Starting phenix.real_space_refine on Mon May 12 22:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl1_36386/05_2025/8jl1_36386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl1_36386/05_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_36386/05_2025/8jl1_36386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl1_36386/05_2025/8jl1_36386.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl1_36386/05_2025/8jl1_36386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl1_36386/05_2025/8jl1_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-5687/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: 7.39, per 1000 atoms: 0.79 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: 2.34 Conformation dependent library (CDL) restraints added in 995.1 milliseconds 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: 0.77 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: 2.47 Time building geometry restraints manager: 2.71 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: 2.670 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.080 Find NCS groups from input model: 0.620 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 1.58170 ( 18) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 1.12536 ( 12) hydrogen bonds : bond 0.15142 ( 478) hydrogen bonds : angle 5.56503 ( 1356) SS BOND : bond 0.00163 ( 6) SS BOND : angle 2.48520 ( 12) covalent geometry : bond 0.00654 ( 9562) covalent geometry : angle 0.61140 (12756) *********************** 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 : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.3052 time to fit residues: 109.4640 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 : 0.956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102378 restraints weight = 10262.206| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.76 r_work: 0.2916 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 9578 Z= 0.136 Angle : 0.501 6.250 12798 Z= 0.259 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 6) link_NAG-ASN : angle 1.55145 ( 18) link_BETA1-4 : bond 0.00122 ( 4) link_BETA1-4 : angle 1.28983 ( 12) hydrogen bonds : bond 0.05091 ( 478) hydrogen bonds : angle 4.04586 ( 1356) SS BOND : bond 0.00177 ( 6) SS BOND : angle 1.35305 ( 12) covalent geometry : bond 0.00318 ( 9562) covalent geometry : angle 0.49505 (12756) *********************** 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 : 0.878 Fit side-chains REVERT: A 416 SER cc_start: 0.8711 (p) cc_final: 0.8487 (m) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.9286 time to fit residues: 70.9191 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 : 1.014 ------------------------------------------------------------------------------- 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 64 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.0870 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.134770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100591 restraints weight = 10509.472| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.76 r_work: 0.2883 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9578 Z= 0.195 Angle : 0.541 6.290 12798 Z= 0.274 Chirality : 0.042 0.150 1426 Planarity : 0.004 0.035 1446 Dihedral : 12.419 59.671 2080 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.53 % Allowed : 9.30 % Favored : 89.17 % 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: 2.77 (0.22), residues: 498 sheet: 1.06 (0.41), residues: 124 loop : -0.01 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.007 0.001 HIS A 614 PHE 0.016 0.002 PHE A 322 TYR 0.012 0.002 TYR A 496 ARG 0.002 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 6) link_NAG-ASN : angle 1.63141 ( 18) link_BETA1-4 : bond 0.00244 ( 4) link_BETA1-4 : angle 1.32968 ( 12) hydrogen bonds : bond 0.05417 ( 478) hydrogen bonds : angle 4.02193 ( 1356) SS BOND : bond 0.00127 ( 6) SS BOND : angle 1.10265 ( 12) covalent geometry : bond 0.00486 ( 9562) covalent geometry : angle 0.53546 (12756) *********************** 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 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.032 Fit side-chains REVERT: A 148 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7265 (ptmt) REVERT: A 556 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: B 148 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7198 (ptmt) outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.8997 time to fit residues: 63.9688 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 : 0.947 ------------------------------------------------------------------------------- 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 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 483 HIS 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 57 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100333 restraints weight = 10381.667| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.76 r_work: 0.2857 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9578 Z= 0.153 Angle : 0.500 6.296 12798 Z= 0.255 Chirality : 0.041 0.147 1426 Planarity : 0.004 0.035 1446 Dihedral : 11.871 56.819 2080 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.42 % Allowed : 10.07 % Favored : 88.51 % 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: 2.34 (0.26), residues: 1038 helix: 2.96 (0.22), residues: 498 sheet: 0.98 (0.40), residues: 130 loop : -0.05 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.005 0.001 HIS B 614 PHE 0.014 0.001 PHE A 322 TYR 0.013 0.001 TYR B 570 ARG 0.001 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 6) link_NAG-ASN : angle 1.58696 ( 18) link_BETA1-4 : bond 0.00266 ( 4) link_BETA1-4 : angle 1.35301 ( 12) hydrogen bonds : bond 0.04807 ( 478) hydrogen bonds : angle 3.88973 ( 1356) SS BOND : bond 0.00172 ( 6) SS BOND : angle 1.09622 ( 12) covalent geometry : bond 0.00374 ( 9562) covalent geometry : angle 0.49421 (12756) *********************** 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 68 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.889 Fit side-chains REVERT: A 148 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7222 (ptmt) REVERT: A 614 HIS cc_start: 0.9214 (OUTLIER) cc_final: 0.8804 (p-80) REVERT: B 148 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7174 (ptmt) REVERT: B 164 SER cc_start: 0.8613 (p) cc_final: 0.8385 (t) REVERT: B 556 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 614 HIS cc_start: 0.9211 (OUTLIER) cc_final: 0.8799 (p-80) outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 0.9257 time to fit residues: 63.5381 Evaluate side-chains 65 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101554 restraints weight = 10250.107| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.79 r_work: 0.2881 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9578 Z= 0.107 Angle : 0.454 6.310 12798 Z= 0.233 Chirality : 0.039 0.147 1426 Planarity : 0.003 0.033 1446 Dihedral : 10.851 59.980 2080 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.53 % Allowed : 10.72 % Favored : 87.75 % 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: 2.62 (0.26), residues: 1038 helix: 3.30 (0.22), residues: 498 sheet: 1.04 (0.40), residues: 130 loop : -0.02 (0.33), residues: 410 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 0.012 0.001 PHE A 322 TYR 0.013 0.001 TYR A 570 ARG 0.001 0.000 ARG A 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 6) link_NAG-ASN : angle 1.49512 ( 18) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 1.34628 ( 12) hydrogen bonds : bond 0.04035 ( 478) hydrogen bonds : angle 3.70310 ( 1356) SS BOND : bond 0.00218 ( 6) SS BOND : angle 1.02976 ( 12) covalent geometry : bond 0.00245 ( 9562) covalent geometry : angle 0.44800 (12756) *********************** 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 67 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.871 Fit side-chains REVERT: A 556 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: A 614 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8682 (p-80) REVERT: A 630 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8047 (t0) REVERT: B 556 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: B 614 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8684 (p-80) REVERT: B 630 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8046 (t0) outliers start: 14 outliers final: 3 residues processed: 62 average time/residue: 1.0160 time to fit residues: 69.2572 Evaluate side-chains 61 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 164 SER 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 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 85 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099523 restraints weight = 10241.794| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.79 r_work: 0.2865 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9578 Z= 0.128 Angle : 0.467 6.340 12798 Z= 0.239 Chirality : 0.040 0.149 1426 Planarity : 0.003 0.033 1446 Dihedral : 10.625 57.301 2080 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.75 % Allowed : 10.72 % Favored : 87.53 % 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: 2.56 (0.26), residues: 1038 helix: 3.20 (0.21), residues: 500 sheet: 1.05 (0.40), residues: 130 loop : -0.02 (0.33), residues: 408 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 0.014 0.001 PHE A 322 TYR 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 6) link_NAG-ASN : angle 1.57399 ( 18) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 1.29365 ( 12) hydrogen bonds : bond 0.04345 ( 478) hydrogen bonds : angle 3.72184 ( 1356) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.97012 ( 12) covalent geometry : bond 0.00306 ( 9562) covalent geometry : angle 0.46129 (12756) *********************** 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 : 0.899 Fit side-chains REVERT: A 148 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7213 (ptmt) REVERT: A 325 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7850 (tpp) REVERT: A 333 CYS cc_start: 0.8200 (t) cc_final: 0.7862 (m) REVERT: A 614 HIS cc_start: 0.9189 (OUTLIER) cc_final: 0.8762 (p-80) REVERT: A 630 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 325 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7835 (tpp) REVERT: B 333 CYS cc_start: 0.8210 (t) cc_final: 0.7871 (m) REVERT: B 614 HIS cc_start: 0.9187 (OUTLIER) cc_final: 0.8754 (p-80) REVERT: B 630 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8059 (t0) outliers start: 16 outliers final: 4 residues processed: 62 average time/residue: 1.0114 time to fit residues: 69.1719 Evaluate side-chains 64 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 164 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 45 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101732 restraints weight = 10278.646| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.79 r_work: 0.2899 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9578 Z= 0.107 Angle : 0.445 6.337 12798 Z= 0.228 Chirality : 0.039 0.147 1426 Planarity : 0.003 0.034 1446 Dihedral : 10.138 58.873 2080 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.20 % Allowed : 11.27 % Favored : 87.53 % 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: 3.33 (0.21), residues: 500 sheet: 1.05 (0.40), residues: 130 loop : -0.03 (0.33), 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 A 322 TYR 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 6) link_NAG-ASN : angle 1.48842 ( 18) link_BETA1-4 : bond 0.00310 ( 4) link_BETA1-4 : angle 1.25995 ( 12) hydrogen bonds : bond 0.03985 ( 478) hydrogen bonds : angle 3.63686 ( 1356) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.95398 ( 12) covalent geometry : bond 0.00247 ( 9562) covalent geometry : angle 0.43945 (12756) *********************** 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 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.962 Fit side-chains REVERT: A 325 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7829 (tpp) REVERT: A 333 CYS cc_start: 0.8201 (t) cc_final: 0.7873 (m) REVERT: A 614 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8747 (p-80) REVERT: A 630 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8070 (t0) REVERT: B 148 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7173 (ptmt) REVERT: B 325 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7839 (tpp) REVERT: B 333 CYS cc_start: 0.8219 (t) cc_final: 0.7891 (m) REVERT: B 614 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.8745 (p-80) REVERT: B 630 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (t0) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 1.0012 time to fit residues: 62.0052 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 164 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 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 5 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.099828 restraints weight = 10524.663| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.82 r_work: 0.2957 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9578 Z= 0.202 Angle : 0.522 6.446 12798 Z= 0.266 Chirality : 0.043 0.152 1426 Planarity : 0.004 0.030 1446 Dihedral : 11.054 59.872 2080 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.64 % Allowed : 11.27 % 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: 2.35 (0.26), residues: 1038 helix: 2.97 (0.21), residues: 500 sheet: 1.01 (0.40), residues: 130 loop : -0.05 (0.33), 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 A 322 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 6) link_NAG-ASN : angle 1.71635 ( 18) link_BETA1-4 : bond 0.00223 ( 4) link_BETA1-4 : angle 1.25885 ( 12) hydrogen bonds : bond 0.05204 ( 478) hydrogen bonds : angle 3.86619 ( 1356) SS BOND : bond 0.00116 ( 6) SS BOND : angle 0.94374 ( 12) covalent geometry : bond 0.00506 ( 9562) covalent geometry : angle 0.51629 (12756) *********************** 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 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.907 Fit side-chains REVERT: A 148 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7236 (ptmt) REVERT: A 325 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: A 333 CYS cc_start: 0.8188 (t) cc_final: 0.7896 (m) REVERT: A 614 HIS cc_start: 0.9230 (OUTLIER) cc_final: 0.8865 (p-80) REVERT: A 630 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 148 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7192 (ptmt) REVERT: B 325 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: B 333 CYS cc_start: 0.8197 (t) cc_final: 0.7904 (m) REVERT: B 614 HIS cc_start: 0.9228 (OUTLIER) cc_final: 0.8862 (p-80) REVERT: B 630 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (t0) outliers start: 15 outliers final: 4 residues processed: 63 average time/residue: 0.9809 time to fit residues: 67.9868 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 : 0.980 ------------------------------------------------------------------------------- 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 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 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 82 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.096585 restraints weight = 10414.342| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.76 r_work: 0.2841 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9578 Z= 0.200 Angle : 0.528 6.481 12798 Z= 0.270 Chirality : 0.043 0.155 1426 Planarity : 0.004 0.030 1446 Dihedral : 11.341 56.129 2080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.53 % Allowed : 11.60 % Favored : 86.87 % 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: 2.26 (0.26), residues: 1038 helix: 2.90 (0.21), residues: 500 sheet: 0.95 (0.40), residues: 130 loop : -0.10 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.006 0.001 HIS A 614 PHE 0.016 0.001 PHE A 322 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 6) link_NAG-ASN : angle 1.73643 ( 18) link_BETA1-4 : bond 0.00236 ( 4) link_BETA1-4 : angle 1.27396 ( 12) hydrogen bonds : bond 0.05222 ( 478) hydrogen bonds : angle 3.89627 ( 1356) SS BOND : bond 0.00124 ( 6) SS BOND : angle 1.01207 ( 12) covalent geometry : bond 0.00499 ( 9562) covalent geometry : angle 0.52224 (12756) *********************** 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 67 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.965 Fit side-chains REVERT: A 148 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7195 (ptmt) REVERT: A 325 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: A 333 CYS cc_start: 0.8182 (t) cc_final: 0.7916 (m) REVERT: A 556 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 614 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8786 (p-80) REVERT: B 148 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7124 (ptmt) REVERT: B 325 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7844 (tpp) REVERT: B 333 CYS cc_start: 0.8172 (t) cc_final: 0.7913 (m) REVERT: B 556 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 614 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8782 (p-80) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 1.1002 time to fit residues: 72.1090 Evaluate side-chains 67 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.100521 restraints weight = 10448.866| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.81 r_work: 0.2967 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9578 Z= 0.159 Angle : 0.497 6.463 12798 Z= 0.255 Chirality : 0.041 0.152 1426 Planarity : 0.004 0.030 1446 Dihedral : 11.049 57.893 2080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.31 % Allowed : 11.71 % Favored : 86.98 % 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: 2.38 (0.26), residues: 1038 helix: 3.05 (0.21), residues: 498 sheet: 0.97 (0.40), residues: 130 loop : -0.10 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE B 322 TYR 0.013 0.001 TYR B 570 ARG 0.002 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 6) link_NAG-ASN : angle 1.66139 ( 18) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.27864 ( 12) hydrogen bonds : bond 0.04790 ( 478) hydrogen bonds : angle 3.82594 ( 1356) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.98713 ( 12) covalent geometry : bond 0.00391 ( 9562) covalent geometry : angle 0.49153 (12756) ********************** 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: 12 poor density : 51 time to evaluate : 0.891 Fit side-chains REVERT: A 148 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7186 (ptmt) REVERT: A 325 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: A 333 CYS cc_start: 0.8142 (t) cc_final: 0.7876 (m) REVERT: A 614 HIS cc_start: 0.9212 (OUTLIER) cc_final: 0.8795 (p-80) REVERT: A 630 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 148 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7148 (ptmt) REVERT: B 325 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7825 (tpp) REVERT: B 333 CYS cc_start: 0.8164 (t) cc_final: 0.7894 (m) REVERT: B 614 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8788 (p-80) REVERT: B 630 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (t0) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.9783 time to fit residues: 60.4393 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 : 0.939 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102048 restraints weight = 10252.039| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.80 r_work: 0.2884 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9578 Z= 0.125 Angle : 0.467 6.390 12798 Z= 0.240 Chirality : 0.040 0.152 1426 Planarity : 0.003 0.031 1446 Dihedral : 10.455 59.657 2080 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.53 % Allowed : 11.82 % 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: 2.52 (0.26), residues: 1038 helix: 3.21 (0.21), residues: 498 sheet: 0.99 (0.40), residues: 130 loop : -0.07 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 647 HIS 0.004 0.001 HIS A 614 PHE 0.013 0.001 PHE B 322 TYR 0.013 0.001 TYR A 570 ARG 0.001 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 6) link_NAG-ASN : angle 1.57382 ( 18) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 1.23357 ( 12) hydrogen bonds : bond 0.04272 ( 478) hydrogen bonds : angle 3.71884 ( 1356) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.96456 ( 12) covalent geometry : bond 0.00296 ( 9562) covalent geometry : angle 0.46117 (12756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5839.60 seconds wall clock time: 102 minutes 20.44 seconds (6140.44 seconds total)