Starting phenix.real_space_refine on Wed Apr 30 09:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl1_36386/04_2025/8jl1_36386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl1_36386/04_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_36386/04_2025/8jl1_36386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl1_36386/04_2025/8jl1_36386.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl1_36386/04_2025/8jl1_36386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl1_36386/04_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-5669/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: 7.07, per 1000 atoms: 0.75 Number of scatterers: 9384 At special positions: 0 Unit cell: (108.73, 87.15, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1516 8.00 N 1364 7.00 C 6458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 802 " - " ASN A 94 " " NAG B 803 " - " ASN B 94 " " NAG C 1 " - " ASN A 142 " " NAG D 1 " - " ASN A 162 " " NAG E 1 " - " ASN B 142 " " NAG F 1 " - " ASN B 162 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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: 3.06 Time building geometry restraints manager: 3.10 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: 4.390 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:19.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- 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 : 0.930 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.2312 time to fit residues: 103.1763 Evaluate side-chains 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.136520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102385 restraints weight = 10261.279| |-----------------------------------------------------------------------------| 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: 3.80 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 1.55147 ( 18) link_BETA1-4 : bond 0.00122 ( 4) link_BETA1-4 : angle 1.28951 ( 12) hydrogen bonds : bond 0.05091 ( 478) hydrogen bonds : angle 4.04588 ( 1356) SS BOND : bond 0.00177 ( 6) SS BOND : angle 1.35300 ( 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 : 0.910 Fit side-chains REVERT: A 416 SER cc_start: 0.8712 (p) cc_final: 0.8488 (m) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.9435 time to fit residues: 71.6983 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 : 0.983 ------------------------------------------------------------------------------- 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: 0.0770 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100570 restraints weight = 10510.488| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.76 r_work: 0.2884 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0939 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= 0.197 Angle : 0.544 6.315 12798 Z= 0.275 Chirality : 0.043 0.149 1426 Planarity : 0.004 0.034 1446 Dihedral : 12.427 59.677 2080 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.31 % Allowed : 9.63 % Favored : 89.06 % 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: 2.76 (0.22), residues: 498 sheet: 1.06 (0.41), residues: 124 loop : -0.02 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.006 0.001 HIS B 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 0.00125 ( 6) link_NAG-ASN : angle 1.67285 ( 18) link_BETA1-4 : bond 0.00245 ( 4) link_BETA1-4 : angle 1.32189 ( 12) hydrogen bonds : bond 0.05437 ( 478) hydrogen bonds : angle 4.02476 ( 1356) SS BOND : bond 0.00105 ( 6) SS BOND : angle 1.13154 ( 12) covalent geometry : bond 0.00490 ( 9562) covalent geometry : angle 0.53904 (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 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.979 Fit side-chains REVERT: A 148 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7252 (ptmt) REVERT: B 148 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7189 (ptmt) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 1.1059 time to fit residues: 75.5282 Evaluate side-chains 60 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 57 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100664 restraints weight = 10393.001| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.75 r_work: 0.2865 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9578 Z= 0.184 Angle : 0.525 6.327 12798 Z= 0.267 Chirality : 0.042 0.149 1426 Planarity : 0.004 0.036 1446 Dihedral : 12.201 56.481 2080 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 9.96 % 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: 2.27 (0.26), residues: 1038 helix: 2.84 (0.22), residues: 498 sheet: 1.02 (0.40), residues: 128 loop : 0.00 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.007 0.001 HIS A 614 PHE 0.015 0.001 PHE A 322 TYR 0.012 0.002 TYR A 570 ARG 0.002 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 6) link_NAG-ASN : angle 1.69614 ( 18) link_BETA1-4 : bond 0.00276 ( 4) link_BETA1-4 : angle 1.36084 ( 12) hydrogen bonds : bond 0.05168 ( 478) hydrogen bonds : angle 3.96306 ( 1356) SS BOND : bond 0.00118 ( 6) SS BOND : angle 1.09415 ( 12) covalent geometry : bond 0.00458 ( 9562) covalent geometry : angle 0.51878 (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 64 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.052 Fit side-chains REVERT: A 148 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7237 (ptmt) REVERT: A 556 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: A 614 HIS cc_start: 0.9243 (OUTLIER) cc_final: 0.8843 (p-80) REVERT: B 148 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7174 (ptmt) REVERT: B 556 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 614 HIS cc_start: 0.9238 (OUTLIER) cc_final: 0.8835 (p-80) outliers start: 14 outliers final: 6 residues processed: 58 average time/residue: 1.0296 time to fit residues: 65.7880 Evaluate side-chains 60 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.137905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103278 restraints weight = 10197.801| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.80 r_work: 0.2905 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9578 Z= 0.100 Angle : 0.449 6.319 12798 Z= 0.231 Chirality : 0.039 0.144 1426 Planarity : 0.003 0.033 1446 Dihedral : 10.888 59.941 2080 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.09 % Allowed : 11.27 % Favored : 87.64 % 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: 2.60 (0.26), residues: 1038 helix: 3.29 (0.22), residues: 498 sheet: 0.99 (0.40), residues: 130 loop : -0.04 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.002 0.001 HIS B 614 PHE 0.012 0.001 PHE A 322 TYR 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 6) link_NAG-ASN : angle 1.50346 ( 18) link_BETA1-4 : bond 0.00334 ( 4) link_BETA1-4 : angle 1.36764 ( 12) hydrogen bonds : bond 0.03884 ( 478) hydrogen bonds : angle 3.68322 ( 1356) SS BOND : bond 0.00191 ( 6) SS BOND : angle 1.07597 ( 12) covalent geometry : bond 0.00221 ( 9562) covalent geometry : angle 0.44302 (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 63 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 1.082 Fit side-chains REVERT: A 614 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8657 (p-80) REVERT: A 630 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8046 (t0) REVERT: B 614 HIS cc_start: 0.9126 (OUTLIER) cc_final: 0.8653 (p-80) REVERT: B 630 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (t0) outliers start: 10 outliers final: 2 residues processed: 59 average time/residue: 1.1250 time to fit residues: 73.3203 Evaluate side-chains 60 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS 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 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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 87 HIS B 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098292 restraints weight = 10270.557| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.78 r_work: 0.2973 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9578 Z= 0.173 Angle : 0.503 6.402 12798 Z= 0.257 Chirality : 0.041 0.151 1426 Planarity : 0.004 0.031 1446 Dihedral : 11.198 58.504 2080 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.09 % Allowed : 11.71 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.26), residues: 1038 helix: 3.06 (0.21), residues: 498 sheet: 1.00 (0.41), residues: 130 loop : -0.04 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE A 322 TYR 0.012 0.001 TYR A 570 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 6) link_NAG-ASN : angle 1.67282 ( 18) link_BETA1-4 : bond 0.00262 ( 4) link_BETA1-4 : angle 1.31482 ( 12) hydrogen bonds : bond 0.04882 ( 478) hydrogen bonds : angle 3.83226 ( 1356) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.98174 ( 12) covalent geometry : bond 0.00427 ( 9562) covalent geometry : angle 0.49748 (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 62 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 1.064 Fit side-chains REVERT: A 325 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7863 (tpp) REVERT: A 614 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8789 (p-80) REVERT: A 630 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 614 HIS cc_start: 0.9225 (OUTLIER) cc_final: 0.8788 (p-80) REVERT: B 630 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8133 (t0) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 1.0570 time to fit residues: 65.2788 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 : 1.010 ------------------------------------------------------------------------------- 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 164 SER 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: 1.9990 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.128435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093044 restraints weight = 10429.074| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.77 r_work: 0.2805 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1209 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= 0.242 Angle : 0.562 6.465 12798 Z= 0.286 Chirality : 0.044 0.155 1426 Planarity : 0.004 0.031 1446 Dihedral : 12.066 59.452 2080 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.19 % Allowed : 11.05 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1038 helix: 2.74 (0.21), residues: 500 sheet: 0.92 (0.41), residues: 130 loop : -0.10 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 647 HIS 0.006 0.001 HIS B 614 PHE 0.017 0.002 PHE A 322 TYR 0.014 0.002 TYR A 496 ARG 0.003 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 1.82322 ( 18) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 1.33787 ( 12) hydrogen bonds : bond 0.05717 ( 478) hydrogen bonds : angle 4.02417 ( 1356) SS BOND : bond 0.00109 ( 6) SS BOND : angle 1.06634 ( 12) covalent geometry : bond 0.00609 ( 9562) covalent geometry : angle 0.55627 (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 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 1.244 Fit side-chains REVERT: A 148 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7145 (ptmt) REVERT: A 325 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7807 (tpp) REVERT: A 337 ARG cc_start: 0.7439 (mtp-110) cc_final: 0.7193 (ttm110) REVERT: A 556 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: A 614 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8873 (p-80) REVERT: B 148 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7150 (ptmt) REVERT: B 325 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7841 (tpp) REVERT: B 337 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7191 (ttm110) REVERT: B 556 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 614 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8871 (p-80) outliers start: 20 outliers final: 8 residues processed: 64 average time/residue: 1.1699 time to fit residues: 81.4766 Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096659 restraints weight = 10615.961| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.76 r_work: 0.2840 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9578 Z= 0.184 Angle : 0.519 6.431 12798 Z= 0.266 Chirality : 0.042 0.154 1426 Planarity : 0.004 0.030 1446 Dihedral : 11.759 58.839 2080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 (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: 2.20 (0.26), residues: 1038 helix: 2.85 (0.21), residues: 500 sheet: 0.94 (0.41), residues: 130 loop : -0.14 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE B 322 TYR 0.013 0.002 TYR A 570 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 6) link_NAG-ASN : angle 1.72110 ( 18) link_BETA1-4 : bond 0.00239 ( 4) link_BETA1-4 : angle 1.33473 ( 12) hydrogen bonds : bond 0.05131 ( 478) hydrogen bonds : angle 3.92459 ( 1356) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.01906 ( 12) covalent geometry : bond 0.00457 ( 9562) covalent geometry : angle 0.51294 (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 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.012 Fit side-chains REVERT: A 148 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7160 (ptmt) REVERT: A 325 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7826 (tpp) REVERT: A 556 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: A 614 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8793 (p-80) REVERT: B 148 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7175 (ptmt) REVERT: B 325 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7796 (tpp) REVERT: B 556 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 614 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8789 (p-80) outliers start: 18 outliers final: 8 residues processed: 62 average time/residue: 1.1359 time to fit residues: 77.0933 Evaluate side-chains 67 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.9980 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: 4.9990 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: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.130760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096016 restraints weight = 10420.774| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.75 r_work: 0.2865 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9578 Z= 0.215 Angle : 0.543 6.464 12798 Z= 0.278 Chirality : 0.043 0.156 1426 Planarity : 0.004 0.031 1446 Dihedral : 11.888 55.904 2080 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.75 % Allowed : 12.25 % 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 (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: 2.11 (0.26), residues: 1038 helix: 2.74 (0.21), residues: 500 sheet: 0.90 (0.41), residues: 130 loop : -0.14 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.006 0.001 HIS A 614 PHE 0.016 0.002 PHE A 322 TYR 0.013 0.002 TYR B 570 ARG 0.002 0.000 ARG A 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 6) link_NAG-ASN : angle 1.78718 ( 18) link_BETA1-4 : bond 0.00234 ( 4) link_BETA1-4 : angle 1.33589 ( 12) hydrogen bonds : bond 0.05462 ( 478) hydrogen bonds : angle 3.98921 ( 1356) SS BOND : bond 0.00121 ( 6) SS BOND : angle 1.03126 ( 12) covalent geometry : bond 0.00540 ( 9562) covalent geometry : angle 0.53727 (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 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.261 Fit side-chains REVERT: A 148 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7154 (ptmt) REVERT: A 325 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (tpp) REVERT: A 337 ARG cc_start: 0.7432 (mtp-110) cc_final: 0.7189 (ttm110) REVERT: A 556 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: A 614 HIS cc_start: 0.9236 (OUTLIER) cc_final: 0.8872 (p-80) REVERT: B 148 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7128 (ptmt) REVERT: B 325 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7843 (tpp) REVERT: B 337 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7191 (ttm110) REVERT: B 556 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: B 614 HIS cc_start: 0.9237 (OUTLIER) cc_final: 0.8870 (p-80) outliers start: 16 outliers final: 8 residues processed: 60 average time/residue: 1.2613 time to fit residues: 81.9564 Evaluate side-chains 70 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 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: 0.8980 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.135620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101160 restraints weight = 10414.914| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.78 r_work: 0.2852 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1357 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= 0.154 Angle : 0.490 6.423 12798 Z= 0.252 Chirality : 0.041 0.152 1426 Planarity : 0.004 0.031 1446 Dihedral : 11.280 57.861 2080 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.86 % Allowed : 12.14 % 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 (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: 2.31 (0.26), residues: 1038 helix: 2.98 (0.21), residues: 498 sheet: 0.95 (0.41), residues: 130 loop : -0.11 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.005 0.001 HIS B 614 PHE 0.014 0.001 PHE B 322 TYR 0.014 0.001 TYR A 570 ARG 0.002 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 6) link_NAG-ASN : angle 1.64291 ( 18) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.30948 ( 12) hydrogen bonds : bond 0.04729 ( 478) hydrogen bonds : angle 3.86077 ( 1356) SS BOND : bond 0.00157 ( 6) SS BOND : angle 0.99277 ( 12) covalent geometry : bond 0.00377 ( 9562) covalent geometry : angle 0.48445 (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 68 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.948 Fit side-chains REVERT: A 148 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7143 (ptmt) REVERT: A 325 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: A 556 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: A 614 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8789 (p-80) REVERT: A 630 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 148 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7161 (ptmt) REVERT: B 325 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (tpp) REVERT: B 556 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 614 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8785 (p-80) REVERT: B 630 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8088 (t0) outliers start: 17 outliers final: 7 residues processed: 59 average time/residue: 1.2905 time to fit residues: 82.7285 Evaluate side-chains 66 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 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 79 MET Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 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 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.133733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099110 restraints weight = 10320.608| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.75 r_work: 0.2867 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9578 Z= 0.116 Angle : 0.459 6.442 12798 Z= 0.236 Chirality : 0.039 0.149 1426 Planarity : 0.003 0.033 1446 Dihedral : 10.407 59.698 2080 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.54 % Favored : 98.36 % Rotamer: Outliers : 1.86 % Allowed : 12.80 % Favored : 85.34 % 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: 2.51 (0.26), residues: 1038 helix: 3.20 (0.21), residues: 498 sheet: 1.00 (0.41), residues: 130 loop : -0.08 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.003 0.001 HIS B 614 PHE 0.013 0.001 PHE A 322 TYR 0.012 0.001 TYR A 570 ARG 0.001 0.000 ARG B 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 6) link_NAG-ASN : angle 1.55184 ( 18) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 1.26214 ( 12) hydrogen bonds : bond 0.04134 ( 478) hydrogen bonds : angle 3.72149 ( 1356) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.96566 ( 12) covalent geometry : bond 0.00274 ( 9562) covalent geometry : angle 0.45307 (12756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6367.61 seconds wall clock time: 111 minutes 48.31 seconds (6708.31 seconds total)