Starting phenix.real_space_refine on Thu Feb 13 19:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkv_36376/02_2025/8jkv_36376.cif" } resolution = 2.87 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= 0.043 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6396 2.51 5 N 1350 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9266 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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 396 Unusual residues: {'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 35} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 380 Unusual residues: {'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 14, 'R16': 1} Classifications: {'undetermined': 33} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.88, per 1000 atoms: 0.74 Number of scatterers: 9266 At special positions: 0 Unit cell: (110.39, 88.81, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1482 8.00 N 1350 7.00 C 6396 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 801 " - " ASN A 94 " " NAG B 802 " - " 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: 2.80 Conformation dependent library (CDL) restraints added in 903.4 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: 38 helices and 4 sheets defined 56.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 288 removed outlier: 3.727A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 6.715A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 296 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 331 removed outlier: 3.514A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 437 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.644A pdb=" N PHE A 456 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 477 through 480 removed outlier: 3.591A pdb=" N LEU A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 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 removed outlier: 3.537A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 removed outlier: 3.521A pdb=" N HIS A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 Processing helix chain 'B' and resid 268 through 288 removed outlier: 3.728A pdb=" N ASP B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 288 " --> pdb=" O PHE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 6.715A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.514A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 437 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.645A pdb=" N PHE B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 458 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 477 through 480 removed outlier: 3.591A pdb=" N LEU B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 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 removed outlier: 3.536A pdb=" N ILE B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 removed outlier: 3.522A pdb=" N HIS B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.989A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 178 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.825A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 8.989A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 178 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.824A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1380 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: 2.79 Time building geometry restraints manager: 2.74 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: 2529 1.34 - 1.46: 1871 1.46 - 1.58: 4992 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9442 Sorted by residual: bond pdb=" CB PRO A 311 " pdb=" CG PRO A 311 " ideal model delta sigma weight residual 1.492 1.413 0.079 5.00e-02 4.00e+02 2.53e+00 bond pdb=" CB PRO B 311 " pdb=" CG PRO B 311 " ideal model delta sigma weight residual 1.492 1.413 0.079 5.00e-02 4.00e+02 2.50e+00 bond pdb=" C1 NAG B 802 " pdb=" O5 NAG B 802 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.14e+00 ... (remaining 9437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12033 1.42 - 2.83: 446 2.83 - 4.25: 79 4.25 - 5.66: 24 5.66 - 7.08: 4 Bond angle restraints: 12586 Sorted by residual: angle pdb=" C GLY B 613 " pdb=" N HIS B 614 " pdb=" CA HIS B 614 " ideal model delta sigma weight residual 121.14 116.42 4.72 1.75e+00 3.27e-01 7.27e+00 angle pdb=" C GLY A 613 " pdb=" N HIS A 614 " pdb=" CA HIS A 614 " ideal model delta sigma weight residual 121.14 116.44 4.70 1.75e+00 3.27e-01 7.21e+00 angle pdb=" C LYS A 551 " pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 121.97 126.62 -4.65 1.80e+00 3.09e-01 6.66e+00 angle pdb=" C LYS B 551 " pdb=" N VAL B 552 " pdb=" CA VAL B 552 " ideal model delta sigma weight residual 121.97 126.58 -4.61 1.80e+00 3.09e-01 6.55e+00 angle pdb=" CA TYR A 570 " pdb=" CB TYR A 570 " pdb=" CG TYR A 570 " ideal model delta sigma weight residual 113.90 118.35 -4.45 1.80e+00 3.09e-01 6.12e+00 ... (remaining 12581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 5163 19.02 - 38.05: 519 38.05 - 57.07: 112 57.07 - 76.09: 20 76.09 - 95.11: 10 Dihedral angle restraints: 5824 sinusoidal: 2782 harmonic: 3042 Sorted by residual: 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 -178.52 -88.48 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual 93.00 -178.59 -88.41 1 1.00e+01 1.00e-02 9.33e+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 93.00 170.43 -77.43 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 5821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 627 0.028 - 0.055: 476 0.055 - 0.083: 210 0.083 - 0.111: 75 0.111 - 0.139: 28 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA ILE A 559 " pdb=" N ILE A 559 " pdb=" C ILE A 559 " pdb=" CB ILE A 559 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE B 559 " pdb=" N ILE B 559 " pdb=" C ILE B 559 " pdb=" CB ILE B 559 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA PRO B 622 " pdb=" N PRO B 622 " pdb=" C PRO B 622 " pdb=" CB PRO B 622 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1413 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 274 " -0.022 2.00e-02 2.50e+03 1.91e-02 6.39e+00 pdb=" CG PHE B 274 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 274 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 274 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 274 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 274 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 274 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 274 " 0.022 2.00e-02 2.50e+03 1.90e-02 6.31e+00 pdb=" CG PHE A 274 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 274 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 274 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 274 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 274 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 459 " 0.021 2.00e-02 2.50e+03 1.75e-02 6.11e+00 pdb=" CG TYR A 459 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 459 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 459 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 459 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 459 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 459 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 459 " 0.001 2.00e-02 2.50e+03 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1829 2.78 - 3.31: 7883 3.31 - 3.84: 14333 3.84 - 4.37: 18409 4.37 - 4.90: 31863 Nonbonded interactions: 74317 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" OG1 THR A 573 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 546 " pdb=" OG1 THR B 573 " model vdw 2.253 3.040 nonbonded pdb=" O LYS B 296 " pdb=" OG1 THR B 304 " model vdw 2.287 3.040 nonbonded pdb=" O LYS A 296 " pdb=" OG1 THR A 304 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 447 " pdb=" OD2 ASP B 455 " model vdw 2.323 3.040 ... (remaining 74312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 663 or resid 804 or (resid 806 and (name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C1 \ 0 or name C11 or name C12 or name C13 or name C14)) or resid 807 through 809 or \ resid 816 or resid 821 through 833)) selection = (chain 'B' and (resid 75 through 663 or resid 804 or resid 806 through 809 or re \ sid 816 or resid 821 through 833)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:20.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 9442 Z= 0.424 Angle : 0.654 7.077 12586 Z= 0.329 Chirality : 0.046 0.139 1416 Planarity : 0.005 0.039 1438 Dihedral : 15.121 95.113 3858 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.73 (0.25), residues: 1038 helix: 1.38 (0.21), residues: 502 sheet: 1.28 (0.47), residues: 128 loop : -0.92 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 566 HIS 0.011 0.002 HIS A 614 PHE 0.044 0.002 PHE B 274 TYR 0.043 0.003 TYR A 459 ARG 0.002 0.000 ARG B 337 *********************** 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 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.984 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.7737 time to fit residues: 65.8134 Evaluate side-chains 68 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131562 restraints weight = 9261.800| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.74 r_work: 0.3309 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9442 Z= 0.215 Angle : 0.537 6.609 12586 Z= 0.275 Chirality : 0.041 0.138 1416 Planarity : 0.004 0.040 1438 Dihedral : 11.797 59.735 1966 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.88 % Allowed : 4.49 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1038 helix: 2.46 (0.22), residues: 504 sheet: 1.20 (0.45), residues: 128 loop : -0.67 (0.30), residues: 406 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 0.022 0.001 PHE B 274 TYR 0.023 0.002 TYR B 459 ARG 0.003 0.000 ARG B 379 *********************** 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 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.884 Fit side-chains REVERT: A 618 GLU cc_start: 0.8237 (tt0) cc_final: 0.7478 (pt0) REVERT: B 618 GLU cc_start: 0.8264 (tt0) cc_final: 0.7484 (pt0) outliers start: 8 outliers final: 0 residues processed: 74 average time/residue: 0.8104 time to fit residues: 67.1444 Evaluate side-chains 70 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128812 restraints weight = 9407.378| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.84 r_work: 0.3286 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9442 Z= 0.300 Angle : 0.558 6.340 12586 Z= 0.283 Chirality : 0.042 0.146 1416 Planarity : 0.004 0.039 1438 Dihedral : 11.506 59.819 1966 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.09 % Allowed : 6.89 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1038 helix: 2.28 (0.21), residues: 520 sheet: 0.95 (0.45), residues: 116 loop : -0.70 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 647 HIS 0.004 0.001 HIS B 614 PHE 0.020 0.002 PHE B 274 TYR 0.022 0.002 TYR B 570 ARG 0.002 0.000 ARG A 379 *********************** 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 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.939 Fit side-chains REVERT: A 614 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.7684 (p-80) REVERT: B 614 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.7702 (p-80) REVERT: B 618 GLU cc_start: 0.8178 (tt0) cc_final: 0.7301 (pt0) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.7521 time to fit residues: 61.0401 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 113 VAL 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 81 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129994 restraints weight = 9318.948| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.66 r_work: 0.3308 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9442 Z= 0.272 Angle : 0.533 6.397 12586 Z= 0.271 Chirality : 0.042 0.142 1416 Planarity : 0.004 0.039 1438 Dihedral : 11.163 59.673 1966 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.75 % Allowed : 7.11 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1038 helix: 2.42 (0.21), residues: 520 sheet: 0.86 (0.44), residues: 116 loop : -0.62 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.003 0.001 HIS B 614 PHE 0.017 0.001 PHE A 315 TYR 0.020 0.002 TYR B 570 ARG 0.002 0.000 ARG B 379 *********************** 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 86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.971 Fit side-chains REVERT: A 614 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.7760 (p-80) REVERT: B 614 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.7765 (p-80) outliers start: 16 outliers final: 7 residues processed: 76 average time/residue: 0.6985 time to fit residues: 60.6015 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 0.0980 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.169475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133430 restraints weight = 9234.944| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.65 r_work: 0.3359 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9442 Z= 0.144 Angle : 0.454 6.477 12586 Z= 0.234 Chirality : 0.039 0.129 1416 Planarity : 0.004 0.043 1438 Dihedral : 10.100 58.120 1966 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.77 % Allowed : 7.88 % Favored : 91.36 % 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: 2.23 (0.25), residues: 1038 helix: 3.07 (0.21), residues: 504 sheet: 0.91 (0.44), residues: 116 loop : -0.40 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.002 0.001 HIS A 614 PHE 0.013 0.001 PHE A 315 TYR 0.017 0.001 TYR A 570 ARG 0.002 0.000 ARG B 379 *********************** 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 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.918 Fit side-chains REVERT: A 618 GLU cc_start: 0.8272 (tt0) cc_final: 0.7454 (pt0) REVERT: B 618 GLU cc_start: 0.8239 (tt0) cc_final: 0.7452 (pt0) outliers start: 7 outliers final: 1 residues processed: 73 average time/residue: 0.7521 time to fit residues: 62.0927 Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.165022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128458 restraints weight = 9284.908| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.64 r_work: 0.3287 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9442 Z= 0.390 Angle : 0.596 6.462 12586 Z= 0.300 Chirality : 0.045 0.149 1416 Planarity : 0.004 0.046 1438 Dihedral : 10.697 59.652 1966 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.31 % Allowed : 8.10 % Favored : 90.59 % 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: 1.53 (0.25), residues: 1038 helix: 2.31 (0.21), residues: 520 sheet: 0.76 (0.44), residues: 116 loop : -0.66 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 647 HIS 0.003 0.001 HIS A 614 PHE 0.019 0.002 PHE A 315 TYR 0.021 0.002 TYR A 570 ARG 0.002 0.000 ARG A 372 *********************** 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 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.922 Fit side-chains REVERT: A 614 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.7787 (p-80) REVERT: B 614 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.7789 (p-80) outliers start: 12 outliers final: 2 residues processed: 73 average time/residue: 0.7238 time to fit residues: 60.1602 Evaluate side-chains 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 113 VAL 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 40 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131369 restraints weight = 9317.203| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.63 r_work: 0.3321 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9442 Z= 0.200 Angle : 0.485 6.456 12586 Z= 0.249 Chirality : 0.040 0.132 1416 Planarity : 0.004 0.039 1438 Dihedral : 10.046 58.233 1966 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.09 % Allowed : 8.64 % Favored : 90.26 % 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: 1.89 (0.25), residues: 1038 helix: 2.69 (0.21), residues: 520 sheet: 0.82 (0.44), residues: 116 loop : -0.58 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.003 0.001 HIS A 614 PHE 0.015 0.001 PHE B 315 TYR 0.018 0.001 TYR B 570 ARG 0.002 0.000 ARG B 379 *********************** 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 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.913 Fit side-chains REVERT: A 614 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.7738 (p-80) REVERT: B 614 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.7724 (p-80) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.7175 time to fit residues: 59.3855 Evaluate side-chains 73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 515 VAL 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 65 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129396 restraints weight = 9433.053| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.63 r_work: 0.3263 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.006 0.074 9442 Z= 0.375 Angle : 0.584 6.468 12586 Z= 0.295 Chirality : 0.044 0.147 1416 Planarity : 0.004 0.039 1438 Dihedral : 10.526 59.745 1966 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.42 % Allowed : 9.08 % Favored : 89.50 % 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: 1.52 (0.25), residues: 1038 helix: 2.35 (0.21), residues: 520 sheet: 0.70 (0.44), residues: 116 loop : -0.73 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.004 0.001 HIS B 614 PHE 0.017 0.002 PHE B 315 TYR 0.021 0.002 TYR B 570 ARG 0.002 0.000 ARG B 379 *********************** 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 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.917 Fit side-chains REVERT: A 614 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.7809 (p-80) REVERT: B 614 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.7794 (p-80) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.7678 time to fit residues: 65.7526 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 515 VAL 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 58 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.166971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130765 restraints weight = 9248.323| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.62 r_work: 0.3324 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9442 Z= 0.228 Angle : 0.506 6.434 12586 Z= 0.258 Chirality : 0.041 0.137 1416 Planarity : 0.004 0.039 1438 Dihedral : 10.081 58.511 1966 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.31 % Allowed : 9.41 % Favored : 89.28 % 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: 1.77 (0.25), residues: 1038 helix: 2.62 (0.21), residues: 520 sheet: 0.72 (0.44), residues: 116 loop : -0.67 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.003 0.001 HIS A 614 PHE 0.016 0.001 PHE B 315 TYR 0.020 0.001 TYR B 570 ARG 0.002 0.000 ARG B 379 *********************** 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 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.990 Fit side-chains REVERT: A 614 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.7746 (p-80) REVERT: B 614 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.7729 (p-80) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 0.7360 time to fit residues: 65.2139 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 515 VAL 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 100 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.168905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131720 restraints weight = 9412.173| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.64 r_work: 0.3308 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9442 Z= 0.169 Angle : 0.468 6.432 12586 Z= 0.240 Chirality : 0.039 0.127 1416 Planarity : 0.004 0.043 1438 Dihedral : 9.412 55.973 1966 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.09 % Allowed : 9.63 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.26), residues: 1038 helix: 2.88 (0.21), residues: 518 sheet: 0.81 (0.45), residues: 116 loop : -0.57 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.002 0.001 HIS B 614 PHE 0.015 0.001 PHE B 315 TYR 0.017 0.001 TYR B 570 ARG 0.001 0.000 ARG A 269 ********************** 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 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.794 Fit side-chains REVERT: A 614 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.7606 (p-80) REVERT: B 614 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.7631 (p-80) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.7336 time to fit residues: 61.4385 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 515 VAL 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 38 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132495 restraints weight = 9274.071| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.62 r_work: 0.3346 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9442 Z= 0.167 Angle : 0.465 6.414 12586 Z= 0.238 Chirality : 0.039 0.130 1416 Planarity : 0.004 0.048 1438 Dihedral : 9.082 57.448 1966 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.88 % Allowed : 9.85 % Favored : 89.28 % 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: 2.10 (0.25), residues: 1038 helix: 2.92 (0.21), residues: 518 sheet: 0.86 (0.45), residues: 116 loop : -0.54 (0.30), residues: 404 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 0.014 0.001 PHE B 315 TYR 0.018 0.001 TYR B 570 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5761.06 seconds wall clock time: 102 minutes 47.09 seconds (6167.09 seconds total)