040 0.140 1426 Planarity : 0.004 0.033 1446 Dihedral : 11.862 57.033 2080 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.09 % Allowed : 9.96 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.26), residues: 1038 helix: 2.96 (0.22), residues: 498 sheet: 0.91 (0.41), residues: 126 loop : -0.05 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.011 0.001 TYR B 570 PHE 0.014 0.001 PHE A 322 TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9562) covalent geometry : angle 0.49050 (12756) SS BOND : bond 0.00120 ( 6) SS BOND : angle 1.12375 ( 12) hydrogen bonds : bond 0.04717 ( 478) hydrogen bonds : angle 3.88081 ( 1356) link_BETA1-4 : bond 0.00266 ( 4) link_BETA1-4 : angle 1.33832 ( 12) link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 1.54771 ( 18) *********************** 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 70 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.321 Fit side-chains REVERT: A 148 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7244 (ptmt) REVERT: B 148 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7194 (ptmt) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.4578 time to fit residues: 31.2257 Evaluate side-chains 59 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS 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 101 optimal weight: 0.0050 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100989 restraints weight = 10510.013| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.76 r_work: 0.2869 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9578 Z= 0.177 Angle : 0.516 6.327 12798 Z= 0.263 Chirality : 0.042 0.151 1426 Planarity : 0.004 0.032 1446 Dihedral : 11.885 56.885 2080 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.75 % Allowed : 9.63 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.26), residues: 1038 helix: 2.93 (0.21), residues: 498 sheet: 0.96 (0.41), residues: 126 loop : -0.04 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.012 0.002 TYR A 570 PHE 0.015 0.001 PHE B 322 TRP 0.012 0.001 TRP A 647 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9562) covalent geometry : angle 0.51040 (12756) SS BOND : bond 0.00216 ( 6) SS BOND : angle 1.04215 ( 12) hydrogen bonds : bond 0.05084 ( 478) hydrogen bonds : angle 3.91337 ( 1356) link_BETA1-4 : bond 0.00241 ( 4) link_BETA1-4 : angle 1.34142 ( 12) link_NAG-ASN : bond 0.00110 ( 6) link_NAG-ASN : angle 1.61671 ( 18) *********************** 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 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.410 Fit side-chains REVERT: A 148 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7255 (ptmt) REVERT: A 556 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 614 HIS cc_start: 0.9240 (OUTLIER) cc_final: 0.8829 (p-80) REVERT: B 148 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7183 (ptmt) REVERT: B 164 SER cc_start: 0.8653 (p) cc_final: 0.8424 (t) REVERT: B 556 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 614 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8820 (p-80) outliers start: 16 outliers final: 6 residues processed: 63 average time/residue: 0.4908 time to fit residues: 33.8825 Evaluate side-chains 66 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 325 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100090 restraints weight = 10501.990| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.75 r_work: 0.2830 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9578 Z= 0.238 Angle : 0.570 6.407 12798 Z= 0.290 Chirality : 0.044 0.159 1426 Planarity : 0.004 0.032 1446 Dihedral : 12.445 59.160 2080 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.19 % Allowed : 9.96 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.26), residues: 1038 helix: 2.72 (0.21), residues: 498 sheet: 1.02 (0.41), residues: 124 loop : -0.04 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.014 0.002 TYR A 496 PHE 0.017 0.002 PHE A 322 TRP 0.014 0.002 TRP B 647 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9562) covalent geometry : angle 0.56396 (12756) SS BOND : bond 0.00158 ( 6) SS BOND : angle 1.10004 ( 12) hydrogen bonds : bond 0.05783 ( 478) hydrogen bonds : angle 4.06277 ( 1356) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.39588 ( 12) link_NAG-ASN : bond 0.00121 ( 6) link_NAG-ASN : angle 1.77152 ( 18) *********************** 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 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.337 Fit side-chains REVERT: A 148 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7198 (ptmt) REVERT: A 325 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7808 (tpp) REVERT: A 337 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7261 (ttm110) REVERT: A 556 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 614 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.8909 (p-80) REVERT: B 148 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7169 (ptmt) REVERT: B 337 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7264 (ttm110) REVERT: B 556 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: B 614 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8912 (p-80) outliers start: 20 outliers final: 11 residues processed: 66 average time/residue: 0.5832 time to fit residues: 41.5290 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 : 0.359 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 483 HIS 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 325 MET Chi-restraints excluded: chain B residue 358 ASN 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 51 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100247 restraints weight = 10466.210| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.72 r_work: 0.2986 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9578 Z= 0.160 Angle : 0.507 6.349 12798 Z= 0.260 Chirality : 0.041 0.155 1426 Planarity : 0.004 0.033 1446 Dihedral : 11.784 58.894 2080 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.75 % Allowed : 12.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.26), residues: 1038 helix: 2.94 (0.22), residues: 498 sheet: 0.94 (0.40), residues: 130 loop : -0.12 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.014 0.001 TYR B 570 PHE 0.014 0.001 PHE B 322 TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9562) covalent geometry : angle 0.50094 (12756) SS BOND : bond 0.00175 ( 6) SS BOND : angle 1.05437 ( 12) hydrogen bonds : bond 0.04886 ( 478) hydrogen bonds : angle 3.89219 ( 1356) link_BETA1-4 : bond 0.00277 ( 4) link_BETA1-4 : angle 1.36579 ( 12) link_NAG-ASN : bond 0.00082 ( 6) link_NAG-ASN : angle 1.62604 ( 18) *********************** 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 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.353 Fit side-chains REVERT: A 148 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7250 (ptmt) REVERT: A 325 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: A 556 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: A 614 HIS cc_start: 0.9243 (OUTLIER) cc_final: 0.8847 (p-80) REVERT: B 148 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7214 (ptmt) REVERT: B 325 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7829 (tpp) REVERT: B 556 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: B 614 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.8846 (p-80) outliers start: 16 outliers final: 4 residues processed: 61 average time/residue: 0.5708 time to fit residues: 37.7927 Evaluate side-chains 63 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 325 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.099863 restraints weight = 10491.288| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.78 r_work: 0.2931 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9578 Z= 0.245 Angle : 0.571 6.458 12798 Z= 0.290 Chirality : 0.044 0.156 1426 Planarity : 0.004 0.034 1446 Dihedral : 12.225 58.241 2080 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.97 % Allowed : 12.04 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.26), residues: 1038 helix: 2.69 (0.21), residues: 498 sheet: 0.92 (0.40), residues: 130 loop : -0.18 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.014 0.002 TYR A 496 PHE 0.016 0.002 PHE A 322 TRP 0.014 0.002 TRP B 647 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 9562) covalent geometry : angle 0.56521 (12756) SS BOND : bond 0.00133 ( 6) SS BOND : angle 1.05036 ( 12) hydrogen bonds : bond 0.05752 ( 478) hydrogen bonds : angle 4.04783 ( 1356) link_BETA1-4 : bond 0.00206 ( 4) link_BETA1-4 : angle 1.34366 ( 12) link_NAG-ASN : bond 0.00150 ( 6) link_NAG-ASN : angle 1.80313 ( 18) *********************** 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 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.362 Fit side-chains REVERT: A 148 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7182 (ptmt) REVERT: A 325 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: A 337 ARG cc_start: 0.7469 (mtp-110) cc_final: 0.7225 (ttm110) REVERT: A 556 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 614 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.8899 (p-80) REVERT: B 148 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7151 (ptmt) REVERT: B 325 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7803 (tpp) REVERT: B 337 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.7237 (ttm110) REVERT: B 556 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: B 614 HIS cc_start: 0.9250 (OUTLIER) cc_final: 0.8899 (p-80) outliers start: 18 outliers final: 6 residues processed: 61 average time/residue: 0.6263 time to fit residues: 41.1422 Evaluate side-chains 66 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 483 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099161 restraints weight = 10331.905| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.80 r_work: 0.2863 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9578 Z= 0.119 Angle : 0.471 6.384 12798 Z= 0.241 Chirality : 0.039 0.151 1426 Planarity : 0.004 0.033 1446 Dihedral : 11.062 58.621 2080 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.98 % Allowed : 12.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.26), residues: 1038 helix: 3.12 (0.21), residues: 498 sheet: 0.97 (0.40), residues: 130 loop : -0.09 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.014 0.001 TYR A 570 PHE 0.013 0.001 PHE B 322 TRP 0.012 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9562) covalent geometry : angle 0.46485 (12756) SS BOND : bond 0.00206 ( 6) SS BOND : angle 1.01042 ( 12) hydrogen bonds : bond 0.04327 ( 478) hydrogen bonds : angle 3.77787 ( 1356) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 1.34848 ( 12) link_NAG-ASN : bond 0.00107 ( 6) link_NAG-ASN : angle 1.55456 ( 18) *********************** 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 64 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.360 Fit side-chains REVERT: A 325 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (tpp) REVERT: A 333 CYS cc_start: 0.8135 (t) cc_final: 0.7893 (m) REVERT: A 556 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: A 614 HIS cc_start: 0.9179 (OUTLIER) cc_final: 0.8765 (p-80) REVERT: A 630 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (t0) REVERT: B 325 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7777 (tpp) REVERT: B 333 CYS cc_start: 0.8151 (t) cc_final: 0.7905 (m) REVERT: B 614 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8756 (p-80) REVERT: B 630 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8108 (t0) outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 0.5621 time to fit residues: 36.6778 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS 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 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 20 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100432 restraints weight = 10338.117| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.79 r_work: 0.2849 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9578 Z= 0.128 Angle : 0.471 6.394 12798 Z= 0.242 Chirality : 0.040 0.149 1426 Planarity : 0.003 0.032 1446 Dihedral : 10.592 58.130 2080 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.88 % Allowed : 14.00 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.26), residues: 1038 helix: 3.15 (0.21), residues: 498 sheet: 0.93 (0.39), residues: 130 loop : -0.06 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 152 TYR 0.012 0.001 TYR A 570 PHE 0.014 0.001 PHE B 322 TRP 0.012 0.001 TRP A 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9562) covalent geometry : angle 0.46513 (12756) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.95871 ( 12) hydrogen bonds : bond 0.04360 ( 478) hydrogen bonds : angle 3.73434 ( 1356) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.27093 ( 12) link_NAG-ASN : bond 0.00123 ( 6) link_NAG-ASN : angle 1.57272 ( 18) *********************** 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 60 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.364 Fit side-chains REVERT: A 325 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: A 333 CYS cc_start: 0.8164 (t) cc_final: 0.7849 (m) REVERT: A 614 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8750 (p-80) REVERT: A 630 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 325 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7772 (tpp) REVERT: B 333 CYS cc_start: 0.8182 (t) cc_final: 0.7863 (m) REVERT: B 614 HIS cc_start: 0.9185 (OUTLIER) cc_final: 0.8743 (p-80) REVERT: B 630 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8066 (t0) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.4974 time to fit residues: 30.5106 Evaluate side-chains 60 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS 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 325 MET Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098327 restraints weight = 10381.013| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.78 r_work: 0.2848 rms_B_bonded: 2.37 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: 0.8374 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9578 Z= 0.163 Angle : 0.495 6.410 12798 Z= 0.253 Chirality : 0.041 0.151 1426 Planarity : 0.004 0.032 1446 Dihedral : 10.803 56.700 2080 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.98 % Allowed : 13.79 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.26), residues: 1038 helix: 3.00 (0.21), residues: 500 sheet: 0.89 (0.40), residues: 130 loop : -0.13 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.013 0.001 TYR B 570 PHE 0.015 0.001 PHE B 322 TRP 0.012 0.001 TRP A 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9562) covalent geometry : angle 0.48924 (12756) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.96164 ( 12) hydrogen bonds : bond 0.04791 ( 478) hydrogen bonds : angle 3.80665 ( 1356) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.24671 ( 12) link_NAG-ASN : bond 0.00103 ( 6) link_NAG-ASN : angle 1.63996 ( 18) ********************** 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 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.337 Fit side-chains REVERT: A 325 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: A 333 CYS cc_start: 0.8118 (t) cc_final: 0.7850 (m) REVERT: A 614 HIS cc_start: 0.9206 (OUTLIER) cc_final: 0.8769 (p-80) REVERT: A 630 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 333 CYS cc_start: 0.8138 (t) cc_final: 0.7865 (m) REVERT: B 614 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8766 (p-80) REVERT: B 630 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8118 (t0) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 0.5264 time to fit residues: 33.2490 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS 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 325 MET Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 82 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102292 restraints weight = 10164.227| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.78 r_work: 0.2859 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9578 Z= 0.122 Angle : 0.463 6.403 12798 Z= 0.237 Chirality : 0.040 0.150 1426 Planarity : 0.003 0.034 1446 Dihedral : 10.300 58.638 2080 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.98 % Allowed : 13.89 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.26), residues: 1038 helix: 3.16 (0.21), residues: 500 sheet: 0.94 (0.40), residues: 130 loop : -0.10 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.013 0.001 TYR B 570 PHE 0.013 0.001 PHE B 322 TRP 0.011 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9562) covalent geometry : angle 0.45716 (12756) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.95266 ( 12) hydrogen bonds : bond 0.04255 ( 478) hydrogen bonds : angle 3.70136 ( 1356) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 1.24029 ( 12) link_NAG-ASN : bond 0.00124 ( 6) link_NAG-ASN : angle 1.55383 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3039.70 seconds wall clock time: 52 minutes 51.40 seconds (3171.40 seconds total)