Starting phenix.real_space_refine on Mon May 12 22:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl3_36387/05_2025/8jl3_36387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl3_36387/05_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_36387/05_2025/8jl3_36387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl3_36387/05_2025/8jl3_36387.map" model { file = "/net/cci-nas-00/data/ceres_data/8jl3_36387/05_2025/8jl3_36387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl3_36387/05_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-5687/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: 6.33, per 1000 atoms: 0.67 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: 2.33 Conformation dependent library (CDL) restraints added in 888.2 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.511A 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: 2.36 Time building geometry restraints manager: 2.70 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.440 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- 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 : 0.949 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: 1.1249 time to fit residues: 118.1119 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 : 0.882 ------------------------------------------------------------------------------- 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: 0.5980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3471 r_free = 0.3471 target = 0.133537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101245 restraints weight = 8714.292| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.20 r_work: 0.2950 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9602 Z= 0.129 Angle : 0.530 6.562 12832 Z= 0.268 Chirality : 0.041 0.139 1436 Planarity : 0.004 0.057 1446 Dihedral : 13.029 59.804 2124 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.42 % Allowed : 6.46 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.25), residues: 1038 helix: 2.57 (0.22), residues: 500 sheet: 1.37 (0.39), residues: 112 loop : -0.41 (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 614 PHE 0.018 0.001 PHE B 322 TYR 0.010 0.001 TYR A 496 ARG 0.002 0.000 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 6) link_NAG-ASN : angle 2.01092 ( 18) link_BETA1-4 : bond 0.00161 ( 4) link_BETA1-4 : angle 1.36185 ( 12) hydrogen bonds : bond 0.05007 ( 492) hydrogen bonds : angle 4.36756 ( 1386) SS BOND : bond 0.00292 ( 6) SS BOND : angle 1.03433 ( 12) covalent geometry : bond 0.00291 ( 9586) covalent geometry : angle 0.52260 (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 : 0.912 Fit side-chains REVERT: A 153 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 461 ASN cc_start: 0.8757 (m-40) cc_final: 0.8479 (m-40) REVERT: A 478 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: A 630 ASN cc_start: 0.8514 (m-40) cc_final: 0.8268 (t0) REVERT: B 153 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 461 ASN cc_start: 0.8724 (m-40) cc_final: 0.8485 (m-40) REVERT: B 478 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: B 630 ASN cc_start: 0.8498 (m-40) cc_final: 0.8245 (t0) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 1.0659 time to fit residues: 96.9163 Evaluate side-chains 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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: 0.3980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 83 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103534 restraints weight = 8774.334| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.21 r_work: 0.2970 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.002 0.029 9602 Z= 0.111 Angle : 0.481 6.529 12832 Z= 0.246 Chirality : 0.040 0.135 1436 Planarity : 0.004 0.047 1446 Dihedral : 12.252 59.867 2124 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.99 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: 2.29 (0.25), residues: 1038 helix: 2.99 (0.21), residues: 500 sheet: 1.59 (0.38), residues: 112 loop : -0.33 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.002 0.001 HIS B 633 PHE 0.015 0.001 PHE B 322 TYR 0.009 0.001 TYR B 570 ARG 0.001 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 1.77740 ( 18) link_BETA1-4 : bond 0.00215 ( 4) link_BETA1-4 : angle 1.45613 ( 12) hydrogen bonds : bond 0.04409 ( 492) hydrogen bonds : angle 4.05495 ( 1386) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.73122 ( 12) covalent geometry : bond 0.00248 ( 9586) covalent geometry : angle 0.47458 (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 88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.993 Fit side-chains REVERT: A 153 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 369 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7936 (p0) REVERT: A 461 ASN cc_start: 0.8692 (m-40) cc_final: 0.8393 (m-40) REVERT: A 478 ASP cc_start: 0.8032 (m-30) cc_final: 0.7486 (m-30) REVERT: A 630 ASN cc_start: 0.8490 (m-40) cc_final: 0.8243 (t0) REVERT: B 153 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 369 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8021 (p0) REVERT: B 461 ASN cc_start: 0.8662 (m-40) cc_final: 0.8403 (m-40) REVERT: B 630 ASN cc_start: 0.8482 (m-40) cc_final: 0.8219 (t0) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 1.0538 time to fit residues: 98.3918 Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 393 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 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 117 GLN B 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101887 restraints weight = 8703.369| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.20 r_work: 0.2943 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1144 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 : 0.521 6.574 12832 Z= 0.263 Chirality : 0.041 0.138 1436 Planarity : 0.004 0.046 1446 Dihedral : 12.439 60.000 2124 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.86 % Allowed : 8.97 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.25), residues: 1038 helix: 2.91 (0.21), residues: 500 sheet: 1.52 (0.39), residues: 126 loop : -0.20 (0.29), residues: 412 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 0.018 0.001 PHE B 322 TYR 0.010 0.001 TYR A 294 ARG 0.002 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.95500 ( 18) link_BETA1-4 : bond 0.00168 ( 4) link_BETA1-4 : angle 1.42240 ( 12) hydrogen bonds : bond 0.04887 ( 492) hydrogen bonds : angle 4.12542 ( 1386) SS BOND : bond 0.00086 ( 6) SS BOND : angle 0.89837 ( 12) covalent geometry : bond 0.00326 ( 9586) covalent geometry : angle 0.51363 (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 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.904 Fit side-chains REVERT: A 153 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 369 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8015 (p0) REVERT: A 630 ASN cc_start: 0.8519 (m-40) cc_final: 0.8252 (t0) REVERT: B 153 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 369 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7988 (p0) REVERT: B 630 ASN cc_start: 0.8512 (m-40) cc_final: 0.8242 (t0) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 1.0462 time to fit residues: 98.9191 Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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: 1.9990 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: 0.6980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099507 restraints weight = 8642.890| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.23 r_work: 0.2920 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9602 Z= 0.182 Angle : 0.576 6.624 12832 Z= 0.288 Chirality : 0.043 0.140 1436 Planarity : 0.005 0.044 1446 Dihedral : 12.867 61.136 2124 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.41 % Allowed : 9.08 % 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: 2.18 (0.25), residues: 1038 helix: 2.72 (0.21), residues: 500 sheet: 1.65 (0.41), residues: 126 loop : -0.24 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 647 HIS 0.004 0.001 HIS B 614 PHE 0.020 0.002 PHE B 322 TYR 0.012 0.002 TYR B 496 ARG 0.003 0.001 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 6) link_NAG-ASN : angle 2.19694 ( 18) link_BETA1-4 : bond 0.00130 ( 4) link_BETA1-4 : angle 1.45711 ( 12) hydrogen bonds : bond 0.05515 ( 492) hydrogen bonds : angle 4.27192 ( 1386) SS BOND : bond 0.00102 ( 6) SS BOND : angle 1.14037 ( 12) covalent geometry : bond 0.00441 ( 9586) covalent geometry : angle 0.56772 (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 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.896 Fit side-chains REVERT: A 153 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 170 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6078 (mt) REVERT: A 369 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8030 (p0) REVERT: A 630 ASN cc_start: 0.8591 (m-40) cc_final: 0.8291 (t0) REVERT: B 170 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6091 (mt) REVERT: B 369 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8081 (p0) REVERT: B 630 ASN cc_start: 0.8544 (m-40) cc_final: 0.8273 (t0) outliers start: 22 outliers final: 11 residues processed: 91 average time/residue: 1.0646 time to fit residues: 104.8226 Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU 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 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 369 ASP Chi-restraints excluded: chain B residue 393 LEU 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: 1.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 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: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.099029 restraints weight = 8740.225| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.19 r_work: 0.2907 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9602 Z= 0.216 Angle : 0.619 6.652 12832 Z= 0.308 Chirality : 0.045 0.142 1436 Planarity : 0.005 0.042 1446 Dihedral : 13.271 62.402 2124 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.19 % Allowed : 9.52 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1038 helix: 2.53 (0.21), residues: 504 sheet: 1.69 (0.41), residues: 126 loop : -0.29 (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 B 614 PHE 0.021 0.002 PHE A 322 TYR 0.015 0.002 TYR B 496 ARG 0.004 0.001 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 2.40582 ( 18) link_BETA1-4 : bond 0.00137 ( 4) link_BETA1-4 : angle 1.52485 ( 12) hydrogen bonds : bond 0.05947 ( 492) hydrogen bonds : angle 4.38296 ( 1386) SS BOND : bond 0.00166 ( 6) SS BOND : angle 1.28868 ( 12) covalent geometry : bond 0.00531 ( 9586) covalent geometry : angle 0.60998 (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: 20 poor density : 77 time to evaluate : 0.911 Fit side-chains REVERT: A 110 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: A 153 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 170 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6124 (mt) REVERT: A 369 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8108 (p0) REVERT: A 630 ASN cc_start: 0.8623 (m-40) cc_final: 0.8332 (t0) REVERT: B 170 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6127 (mt) REVERT: B 369 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8116 (p0) REVERT: B 630 ASN cc_start: 0.8625 (m-40) cc_final: 0.8333 (t0) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 1.0021 time to fit residues: 102.7715 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 : 1.026 ------------------------------------------------------------------------------- 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 153 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.133837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100492 restraints weight = 8687.466| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.24 r_work: 0.2933 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9602 Z= 0.141 Angle : 0.526 6.631 12832 Z= 0.266 Chirality : 0.041 0.138 1436 Planarity : 0.004 0.039 1446 Dihedral : 12.602 60.889 2124 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.41 % Allowed : 9.52 % 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: 2.28 (0.25), residues: 1038 helix: 2.82 (0.21), residues: 500 sheet: 1.84 (0.42), residues: 126 loop : -0.27 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.003 0.001 HIS B 614 PHE 0.017 0.001 PHE B 322 TYR 0.011 0.001 TYR B 570 ARG 0.002 0.000 ARG B 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 2.11812 ( 18) link_BETA1-4 : bond 0.00135 ( 4) link_BETA1-4 : angle 1.49841 ( 12) hydrogen bonds : bond 0.04889 ( 492) hydrogen bonds : angle 4.17928 ( 1386) SS BOND : bond 0.00450 ( 6) SS BOND : angle 0.87620 ( 12) covalent geometry : bond 0.00332 ( 9586) covalent geometry : angle 0.51834 (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 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.906 Fit side-chains REVERT: A 110 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: A 153 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 170 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6080 (mt) REVERT: A 369 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8045 (p0) REVERT: A 630 ASN cc_start: 0.8580 (m-40) cc_final: 0.8289 (t0) REVERT: B 170 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6092 (mt) REVERT: B 369 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (p0) REVERT: B 630 ASN cc_start: 0.8572 (m-40) cc_final: 0.8303 (t0) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 1.0081 time to fit residues: 101.0558 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 153 LEU 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 614 HIS 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 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: 0.0270 chunk 4 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.137805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105013 restraints weight = 8663.272| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.23 r_work: 0.2994 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9602 Z= 0.090 Angle : 0.451 6.676 12832 Z= 0.231 Chirality : 0.039 0.136 1436 Planarity : 0.004 0.037 1446 Dihedral : 11.434 60.381 2124 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.53 % Allowed : 10.72 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.25), residues: 1038 helix: 3.08 (0.22), residues: 512 sheet: 1.98 (0.42), residues: 126 loop : -0.34 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 418 HIS 0.001 0.000 HIS B 633 PHE 0.013 0.001 PHE B 601 TYR 0.011 0.001 TYR B 570 ARG 0.002 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 6) link_NAG-ASN : angle 1.68889 ( 18) link_BETA1-4 : bond 0.00247 ( 4) link_BETA1-4 : angle 1.38765 ( 12) hydrogen bonds : bond 0.03655 ( 492) hydrogen bonds : angle 3.90505 ( 1386) SS BOND : bond 0.00374 ( 6) SS BOND : angle 0.47862 ( 12) covalent geometry : bond 0.00188 ( 9586) covalent geometry : angle 0.44450 (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 93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.959 Fit side-chains REVERT: A 153 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 170 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6050 (mt) REVERT: A 630 ASN cc_start: 0.8457 (m-40) cc_final: 0.8232 (t0) REVERT: B 110 GLN cc_start: 0.7752 (mt0) cc_final: 0.7543 (mp10) REVERT: B 170 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6095 (mt) REVERT: B 630 ASN cc_start: 0.8476 (m-40) cc_final: 0.8240 (t0) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.9288 time to fit residues: 92.0278 Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 416 SER Chi-restraints excluded: chain A residue 614 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.133168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100863 restraints weight = 8680.073| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.19 r_work: 0.2918 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9602 Z= 0.164 Angle : 0.550 6.694 12832 Z= 0.276 Chirality : 0.042 0.138 1436 Planarity : 0.004 0.040 1446 Dihedral : 12.225 70.492 2124 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.64 % Allowed : 11.16 % 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: 2.34 (0.25), residues: 1038 helix: 2.78 (0.21), residues: 514 sheet: 2.06 (0.42), residues: 126 loop : -0.31 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.019 0.002 PHE B 322 TYR 0.011 0.002 TYR B 294 ARG 0.003 0.000 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.03052 ( 18) link_BETA1-4 : bond 0.00159 ( 4) link_BETA1-4 : angle 1.36026 ( 12) hydrogen bonds : bond 0.05164 ( 492) hydrogen bonds : angle 4.14747 ( 1386) SS BOND : bond 0.00365 ( 6) SS BOND : angle 1.04072 ( 12) covalent geometry : bond 0.00392 ( 9586) covalent geometry : angle 0.54267 (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 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.898 Fit side-chains REVERT: A 153 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 170 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6159 (mt) REVERT: A 630 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8269 (t0) REVERT: B 110 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: B 170 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6145 (mt) REVERT: B 630 ASN cc_start: 0.8531 (m-40) cc_final: 0.8257 (t0) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 1.0469 time to fit residues: 99.9561 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 170 ILE 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 170 ILE Chi-restraints excluded: chain B residue 285 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110157 restraints weight = 9588.725| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.35 r_work: 0.3119 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 9602 Z= 0.333 Angle : 0.746 8.182 12832 Z= 0.366 Chirality : 0.051 0.158 1436 Planarity : 0.006 0.051 1446 Dihedral : 13.873 70.179 2124 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.41 % Allowed : 10.07 % 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: 1.83 (0.24), residues: 1038 helix: 2.13 (0.21), residues: 514 sheet: 1.90 (0.42), residues: 126 loop : -0.24 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 647 HIS 0.006 0.002 HIS B 614 PHE 0.025 0.003 PHE B 322 TYR 0.020 0.003 TYR A 496 ARG 0.007 0.001 ARG A 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 2.73572 ( 18) link_BETA1-4 : bond 0.00236 ( 4) link_BETA1-4 : angle 1.56150 ( 12) hydrogen bonds : bond 0.07060 ( 492) hydrogen bonds : angle 4.56600 ( 1386) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.75606 ( 12) covalent geometry : bond 0.00829 ( 9586) covalent geometry : angle 0.73638 (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: 22 poor density : 71 time to evaluate : 1.055 Fit side-chains REVERT: A 170 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6212 (mt) REVERT: A 369 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8071 (p0) REVERT: A 630 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 110 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: B 170 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6234 (mt) REVERT: B 369 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 630 ASN cc_start: 0.8651 (m-40) cc_final: 0.8389 (t0) outliers start: 22 outliers final: 14 residues processed: 89 average time/residue: 1.0428 time to fit residues: 101.3491 Evaluate side-chains 91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.0010 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.144674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113994 restraints weight = 9444.170| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.33 r_work: 0.3149 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9602 Z= 0.130 Angle : 0.512 6.613 12832 Z= 0.260 Chirality : 0.040 0.140 1436 Planarity : 0.004 0.040 1446 Dihedral : 12.712 70.839 2124 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.86 % Allowed : 10.83 % 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: 2.29 (0.25), residues: 1038 helix: 2.78 (0.21), residues: 502 sheet: 2.02 (0.42), residues: 126 loop : -0.30 (0.28), 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 0.015 0.001 PHE B 322 TYR 0.012 0.001 TYR B 570 ARG 0.002 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 2.05413 ( 18) link_BETA1-4 : bond 0.00189 ( 4) link_BETA1-4 : angle 1.50913 ( 12) hydrogen bonds : bond 0.04742 ( 492) hydrogen bonds : angle 4.16895 ( 1386) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.81968 ( 12) covalent geometry : bond 0.00304 ( 9586) covalent geometry : angle 0.50383 (12790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6432.98 seconds wall clock time: 112 minutes 5.42 seconds (6725.42 seconds total)