Starting phenix.real_space_refine on Fri Oct 10 22:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jl3_36387/10_2025/8jl3_36387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jl3_36387/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jl3_36387/10_2025/8jl3_36387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jl3_36387/10_2025/8jl3_36387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jl3_36387/10_2025/8jl3_36387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jl3_36387/10_2025/8jl3_36387.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.63, per 1000 atoms: 0.28 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: 1.28 Conformation dependent library (CDL) restraints added in 346.7 milliseconds Enol-peptide restraints added in 9.3 microseconds 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: 0.42 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: 1.47 Time building geometry restraints manager: 1.50 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: 0.01 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: 6.690 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (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 ARG 0.003 0.001 ARG A 275 TYR 0.013 0.002 TYR B 496 PHE 0.016 0.002 PHE B 322 TRP 0.025 0.002 TRP B 566 HIS 0.010 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9586) covalent geometry : angle 0.62968 (12790) SS BOND : bond 0.00223 ( 6) SS BOND : angle 2.16307 ( 12) hydrogen bonds : bond 0.15500 ( 492) hydrogen bonds : angle 5.73213 ( 1386) link_BETA1-4 : bond 0.00259 ( 4) link_BETA1-4 : angle 1.39954 ( 12) link_NAG-ASN : bond 0.00128 ( 6) link_NAG-ASN : angle 2.48706 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.300 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: 0.5387 time to fit residues: 56.2353 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 358 ASN B 461 ASN B 491 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099912 restraints weight = 8661.964| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.23 r_work: 0.2909 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9602 Z= 0.168 Angle : 0.582 6.635 12832 Z= 0.292 Chirality : 0.043 0.143 1436 Planarity : 0.005 0.059 1446 Dihedral : 13.460 59.953 2124 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.42 % Allowed : 6.78 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.25), residues: 1038 helix: 2.37 (0.21), residues: 500 sheet: 1.32 (0.39), residues: 112 loop : -0.44 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 275 TYR 0.013 0.002 TYR B 496 PHE 0.020 0.002 PHE B 322 TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9586) covalent geometry : angle 0.57388 (12790) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.27077 ( 12) hydrogen bonds : bond 0.05694 ( 492) hydrogen bonds : angle 4.49330 ( 1386) link_BETA1-4 : bond 0.00106 ( 4) link_BETA1-4 : angle 1.44899 ( 12) link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 2.17786 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.331 Fit side-chains REVERT: A 461 ASN cc_start: 0.8712 (m-40) cc_final: 0.8397 (m-40) REVERT: A 478 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: A 630 ASN cc_start: 0.8485 (m-40) cc_final: 0.8221 (t0) REVERT: B 461 ASN cc_start: 0.8720 (m-40) cc_final: 0.8422 (m-40) REVERT: B 478 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: B 630 ASN cc_start: 0.8482 (m-40) cc_final: 0.8212 (t0) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.5776 time to fit residues: 53.4410 Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 614 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 69 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.134486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102422 restraints weight = 8747.800| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.20 r_work: 0.2956 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9602 Z= 0.121 Angle : 0.496 6.586 12832 Z= 0.254 Chirality : 0.040 0.136 1436 Planarity : 0.004 0.049 1446 Dihedral : 12.600 59.690 2124 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.88 % Allowed : 9.30 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1038 helix: 2.84 (0.21), residues: 500 sheet: 1.57 (0.39), residues: 112 loop : -0.39 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.010 0.001 TYR B 570 PHE 0.016 0.001 PHE B 322 TRP 0.012 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9586) covalent geometry : angle 0.48916 (12790) SS BOND : bond 0.00134 ( 6) SS BOND : angle 0.75344 ( 12) hydrogen bonds : bond 0.04617 ( 492) hydrogen bonds : angle 4.13944 ( 1386) link_BETA1-4 : bond 0.00225 ( 4) link_BETA1-4 : angle 1.49884 ( 12) link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 1.86354 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.341 Fit side-chains REVERT: A 369 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8039 (p0) REVERT: A 461 ASN cc_start: 0.8765 (m-40) cc_final: 0.8473 (m-40) REVERT: A 630 ASN cc_start: 0.8526 (m-40) cc_final: 0.8263 (t0) REVERT: B 461 ASN cc_start: 0.8738 (m-40) cc_final: 0.8454 (m-40) REVERT: B 630 ASN cc_start: 0.8501 (m-40) cc_final: 0.8251 (t0) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.5282 time to fit residues: 49.7359 Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 SER 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 74 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.133791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100157 restraints weight = 8695.480| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.26 r_work: 0.2899 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9602 Z= 0.172 Angle : 0.564 6.616 12832 Z= 0.283 Chirality : 0.042 0.139 1436 Planarity : 0.004 0.047 1446 Dihedral : 13.083 67.276 2124 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.30 % Allowed : 8.86 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.25), residues: 1038 helix: 2.71 (0.21), residues: 500 sheet: 1.54 (0.40), residues: 126 loop : -0.24 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.012 0.002 TYR A 496 PHE 0.019 0.002 PHE B 322 TRP 0.013 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9586) covalent geometry : angle 0.55625 (12790) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.99115 ( 12) hydrogen bonds : bond 0.05421 ( 492) hydrogen bonds : angle 4.25301 ( 1386) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 1.47887 ( 12) link_NAG-ASN : bond 0.00210 ( 6) link_NAG-ASN : angle 2.10879 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.304 Fit side-chains REVERT: A 369 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8078 (p0) REVERT: A 630 ASN cc_start: 0.8535 (m-40) cc_final: 0.8273 (t0) REVERT: B 369 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 630 ASN cc_start: 0.8528 (m-40) cc_final: 0.8260 (t0) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 0.5153 time to fit residues: 51.7787 Evaluate side-chains 88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.133729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101313 restraints weight = 8759.590| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.19 r_work: 0.2931 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1224 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= 0.127 Angle : 0.503 6.619 12832 Z= 0.256 Chirality : 0.040 0.136 1436 Planarity : 0.004 0.044 1446 Dihedral : 12.610 69.584 2124 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.97 % Allowed : 9.41 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.25), residues: 1038 helix: 2.90 (0.21), residues: 500 sheet: 1.70 (0.40), residues: 126 loop : -0.20 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.010 0.001 TYR B 570 PHE 0.016 0.001 PHE B 322 TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9586) covalent geometry : angle 0.49627 (12790) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.74787 ( 12) hydrogen bonds : bond 0.04661 ( 492) hydrogen bonds : angle 4.08989 ( 1386) link_BETA1-4 : bond 0.00169 ( 4) link_BETA1-4 : angle 1.46531 ( 12) link_NAG-ASN : bond 0.00229 ( 6) link_NAG-ASN : angle 1.95778 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.361 Fit side-chains REVERT: A 170 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6160 (mt) REVERT: A 369 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8071 (p0) REVERT: A 630 ASN cc_start: 0.8518 (m-40) cc_final: 0.8255 (t0) REVERT: B 170 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6163 (mt) REVERT: B 369 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8003 (p0) REVERT: B 630 ASN cc_start: 0.8505 (m-40) cc_final: 0.8240 (t0) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.5006 time to fit residues: 51.7069 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 : 0.344 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.131501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.098844 restraints weight = 8772.775| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.21 r_work: 0.2887 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.006 0.059 9602 Z= 0.232 Angle : 0.639 6.701 12832 Z= 0.317 Chirality : 0.045 0.146 1436 Planarity : 0.005 0.043 1446 Dihedral : 13.464 69.492 2124 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.30 % Allowed : 10.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.25), residues: 1038 helix: 2.53 (0.21), residues: 504 sheet: 1.70 (0.41), residues: 126 loop : -0.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 275 TYR 0.015 0.002 TYR B 496 PHE 0.022 0.002 PHE A 322 TRP 0.016 0.002 TRP B 647 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9586) covalent geometry : angle 0.63077 (12790) SS BOND : bond 0.00592 ( 6) SS BOND : angle 1.45005 ( 12) hydrogen bonds : bond 0.06122 ( 492) hydrogen bonds : angle 4.41092 ( 1386) link_BETA1-4 : bond 0.00190 ( 4) link_BETA1-4 : angle 1.51976 ( 12) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 2.37883 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.362 Fit side-chains REVERT: A 170 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6069 (mt) REVERT: A 369 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (p0) REVERT: A 630 ASN cc_start: 0.8599 (m-40) cc_final: 0.8292 (t0) REVERT: B 170 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6086 (mt) REVERT: B 369 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 630 ASN cc_start: 0.8598 (m-40) cc_final: 0.8328 (t0) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.4852 time to fit residues: 46.9525 Evaluate side-chains 89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.133051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100515 restraints weight = 8764.976| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.21 r_work: 0.2933 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9602 Z= 0.138 Angle : 0.523 6.637 12832 Z= 0.265 Chirality : 0.041 0.139 1436 Planarity : 0.004 0.040 1446 Dihedral : 12.763 69.651 2124 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.63 % Allowed : 9.52 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.25), residues: 1038 helix: 2.81 (0.21), residues: 500 sheet: 1.82 (0.42), residues: 126 loop : -0.25 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.001 TYR B 570 PHE 0.017 0.001 PHE A 322 TRP 0.012 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9586) covalent geometry : angle 0.51462 (12790) SS BOND : bond 0.00366 ( 6) SS BOND : angle 1.00376 ( 12) hydrogen bonds : bond 0.04861 ( 492) hydrogen bonds : angle 4.18245 ( 1386) link_BETA1-4 : bond 0.00160 ( 4) link_BETA1-4 : angle 1.50439 ( 12) link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 2.10221 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.337 Fit side-chains REVERT: A 170 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6120 (mt) REVERT: A 369 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 630 ASN cc_start: 0.8612 (m-40) cc_final: 0.8337 (t0) REVERT: B 170 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6177 (mt) REVERT: B 369 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (p0) REVERT: B 630 ASN cc_start: 0.8545 (m-40) cc_final: 0.8296 (t0) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.4915 time to fit residues: 49.4443 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 : 0.323 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.130988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098407 restraints weight = 8779.612| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.22 r_work: 0.2862 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9602 Z= 0.261 Angle : 0.668 7.174 12832 Z= 0.330 Chirality : 0.047 0.144 1436 Planarity : 0.005 0.041 1446 Dihedral : 13.654 68.990 2124 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.74 % Allowed : 9.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.25), residues: 1038 helix: 2.43 (0.21), residues: 504 sheet: 1.70 (0.41), residues: 126 loop : -0.29 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 275 TYR 0.016 0.002 TYR B 496 PHE 0.023 0.002 PHE A 322 TRP 0.017 0.002 TRP B 647 HIS 0.007 0.002 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 9586) covalent geometry : angle 0.65934 (12790) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.53774 ( 12) hydrogen bonds : bond 0.06401 ( 492) hydrogen bonds : angle 4.47141 ( 1386) link_BETA1-4 : bond 0.00170 ( 4) link_BETA1-4 : angle 1.55833 ( 12) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.52646 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.391 Fit side-chains REVERT: A 110 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: A 170 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6154 (mt) REVERT: A 369 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8077 (p0) REVERT: A 630 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8276 (t0) REVERT: B 110 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: B 170 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6166 (mt) REVERT: B 369 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8091 (p0) REVERT: B 630 ASN cc_start: 0.8580 (m-40) cc_final: 0.8269 (t0) outliers start: 25 outliers final: 17 residues processed: 91 average time/residue: 0.4975 time to fit residues: 49.0263 Evaluate side-chains 94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.134363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.101196 restraints weight = 8556.991| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.23 r_work: 0.2942 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9602 Z= 0.126 Angle : 0.514 6.627 12832 Z= 0.261 Chirality : 0.040 0.138 1436 Planarity : 0.004 0.041 1446 Dihedral : 12.735 68.940 2124 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.30 % Allowed : 10.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.25), residues: 1038 helix: 2.81 (0.21), residues: 502 sheet: 1.87 (0.42), residues: 126 loop : -0.24 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 275 TYR 0.012 0.001 TYR B 570 PHE 0.015 0.001 PHE B 322 TRP 0.012 0.001 TRP B 647 HIS 0.004 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9586) covalent geometry : angle 0.50539 (12790) SS BOND : bond 0.00298 ( 6) SS BOND : angle 0.93413 ( 12) hydrogen bonds : bond 0.04746 ( 492) hydrogen bonds : angle 4.17195 ( 1386) link_BETA1-4 : bond 0.00156 ( 4) link_BETA1-4 : angle 1.50263 ( 12) link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 2.11501 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.336 Fit side-chains REVERT: A 110 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: A 170 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6163 (mt) REVERT: A 369 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8055 (p0) REVERT: A 630 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8228 (t0) REVERT: B 110 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: B 170 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6186 (mt) REVERT: B 369 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 630 ASN cc_start: 0.8508 (m-40) cc_final: 0.8224 (t0) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.5178 time to fit residues: 51.5072 Evaluate side-chains 94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 23 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.133798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100502 restraints weight = 8589.643| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.23 r_work: 0.2926 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9602 Z= 0.150 Angle : 0.539 6.658 12832 Z= 0.272 Chirality : 0.041 0.139 1436 Planarity : 0.004 0.041 1446 Dihedral : 12.630 69.878 2124 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.19 % Allowed : 11.05 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.25), residues: 1038 helix: 2.68 (0.21), residues: 512 sheet: 1.92 (0.42), residues: 126 loop : -0.30 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.002 TYR B 570 PHE 0.018 0.001 PHE A 322 TRP 0.013 0.001 TRP B 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9586) covalent geometry : angle 0.53166 (12790) SS BOND : bond 0.00322 ( 6) SS BOND : angle 1.05079 ( 12) hydrogen bonds : bond 0.05034 ( 492) hydrogen bonds : angle 4.19174 ( 1386) link_BETA1-4 : bond 0.00147 ( 4) link_BETA1-4 : angle 1.45065 ( 12) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.11390 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.224 Fit side-chains REVERT: A 110 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: A 170 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6158 (mt) REVERT: A 369 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8082 (p0) REVERT: A 630 ASN cc_start: 0.8509 (m-40) cc_final: 0.8218 (t0) REVERT: B 110 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: B 170 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6228 (mt) REVERT: B 369 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 630 ASN cc_start: 0.8511 (m-40) cc_final: 0.8217 (t0) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.5032 time to fit residues: 50.5639 Evaluate side-chains 93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 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 89 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101329 restraints weight = 8588.467| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.20 r_work: 0.2905 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1365 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 6.652 12832 Z= 0.266 Chirality : 0.041 0.136 1436 Planarity : 0.004 0.041 1446 Dihedral : 12.411 70.086 2124 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.52 % Allowed : 10.50 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.25), residues: 1038 helix: 2.71 (0.21), residues: 514 sheet: 1.95 (0.41), residues: 126 loop : -0.29 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.001 TYR B 570 PHE 0.017 0.001 PHE B 322 TRP 0.013 0.001 TRP B 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9586) covalent geometry : angle 0.51872 (12790) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.00655 ( 12) hydrogen bonds : bond 0.04867 ( 492) hydrogen bonds : angle 4.15422 ( 1386) link_BETA1-4 : bond 0.00162 ( 4) link_BETA1-4 : angle 1.43897 ( 12) link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 2.02114 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.19 seconds wall clock time: 54 minutes 46.01 seconds (3286.01 seconds total)