Starting phenix.real_space_refine on Wed Apr 30 10:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl3_36387/04_2025/8jl3_36387.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 6470 2.51 5 N 1366 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9408 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: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 459 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 2, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 37} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ACO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 459 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 2, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 37} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ACO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.26, per 1000 atoms: 0.77 Number of scatterers: 9408 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 1526 8.00 N 1366 7.00 C 6470 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 803 " - " ASN A 94 " " NAG B 804 " - " 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: 2.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.511A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 6.689A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 3.599A 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 438 removed outlier: 3.564A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 503 through 524 Processing helix chain 'A' and resid 527 through 551 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: 3.510A pdb=" N ASP B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 6.689A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.600A 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 438 removed outlier: 3.564A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 503 through 524 Processing helix chain 'B' and resid 527 through 551 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: 9.048A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.890A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP A 143 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 149 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 9.047A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.890A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 143 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU B 149 " --> pdb=" O ASP B 143 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1386 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: 2.76 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2553 1.34 - 1.46: 2203 1.46 - 1.58: 4776 1.58 - 1.70: 2 1.70 - 1.82: 52 Bond restraints: 9586 Sorted by residual: bond pdb=" C1 NAG A 803 " pdb=" O5 NAG A 803 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG B 804 " pdb=" O5 NAG B 804 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CB PRO A 311 " pdb=" CG PRO A 311 " ideal model delta sigma weight residual 1.492 1.432 0.060 5.00e-02 4.00e+02 1.46e+00 ... (remaining 9581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12557 1.94 - 3.88: 199 3.88 - 5.82: 30 5.82 - 7.76: 2 7.76 - 9.70: 2 Bond angle restraints: 12790 Sorted by residual: angle pdb=" CA LEU A 348 " pdb=" CB LEU A 348 " pdb=" CG LEU A 348 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.69e+00 angle pdb=" CA LEU B 348 " pdb=" CB LEU B 348 " pdb=" CG LEU B 348 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" CA CYS B 104 " pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " ideal model delta sigma weight residual 114.40 119.06 -4.66 2.30e+00 1.89e-01 4.10e+00 angle pdb=" CA CYS A 104 " pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " ideal model delta sigma weight residual 114.40 119.04 -4.64 2.30e+00 1.89e-01 4.07e+00 angle pdb=" N SER A 607 " pdb=" CA SER A 607 " pdb=" C SER A 607 " ideal model delta sigma weight residual 111.07 113.18 -2.11 1.07e+00 8.73e-01 3.91e+00 ... (remaining 12785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 5129 15.80 - 31.60: 593 31.60 - 47.40: 182 47.40 - 63.20: 70 63.20 - 79.00: 8 Dihedral angle restraints: 5982 sinusoidal: 2940 harmonic: 3042 Sorted by residual: 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 93.00 166.74 -73.74 1 1.00e+01 1.00e-02 6.91e+01 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 93.00 166.72 -73.72 1 1.00e+01 1.00e-02 6.91e+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 93.00 141.67 -48.67 1 1.00e+01 1.00e-02 3.26e+01 ... (remaining 5979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 795 0.034 - 0.067: 445 0.067 - 0.101: 157 0.101 - 0.135: 36 0.135 - 0.168: 3 Chirality restraints: 1436 Sorted by residual: 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 -2.23 -0.17 2.00e-01 2.50e+01 7.07e-01 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 -2.24 -0.16 2.00e-01 2.50e+01 6.67e-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 2.58 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1433 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 115 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO B 116 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 115 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A 116 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 566 " -0.002 2.00e-02 2.50e+03 1.07e-02 2.87e+00 pdb=" CG TRP A 566 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 566 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 566 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 566 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 566 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 566 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 566 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 566 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 566 " 0.000 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1440 2.76 - 3.30: 8015 3.30 - 3.83: 15144 3.83 - 4.37: 19548 4.37 - 4.90: 32576 Nonbonded interactions: 76723 Sorted by model distance: nonbonded pdb=" OH TYR A 447 " pdb=" OD2 ASP A 455 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 447 " pdb=" OD2 ASP B 455 " model vdw 2.232 3.040 nonbonded pdb=" O LYS A 296 " pdb=" OG1 THR A 304 " model vdw 2.302 3.040 nonbonded pdb=" O LYS B 296 " pdb=" OG1 THR B 304 " model vdw 2.302 3.040 nonbonded pdb=" ND2 ASN B 506 " pdb=" O TRP B 566 " model vdw 2.355 3.120 ... (remaining 76718 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 663 or resid 806 through 807 or (resid 809 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 810 thr \ ough 812 or resid 819 or resid 824 through 826 or (resid 828 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 829 through 830 or res \ id 832 or resid 835 through 836)) selection = (chain 'B' and (resid 75 through 663 or resid 806 through 807 or resid 809 throu \ gh 812 or resid 819 or resid 824 through 826 or resid 828 through 830 or resid 8 \ 32 or resid 835 through 836)) } 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: 159.270 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.920 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:18.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9602 Z= 0.233 Angle : 0.640 9.704 12832 Z= 0.310 Chirality : 0.045 0.168 1436 Planarity : 0.005 0.078 1446 Dihedral : 15.268 78.999 4016 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 1.16 (0.25), residues: 1038 helix: 1.62 (0.22), residues: 508 sheet: 1.00 (0.40), residues: 114 loop : -0.31 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 566 HIS 0.010 0.001 HIS A 614 PHE 0.016 0.002 PHE B 322 TYR 0.013 0.002 TYR B 496 ARG 0.003 0.001 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 6) link_NAG-ASN : angle 2.48706 ( 18) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.39954 ( 12) hydrogen bonds : bond 0.15500 ( 492) hydrogen bonds : angle 5.73213 ( 1386) SS BOND : bond 0.00223 ( 6) SS BOND : angle 2.16307 ( 12) covalent geometry : bond 0.00574 ( 9586) covalent geometry : angle 0.62968 (12790) *********************** 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 97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.867 Fit side-chains REVERT: A 461 ASN cc_start: 0.8740 (m110) cc_final: 0.8438 (m-40) REVERT: B 461 ASN cc_start: 0.8709 (m110) cc_final: 0.8440 (m-40) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 1.4618 time to fit residues: 155.8297 Evaluate side-chains 71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 286 ASN A 461 ASN A 491 HIS B 114 ASN B 286 ASN B 461 ASN B 491 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102272 restraints weight = 8710.188| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.19 r_work: 0.2950 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9602 Z= 0.119 Angle : 0.519 6.589 12832 Z= 0.264 Chirality : 0.040 0.136 1436 Planarity : 0.004 0.057 1446 Dihedral : 12.937 59.821 2124 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.42 % Allowed : 6.56 % Favored : 92.01 % 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: 1.91 (0.25), residues: 1038 helix: 2.61 (0.22), residues: 500 sheet: 1.38 (0.39), residues: 112 loop : -0.42 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS A 491 PHE 0.017 0.001 PHE B 322 TYR 0.010 0.001 TYR B 155 ARG 0.002 0.000 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 6) link_NAG-ASN : angle 1.97278 ( 18) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.36221 ( 12) hydrogen bonds : bond 0.04787 ( 492) hydrogen bonds : angle 4.34291 ( 1386) SS BOND : bond 0.00812 ( 6) SS BOND : angle 0.96722 ( 12) covalent geometry : bond 0.00261 ( 9586) covalent geometry : angle 0.51229 (12790) *********************** 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 88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.901 Fit side-chains REVERT: A 153 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7934 (mp) REVERT: A 461 ASN cc_start: 0.8690 (m-40) cc_final: 0.8403 (m-40) REVERT: A 478 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 630 ASN cc_start: 0.8463 (m-40) cc_final: 0.8215 (t0) REVERT: B 153 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7952 (mp) REVERT: B 461 ASN cc_start: 0.8671 (m-40) cc_final: 0.8432 (m-40) REVERT: B 478 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: B 630 ASN cc_start: 0.8464 (m-40) cc_final: 0.8202 (t0) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 1.0192 time to fit residues: 93.7344 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 478 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100549 restraints weight = 8817.342| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.21 r_work: 0.2922 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9602 Z= 0.155 Angle : 0.549 6.553 12832 Z= 0.277 Chirality : 0.042 0.140 1436 Planarity : 0.004 0.050 1446 Dihedral : 13.083 66.689 2124 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.20 % Allowed : 9.08 % Favored : 89.72 % 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 (0.25), residues: 1038 helix: 2.70 (0.21), residues: 500 sheet: 1.38 (0.40), residues: 126 loop : -0.20 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.003 0.001 HIS A 636 PHE 0.018 0.002 PHE B 322 TYR 0.011 0.002 TYR A 496 ARG 0.003 0.000 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 2.05915 ( 18) link_BETA1-4 : bond 0.00124 ( 4) link_BETA1-4 : angle 1.45881 ( 12) hydrogen bonds : bond 0.05302 ( 492) hydrogen bonds : angle 4.26788 ( 1386) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.96290 ( 12) covalent geometry : bond 0.00367 ( 9586) covalent geometry : angle 0.54174 (12790) *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.957 Fit side-chains REVERT: A 153 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 369 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (p0) REVERT: A 461 ASN cc_start: 0.8747 (m-40) cc_final: 0.8418 (m-40) REVERT: A 630 ASN cc_start: 0.8506 (m-40) cc_final: 0.8247 (t0) REVERT: B 153 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 369 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8025 (p0) REVERT: B 461 ASN cc_start: 0.8726 (m-40) cc_final: 0.8397 (m-40) REVERT: B 630 ASN cc_start: 0.8493 (m-40) cc_final: 0.8230 (t0) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 1.2428 time to fit residues: 112.8845 Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN 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 = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.100677 restraints weight = 8741.071| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.20 r_work: 0.2922 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9602 Z= 0.139 Angle : 0.518 6.588 12832 Z= 0.263 Chirality : 0.041 0.137 1436 Planarity : 0.004 0.045 1446 Dihedral : 12.785 68.491 2124 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.19 % Allowed : 9.30 % 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: 2.26 (0.25), residues: 1038 helix: 2.82 (0.21), residues: 500 sheet: 1.48 (0.40), residues: 126 loop : -0.20 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.017 0.001 PHE A 322 TYR 0.010 0.001 TYR B 294 ARG 0.002 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 1.95784 ( 18) link_BETA1-4 : bond 0.00158 ( 4) link_BETA1-4 : angle 1.47664 ( 12) hydrogen bonds : bond 0.04857 ( 492) hydrogen bonds : angle 4.16072 ( 1386) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.89226 ( 12) covalent geometry : bond 0.00324 ( 9586) covalent geometry : angle 0.51081 (12790) *********************** 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 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.962 Fit side-chains REVERT: A 153 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 369 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8027 (p0) REVERT: A 461 ASN cc_start: 0.8739 (m-40) cc_final: 0.8537 (m-40) REVERT: A 630 ASN cc_start: 0.8514 (m-40) cc_final: 0.8240 (t0) REVERT: B 153 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 369 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8052 (p0) REVERT: B 630 ASN cc_start: 0.8507 (m-40) cc_final: 0.8231 (t0) outliers start: 20 outliers final: 10 residues processed: 89 average time/residue: 1.0784 time to fit residues: 104.1590 Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099917 restraints weight = 8757.321| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.21 r_work: 0.2915 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9602 Z= 0.169 Angle : 0.558 6.630 12832 Z= 0.280 Chirality : 0.042 0.140 1436 Planarity : 0.004 0.044 1446 Dihedral : 13.016 69.555 2124 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.41 % Allowed : 9.41 % Favored : 88.18 % 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: 2.22 (0.25), residues: 1038 helix: 2.74 (0.21), residues: 502 sheet: 1.63 (0.41), residues: 126 loop : -0.22 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.003 0.001 HIS A 636 PHE 0.019 0.002 PHE A 322 TYR 0.012 0.002 TYR B 294 ARG 0.003 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 2.15398 ( 18) link_BETA1-4 : bond 0.00137 ( 4) link_BETA1-4 : angle 1.47028 ( 12) hydrogen bonds : bond 0.05347 ( 492) hydrogen bonds : angle 4.24562 ( 1386) SS BOND : bond 0.00091 ( 6) SS BOND : angle 1.05470 ( 12) covalent geometry : bond 0.00407 ( 9586) covalent geometry : angle 0.55071 (12790) *********************** 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 97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.036 Fit side-chains REVERT: A 170 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6130 (mt) REVERT: A 369 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 461 ASN cc_start: 0.8724 (m-40) cc_final: 0.8521 (m-40) REVERT: A 630 ASN cc_start: 0.8526 (m-40) cc_final: 0.8238 (t0) REVERT: B 170 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6136 (mt) REVERT: B 630 ASN cc_start: 0.8527 (m-40) cc_final: 0.8266 (t0) outliers start: 22 outliers final: 14 residues processed: 93 average time/residue: 1.0993 time to fit residues: 111.8938 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099451 restraints weight = 8727.779| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.20 r_work: 0.2913 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9602 Z= 0.194 Angle : 0.589 6.652 12832 Z= 0.294 Chirality : 0.044 0.141 1436 Planarity : 0.005 0.042 1446 Dihedral : 13.226 68.665 2124 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.30 % Allowed : 9.63 % Favored : 88.07 % 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: 2.14 (0.25), residues: 1038 helix: 2.62 (0.21), residues: 504 sheet: 1.71 (0.41), residues: 126 loop : -0.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.020 0.002 PHE A 322 TYR 0.013 0.002 TYR B 496 ARG 0.004 0.001 ARG A 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.30307 ( 18) link_BETA1-4 : bond 0.00147 ( 4) link_BETA1-4 : angle 1.51018 ( 12) hydrogen bonds : bond 0.05656 ( 492) hydrogen bonds : angle 4.31695 ( 1386) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.15201 ( 12) covalent geometry : bond 0.00471 ( 9586) covalent geometry : angle 0.58047 (12790) *********************** 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 97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.949 Fit side-chains REVERT: A 110 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: A 170 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6123 (mt) REVERT: A 369 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8097 (p0) REVERT: A 630 ASN cc_start: 0.8616 (m-40) cc_final: 0.8352 (t0) REVERT: B 110 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 170 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6122 (mt) REVERT: B 630 ASN cc_start: 0.8617 (m-40) cc_final: 0.8359 (t0) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 1.0744 time to fit residues: 109.4619 Evaluate side-chains 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.098414 restraints weight = 8689.085| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.24 r_work: 0.2909 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9602 Z= 0.214 Angle : 0.619 6.662 12832 Z= 0.308 Chirality : 0.045 0.143 1436 Planarity : 0.005 0.041 1446 Dihedral : 13.498 67.995 2124 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.63 % Allowed : 9.19 % Favored : 88.18 % 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 (0.25), residues: 1038 helix: 2.54 (0.21), residues: 504 sheet: 1.68 (0.41), residues: 126 loop : -0.28 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 647 HIS 0.004 0.001 HIS A 614 PHE 0.020 0.002 PHE B 322 TYR 0.014 0.002 TYR A 496 ARG 0.004 0.001 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.43732 ( 18) link_BETA1-4 : bond 0.00141 ( 4) link_BETA1-4 : angle 1.55616 ( 12) hydrogen bonds : bond 0.05913 ( 492) hydrogen bonds : angle 4.40262 ( 1386) SS BOND : bond 0.00636 ( 6) SS BOND : angle 1.22591 ( 12) covalent geometry : bond 0.00525 ( 9586) covalent geometry : angle 0.61049 (12790) *********************** 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 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.185 Fit side-chains REVERT: A 110 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: A 170 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6103 (mt) REVERT: A 369 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (p0) REVERT: A 630 ASN cc_start: 0.8589 (m-40) cc_final: 0.8314 (t0) REVERT: B 110 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: B 170 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6168 (mt) REVERT: B 369 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (p0) REVERT: B 630 ASN cc_start: 0.8579 (m-40) cc_final: 0.8308 (t0) outliers start: 24 outliers final: 17 residues processed: 88 average time/residue: 1.0575 time to fit residues: 102.6881 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 0.2980 chunk 4 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102094 restraints weight = 8681.885| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.24 r_work: 0.2945 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9602 Z= 0.109 Angle : 0.484 6.621 12832 Z= 0.247 Chirality : 0.039 0.137 1436 Planarity : 0.004 0.040 1446 Dihedral : 12.385 67.406 2124 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.08 % Allowed : 10.07 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1038 helix: 2.85 (0.22), residues: 512 sheet: 1.85 (0.42), residues: 126 loop : -0.32 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.002 0.001 HIS B 633 PHE 0.014 0.001 PHE B 322 TYR 0.012 0.001 TYR A 570 ARG 0.002 0.000 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 1.93981 ( 18) link_BETA1-4 : bond 0.00212 ( 4) link_BETA1-4 : angle 1.48873 ( 12) hydrogen bonds : bond 0.04260 ( 492) hydrogen bonds : angle 4.07044 ( 1386) SS BOND : bond 0.00368 ( 6) SS BOND : angle 0.70128 ( 12) covalent geometry : bond 0.00244 ( 9586) covalent geometry : angle 0.47695 (12790) *********************** 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 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.017 Fit side-chains REVERT: A 170 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6108 (mt) REVERT: A 630 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (t0) REVERT: B 170 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6109 (mt) REVERT: B 369 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 630 ASN cc_start: 0.8491 (m-40) cc_final: 0.8232 (t0) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 1.1596 time to fit residues: 118.1011 Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100401 restraints weight = 8559.719| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.23 r_work: 0.2933 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9602 Z= 0.155 Angle : 0.542 6.678 12832 Z= 0.273 Chirality : 0.042 0.138 1436 Planarity : 0.004 0.041 1446 Dihedral : 12.573 68.659 2124 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.19 % Allowed : 10.50 % Favored : 87.31 % 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 (0.25), residues: 1038 helix: 2.72 (0.21), residues: 512 sheet: 1.92 (0.42), residues: 126 loop : -0.29 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.018 0.002 PHE B 322 TYR 0.011 0.002 TYR B 294 ARG 0.002 0.000 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 2.08790 ( 18) link_BETA1-4 : bond 0.00134 ( 4) link_BETA1-4 : angle 1.42216 ( 12) hydrogen bonds : bond 0.05049 ( 492) hydrogen bonds : angle 4.17207 ( 1386) SS BOND : bond 0.00371 ( 6) SS BOND : angle 0.97106 ( 12) covalent geometry : bond 0.00370 ( 9586) covalent geometry : angle 0.53476 (12790) *********************** 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 94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.888 Fit side-chains REVERT: A 110 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: A 170 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6164 (mt) REVERT: A 630 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 110 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: B 170 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6167 (mt) REVERT: B 369 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8089 (p0) REVERT: B 630 ASN cc_start: 0.8521 (m-40) cc_final: 0.8252 (t0) outliers start: 20 outliers final: 11 residues processed: 89 average time/residue: 1.1172 time to fit residues: 108.0953 Evaluate side-chains 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110047 restraints weight = 9590.197| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.35 r_work: 0.3129 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 : 0.008 0.078 9602 Z= 0.331 Angle : 0.748 8.338 12832 Z= 0.367 Chirality : 0.051 0.156 1436 Planarity : 0.006 0.047 1446 Dihedral : 13.900 68.485 2124 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.52 % Allowed : 9.85 % 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: 1.79 (0.24), residues: 1038 helix: 2.11 (0.21), residues: 514 sheet: 1.75 (0.41), residues: 126 loop : -0.21 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 647 HIS 0.005 0.002 HIS B 614 PHE 0.025 0.003 PHE B 322 TYR 0.020 0.003 TYR B 496 ARG 0.007 0.001 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.72651 ( 18) link_BETA1-4 : bond 0.00300 ( 4) link_BETA1-4 : angle 1.57428 ( 12) hydrogen bonds : bond 0.07085 ( 492) hydrogen bonds : angle 4.59084 ( 1386) SS BOND : bond 0.00566 ( 6) SS BOND : angle 1.76548 ( 12) covalent geometry : bond 0.00821 ( 9586) covalent geometry : angle 0.73899 (12790) ********************** 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 93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.038 Fit side-chains REVERT: A 110 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: A 170 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6233 (mt) REVERT: A 630 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8406 (t0) REVERT: B 110 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: B 170 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6253 (mt) REVERT: B 369 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 630 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8407 (t0) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 1.0378 time to fit residues: 100.5497 Evaluate side-chains 93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 416 SER 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 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114191 restraints weight = 9446.217| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.33 r_work: 0.3151 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9602 Z= 0.126 Angle : 0.510 6.582 12832 Z= 0.260 Chirality : 0.040 0.140 1436 Planarity : 0.004 0.040 1446 Dihedral : 12.684 67.832 2124 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.97 % Allowed : 10.50 % 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: 2.29 (0.25), residues: 1038 helix: 2.77 (0.21), residues: 502 sheet: 1.91 (0.42), residues: 126 loop : -0.23 (0.29), 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 636 PHE 0.014 0.001 PHE B 322 TYR 0.012 0.001 TYR A 570 ARG 0.002 0.000 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 6) link_NAG-ASN : angle 2.07527 ( 18) link_BETA1-4 : bond 0.00155 ( 4) link_BETA1-4 : angle 1.52820 ( 12) hydrogen bonds : bond 0.04635 ( 492) hydrogen bonds : angle 4.16644 ( 1386) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.78623 ( 12) covalent geometry : bond 0.00291 ( 9586) covalent geometry : angle 0.50256 (12790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6992.40 seconds wall clock time: 122 minutes 37.12 seconds (7357.12 seconds total)