Starting phenix.real_space_refine on Sat Dec 28 22:56:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkv_36376/12_2024/8jkv_36376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkv_36376/12_2024/8jkv_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_36376/12_2024/8jkv_36376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkv_36376/12_2024/8jkv_36376.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkv_36376/12_2024/8jkv_36376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkv_36376/12_2024/8jkv_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.61, per 1000 atoms: 0.71 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: 2.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 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: 0.79 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: 2.65 Time building geometry restraints manager: 2.81 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: 9.300 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.510 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.900 ------------------------------------------------------------------------------- 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 : 1.221 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.7666 time to fit residues: 65.0106 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 : 1.022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.854 Fit side-chains REVERT: A 618 GLU cc_start: 0.7836 (tt0) cc_final: 0.7379 (pt0) REVERT: B 618 GLU cc_start: 0.7859 (tt0) cc_final: 0.7385 (pt0) outliers start: 8 outliers final: 0 residues processed: 74 average time/residue: 0.7851 time to fit residues: 65.1606 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 chunk 75 optimal weight: 1.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0951 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 : 0.539 6.374 12586 Z= 0.274 Chirality : 0.042 0.143 1416 Planarity : 0.004 0.039 1438 Dihedral : 11.429 59.906 1966 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.77 % Allowed : 6.56 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1038 helix: 2.35 (0.21), residues: 520 sheet: 1.02 (0.44), residues: 128 loop : -0.60 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 647 HIS 0.004 0.001 HIS A 614 PHE 0.018 0.002 PHE B 274 TYR 0.021 0.002 TYR B 570 ARG 0.001 0.000 ARG B 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 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.872 Fit side-chains REVERT: A 614 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.7917 (p-80) REVERT: B 618 GLU cc_start: 0.7873 (tt0) cc_final: 0.7394 (pt0) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.7598 time to fit residues: 60.9357 Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9442 Z= 0.214 Angle : 0.498 6.416 12586 Z= 0.255 Chirality : 0.040 0.137 1416 Planarity : 0.004 0.039 1438 Dihedral : 10.814 59.423 1966 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.53 % Allowed : 7.00 % Favored : 91.47 % 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: 1.94 (0.25), residues: 1038 helix: 2.76 (0.21), residues: 506 sheet: 0.94 (0.44), residues: 116 loop : -0.52 (0.29), residues: 416 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 0.016 0.001 PHE B 315 TYR 0.019 0.001 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: 14 poor density : 72 time to evaluate : 0.905 Fit side-chains REVERT: A 614 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.7890 (p-80) REVERT: A 618 GLU cc_start: 0.7887 (tt0) cc_final: 0.7403 (pt0) REVERT: B 614 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.7913 (p-80) REVERT: B 618 GLU cc_start: 0.7917 (tt0) cc_final: 0.7420 (pt0) outliers start: 14 outliers final: 2 residues processed: 76 average time/residue: 0.7513 time to fit residues: 64.5402 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9442 Z= 0.270 Angle : 0.529 6.418 12586 Z= 0.268 Chirality : 0.042 0.141 1416 Planarity : 0.004 0.045 1438 Dihedral : 10.688 59.439 1966 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.31 % Allowed : 7.44 % Favored : 91.25 % 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: 1.85 (0.25), residues: 1038 helix: 2.67 (0.21), residues: 508 sheet: 0.84 (0.44), residues: 116 loop : -0.54 (0.29), residues: 414 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 0.017 0.001 PHE A 315 TYR 0.020 0.002 TYR B 570 ARG 0.002 0.000 ARG A 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 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.962 Fit side-chains REVERT: A 614 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.7902 (p-80) REVERT: B 614 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.7883 (p-80) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.7239 time to fit residues: 62.3786 Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9442 Z= 0.218 Angle : 0.497 6.450 12586 Z= 0.254 Chirality : 0.040 0.135 1416 Planarity : 0.004 0.040 1438 Dihedral : 10.268 58.732 1966 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.53 % Allowed : 7.44 % Favored : 91.03 % 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: 1.99 (0.25), residues: 1038 helix: 2.83 (0.21), residues: 508 sheet: 0.80 (0.44), residues: 116 loop : -0.48 (0.29), residues: 414 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 0.019 0.001 TYR B 570 ARG 0.002 0.000 ARG B 379 *********************** 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 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.966 Fit side-chains REVERT: A 614 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.7882 (p-80) REVERT: B 614 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.7867 (p-80) outliers start: 14 outliers final: 4 residues processed: 77 average time/residue: 0.7349 time to fit residues: 64.3857 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1352 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= 0.195 Angle : 0.482 6.442 12586 Z= 0.246 Chirality : 0.040 0.132 1416 Planarity : 0.004 0.046 1438 Dihedral : 9.818 57.590 1966 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.31 % Allowed : 8.32 % Favored : 90.37 % 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: 2.09 (0.25), residues: 1038 helix: 2.91 (0.21), residues: 508 sheet: 0.81 (0.44), residues: 116 loop : -0.42 (0.30), residues: 414 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 0.015 0.001 PHE B 315 TYR 0.018 0.001 TYR B 570 ARG 0.002 0.000 ARG A 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 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.761 Fit side-chains REVERT: A 614 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.7832 (p-80) REVERT: B 614 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.7881 (p-80) REVERT: B 618 GLU cc_start: 0.7914 (tt0) cc_final: 0.7394 (pt0) outliers start: 12 outliers final: 6 residues processed: 77 average time/residue: 0.8086 time to fit residues: 69.6821 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9442 Z= 0.300 Angle : 0.543 6.441 12586 Z= 0.275 Chirality : 0.042 0.143 1416 Planarity : 0.004 0.040 1438 Dihedral : 10.073 57.750 1966 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.20 % Allowed : 8.64 % Favored : 90.15 % 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: 1.72 (0.25), residues: 1038 helix: 2.51 (0.21), residues: 520 sheet: 0.68 (0.44), residues: 116 loop : -0.59 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 647 HIS 0.003 0.001 HIS A 614 PHE 0.017 0.001 PHE B 315 TYR 0.020 0.002 TYR B 570 ARG 0.002 0.000 ARG A 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: 11 poor density : 70 time to evaluate : 0.931 Fit side-chains REVERT: A 614 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.7853 (p-80) REVERT: B 614 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.7889 (p-80) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.7723 time to fit residues: 66.9565 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9442 Z= 0.207 Angle : 0.491 6.452 12586 Z= 0.251 Chirality : 0.040 0.134 1416 Planarity : 0.004 0.040 1438 Dihedral : 9.707 56.645 1966 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.86 % Allowed : 7.88 % 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: 1.91 (0.25), residues: 1038 helix: 2.70 (0.21), residues: 520 sheet: 0.72 (0.44), residues: 116 loop : -0.53 (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 0.015 0.001 PHE B 315 TYR 0.019 0.001 TYR A 570 ARG 0.002 0.000 ARG A 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 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.008 Fit side-chains REVERT: A 614 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.7859 (p-80) REVERT: B 614 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.7864 (p-80) outliers start: 17 outliers final: 6 residues processed: 79 average time/residue: 0.7639 time to fit residues: 68.1092 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 : 0.986 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9442 Z= 0.208 Angle : 0.493 6.435 12586 Z= 0.252 Chirality : 0.040 0.134 1416 Planarity : 0.004 0.045 1438 Dihedral : 9.541 55.955 1966 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.98 % Allowed : 8.86 % Favored : 90.15 % 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: 1.92 (0.25), residues: 1038 helix: 2.73 (0.21), residues: 520 sheet: 0.68 (0.44), residues: 116 loop : -0.53 (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 0.014 0.001 PHE A 315 TYR 0.019 0.001 TYR A 570 ARG 0.001 0.000 ARG A 372 ********************** 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 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.849 Fit side-chains REVERT: A 614 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.7876 (p-80) REVERT: B 614 HIS cc_start: 0.8938 (OUTLIER) cc_final: 0.7868 (p-80) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.7461 time to fit residues: 61.4108 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 : 0.841 ------------------------------------------------------------------------------- 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 81 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.165938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129737 restraints weight = 9245.306| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.78 r_work: 0.3280 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9442 Z= 0.319 Angle : 0.555 6.462 12586 Z= 0.281 Chirality : 0.043 0.144 1416 Planarity : 0.004 0.052 1438 Dihedral : 9.936 55.913 1966 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.20 % Allowed : 8.75 % Favored : 90.04 % 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: 1.62 (0.25), residues: 1038 helix: 2.47 (0.21), residues: 520 sheet: 0.62 (0.44), residues: 116 loop : -0.70 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 647 HIS 0.004 0.001 HIS A 614 PHE 0.017 0.002 PHE B 315 TYR 0.020 0.002 TYR B 570 ARG 0.002 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.94 seconds wall clock time: 43 minutes 58.30 seconds (2638.30 seconds total)