Starting phenix.real_space_refine on Thu Mar 5 13:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdf_31916/03_2026/7vdf_31916_trim.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.151 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7251 2.51 5 N 2025 2.21 5 O 2316 1.98 5 H 11043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.84, per 1000 atoms: 0.17 Number of scatterers: 22692 At special positions: 0 Unit cell: (84.36, 85.88, 144.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2316 8.00 N 2025 7.00 C 7251 6.00 H 11043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " 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 NAG-ASN " NAG A 601 " - " ASN A 285 " " NAG A 602 " - " ASN A 165 " " NAG A 603 " - " ASN A 81 " " NAG B 601 " - " ASN B 285 " " NAG B 602 " - " ASN B 165 " " NAG B 603 " - " ASN B 81 " " NAG C 603 " - " ASN C 285 " " NAG C 604 " - " ASN C 165 " " NAG C 605 " - " ASN C 81 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 649.6 milliseconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 34 sheets defined 26.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.907A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 367 through 379 removed outlier: 4.202A pdb=" N GLY A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.264A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.940A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 379 removed outlier: 4.231A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.250A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.853A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 367 through 379 removed outlier: 4.239A pdb=" N GLY C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.330A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366 removed outlier: 3.764A pdb=" N ASN A 357 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.838A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.971A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.461A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.493A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.306A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.590A pdb=" N TYR B 351 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 357 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.906A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.013A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.072A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.265A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 366 removed outlier: 3.781A pdb=" N ASN C 357 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.000A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.050A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 286 through 287 524 hydrogen bonds defined for protein. 1434 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: 5.58 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11037 1.04 - 1.24: 1448 1.24 - 1.44: 3768 1.44 - 1.64: 6598 1.64 - 1.84: 78 Bond restraints: 22929 Sorted by residual: bond pdb=" N SER A 9 " pdb=" CA SER A 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" N SER C 9 " pdb=" H SER C 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N SER B 9 " pdb=" H SER B 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39585 1.20 - 2.39: 1453 2.39 - 3.59: 111 3.59 - 4.79: 33 4.79 - 5.99: 14 Bond angle restraints: 41196 Sorted by residual: angle pdb=" CA CYS B 14 " pdb=" CB CYS B 14 " pdb=" SG CYS B 14 " ideal model delta sigma weight residual 114.40 120.12 -5.72 2.30e+00 1.89e-01 6.18e+00 angle pdb=" C LYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta sigma weight residual 122.56 119.39 3.17 1.50e+00 4.44e-01 4.47e+00 angle pdb=" C PHE C 392 " pdb=" N HIS C 393 " pdb=" CA HIS C 393 " ideal model delta sigma weight residual 122.93 119.88 3.05 1.45e+00 4.76e-01 4.41e+00 angle pdb=" C LEU B 13 " pdb=" N CYS B 14 " pdb=" CA CYS B 14 " ideal model delta sigma weight residual 122.45 118.79 3.66 1.78e+00 3.16e-01 4.22e+00 angle pdb=" N CYS B 14 " pdb=" CA CYS B 14 " pdb=" C CYS B 14 " ideal model delta sigma weight residual 107.88 110.71 -2.83 1.41e+00 5.03e-01 4.03e+00 ... (remaining 41191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 10310 21.72 - 43.45: 579 43.45 - 65.17: 142 65.17 - 86.89: 39 86.89 - 108.62: 15 Dihedral angle restraints: 11085 sinusoidal: 6192 harmonic: 4893 Sorted by residual: dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual 79.00 8.95 70.05 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA CYS B 14 " pdb=" C CYS B 14 " pdb=" N LEU B 15 " pdb=" CA LEU B 15 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" O4 BMA B 605 " pdb=" C4 BMA B 605 " pdb=" C5 BMA B 605 " pdb=" O5 BMA B 605 " ideal model delta sinusoidal sigma weight residual -71.29 -179.91 108.62 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 11082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1570 0.061 - 0.121: 211 0.121 - 0.181: 27 0.181 - 0.242: 1 0.242 - 0.302: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C5 BMA A 605 " pdb=" C4 BMA A 605 " pdb=" C6 BMA A 605 " pdb=" O5 BMA A 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C5 BMA B 605 " pdb=" C4 BMA B 605 " pdb=" C6 BMA B 605 " pdb=" O5 BMA B 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1809 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 21 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 74 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO B 284 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.015 5.00e-02 4.00e+02 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 935 2.15 - 2.76: 45082 2.76 - 3.37: 68804 3.37 - 3.99: 94764 3.99 - 4.60: 143378 Nonbonded interactions: 352963 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.537 2.450 nonbonded pdb=" HZ2 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.540 2.450 nonbonded pdb=" OD2 ASP A 415 " pdb=" HZ2 LYS B 391 " model vdw 1.569 2.450 nonbonded pdb=" H MET B 462 " pdb=" O CYS B 466 " model vdw 1.575 2.450 nonbonded pdb=" HZ1 LYS A 391 " pdb=" OD2 ASP C 419 " model vdw 1.583 2.450 ... (remaining 352958 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 9 through 601 or resid 603 through 604)) selection = (chain 'B' and (resid 9 through 601 or resid 603 through 604)) selection = (chain 'C' and (resid 9 through 601 or resid 603 through 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.810 Find NCS groups from input model: 0.250 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.004 0.042 11910 Z= 0.166 Angle : 0.557 5.986 16179 Z= 0.278 Chirality : 0.046 0.302 1812 Planarity : 0.003 0.035 2094 Dihedral : 15.734 108.615 4599 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1443 helix: 2.24 (0.26), residues: 339 sheet: -0.79 (0.29), residues: 315 loop : -0.70 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 261 TYR 0.007 0.001 TYR C 308 PHE 0.012 0.001 PHE C 120 TRP 0.006 0.001 TRP A 222 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00355 (11886) covalent geometry : angle 0.54837 (16122) SS BOND : bond 0.00320 ( 15) SS BOND : angle 1.78711 ( 30) hydrogen bonds : bond 0.12094 ( 492) hydrogen bonds : angle 6.64677 ( 1434) link_NAG-ASN : bond 0.00315 ( 9) link_NAG-ASN : angle 1.74666 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7234 (ttm-80) REVERT: B 450 LYS cc_start: 0.6872 (mtmt) cc_final: 0.6569 (mttt) REVERT: B 452 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7309 (ttm170) REVERT: C 57 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7138 (ttt-90) REVERT: C 493 ASP cc_start: 0.7412 (m-30) cc_final: 0.7146 (m-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.9996 time to fit residues: 202.2173 Evaluate side-chains 149 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 211 GLN A 248 ASN B 394 GLN C 173 ASN C 211 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119707 restraints weight = 34767.330| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.60 r_work: 0.3390 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11910 Z= 0.175 Angle : 0.537 7.645 16179 Z= 0.278 Chirality : 0.044 0.184 1812 Planarity : 0.004 0.047 2094 Dihedral : 8.275 56.365 1878 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 5.58 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1443 helix: 1.94 (0.25), residues: 339 sheet: -0.51 (0.33), residues: 261 loop : -0.87 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.009 0.001 TYR A 302 PHE 0.011 0.001 PHE C 79 TRP 0.005 0.001 TRP B 127 HIS 0.004 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00388 (11886) covalent geometry : angle 0.52683 (16122) SS BOND : bond 0.00371 ( 15) SS BOND : angle 1.78122 ( 30) hydrogen bonds : bond 0.03894 ( 492) hydrogen bonds : angle 5.65328 ( 1434) link_NAG-ASN : bond 0.00307 ( 9) link_NAG-ASN : angle 1.80022 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7103 (ttt-90) REVERT: B 450 LYS cc_start: 0.6891 (mtmt) cc_final: 0.6533 (mttp) REVERT: B 493 ASP cc_start: 0.7086 (m-30) cc_final: 0.6677 (m-30) REVERT: C 57 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7039 (ttm-80) outliers start: 9 outliers final: 5 residues processed: 175 average time/residue: 0.9373 time to fit residues: 182.2215 Evaluate side-chains 158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 173 ASN C 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129872 restraints weight = 34549.750| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.55 r_work: 0.3533 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11910 Z= 0.143 Angle : 0.485 7.754 16179 Z= 0.254 Chirality : 0.042 0.158 1812 Planarity : 0.004 0.041 2094 Dihedral : 6.285 56.202 1878 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.63 % Allowed : 7.63 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.21), residues: 1443 helix: 2.03 (0.26), residues: 339 sheet: -0.87 (0.29), residues: 327 loop : -0.94 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 405 TYR 0.008 0.001 TYR C 302 PHE 0.009 0.001 PHE B 120 TRP 0.005 0.001 TRP B 127 HIS 0.004 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00311 (11886) covalent geometry : angle 0.47718 (16122) SS BOND : bond 0.00279 ( 15) SS BOND : angle 1.46636 ( 30) hydrogen bonds : bond 0.03524 ( 492) hydrogen bonds : angle 5.39537 ( 1434) link_NAG-ASN : bond 0.00193 ( 9) link_NAG-ASN : angle 1.61194 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7321 (ttm-80) REVERT: B 449 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 450 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6765 (mttp) REVERT: C 57 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7241 (ttt-90) outliers start: 8 outliers final: 5 residues processed: 178 average time/residue: 0.9208 time to fit residues: 182.1958 Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN B 33 GLN B 173 ASN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125825 restraints weight = 34572.193| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.55 r_work: 0.3488 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11910 Z= 0.226 Angle : 0.547 8.717 16179 Z= 0.285 Chirality : 0.043 0.146 1812 Planarity : 0.005 0.063 2094 Dihedral : 6.182 55.422 1878 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.94 % Allowed : 9.20 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1443 helix: 1.81 (0.26), residues: 339 sheet: -0.70 (0.32), residues: 279 loop : -1.05 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.008 0.002 TYR B 308 PHE 0.010 0.002 PHE B 120 TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00510 (11886) covalent geometry : angle 0.53395 (16122) SS BOND : bond 0.00310 ( 15) SS BOND : angle 2.23635 ( 30) hydrogen bonds : bond 0.03785 ( 492) hydrogen bonds : angle 5.45596 ( 1434) link_NAG-ASN : bond 0.00439 ( 9) link_NAG-ASN : angle 1.88775 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7315 (ttt-90) REVERT: B 449 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7183 (mm-30) REVERT: C 14 CYS cc_start: 0.7080 (m) cc_final: 0.6861 (m) REVERT: C 57 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7230 (ttt-90) outliers start: 12 outliers final: 5 residues processed: 177 average time/residue: 0.8796 time to fit residues: 174.0681 Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 407 GLN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125130 restraints weight = 34279.450| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.54 r_work: 0.3482 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11910 Z= 0.224 Angle : 0.543 9.522 16179 Z= 0.283 Chirality : 0.043 0.147 1812 Planarity : 0.005 0.062 2094 Dihedral : 6.007 53.552 1878 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.94 % Allowed : 10.69 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1443 helix: 1.73 (0.26), residues: 339 sheet: -0.74 (0.32), residues: 279 loop : -1.10 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.008 0.002 TYR A 302 PHE 0.011 0.002 PHE B 120 TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00502 (11886) covalent geometry : angle 0.53214 (16122) SS BOND : bond 0.00340 ( 15) SS BOND : angle 1.98045 ( 30) hydrogen bonds : bond 0.03742 ( 492) hydrogen bonds : angle 5.47725 ( 1434) link_NAG-ASN : bond 0.00387 ( 9) link_NAG-ASN : angle 1.87583 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7356 (ttt-90) REVERT: B 346 MET cc_start: 0.8378 (ttm) cc_final: 0.8029 (ttm) REVERT: C 14 CYS cc_start: 0.7073 (m) cc_final: 0.6847 (m) REVERT: C 57 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7254 (ttt-90) outliers start: 12 outliers final: 4 residues processed: 172 average time/residue: 0.9342 time to fit residues: 178.2244 Evaluate side-chains 158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 407 GLN B 454 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123174 restraints weight = 34639.115| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.55 r_work: 0.3457 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11910 Z= 0.274 Angle : 0.583 10.525 16179 Z= 0.303 Chirality : 0.044 0.150 1812 Planarity : 0.005 0.075 2094 Dihedral : 6.194 54.824 1878 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.02 % Allowed : 12.03 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1443 helix: 1.55 (0.26), residues: 339 sheet: -0.92 (0.31), residues: 285 loop : -1.10 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.008 0.002 TYR B 233 PHE 0.011 0.002 PHE A 120 TRP 0.006 0.001 TRP C 421 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00621 (11886) covalent geometry : angle 0.57116 (16122) SS BOND : bond 0.00374 ( 15) SS BOND : angle 1.99116 ( 30) hydrogen bonds : bond 0.03984 ( 492) hydrogen bonds : angle 5.58881 ( 1434) link_NAG-ASN : bond 0.00545 ( 9) link_NAG-ASN : angle 2.07376 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7413 (mppt) cc_final: 0.6783 (ttpp) REVERT: B 57 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7353 (ttt-90) REVERT: C 452 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7597 (ttm-80) outliers start: 13 outliers final: 5 residues processed: 168 average time/residue: 0.9431 time to fit residues: 175.4348 Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 498 ASN B 33 GLN B 173 ASN B 407 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125016 restraints weight = 34457.631| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.54 r_work: 0.3480 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11910 Z= 0.194 Angle : 0.539 9.904 16179 Z= 0.280 Chirality : 0.043 0.146 1812 Planarity : 0.005 0.055 2094 Dihedral : 5.893 53.665 1878 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.34 % Allowed : 12.50 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1443 helix: 1.66 (0.26), residues: 339 sheet: -0.83 (0.32), residues: 276 loop : -1.14 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.008 0.002 TYR C 195 PHE 0.011 0.001 PHE B 120 TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00429 (11886) covalent geometry : angle 0.52761 (16122) SS BOND : bond 0.00340 ( 15) SS BOND : angle 2.05110 ( 30) hydrogen bonds : bond 0.03681 ( 492) hydrogen bonds : angle 5.50109 ( 1434) link_NAG-ASN : bond 0.00311 ( 9) link_NAG-ASN : angle 1.85000 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.8381 (ttm) cc_final: 0.7973 (ttm) REVERT: A 403 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 57 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7335 (ttt-90) REVERT: C 57 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7264 (ttt-90) REVERT: C 385 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6839 (mt) REVERT: C 452 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7504 (ttm-80) outliers start: 17 outliers final: 8 residues processed: 170 average time/residue: 0.8648 time to fit residues: 163.9451 Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN B 33 GLN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124250 restraints weight = 34501.789| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.55 r_work: 0.3469 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11910 Z= 0.223 Angle : 0.556 9.961 16179 Z= 0.288 Chirality : 0.043 0.146 1812 Planarity : 0.005 0.061 2094 Dihedral : 5.909 54.468 1878 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.10 % Allowed : 13.52 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1443 helix: 1.61 (0.26), residues: 339 sheet: -0.88 (0.32), residues: 270 loop : -1.13 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.015 0.002 TYR C 195 PHE 0.011 0.001 PHE B 120 TRP 0.005 0.001 TRP C 421 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (11886) covalent geometry : angle 0.54340 (16122) SS BOND : bond 0.00357 ( 15) SS BOND : angle 2.20902 ( 30) hydrogen bonds : bond 0.03787 ( 492) hydrogen bonds : angle 5.51746 ( 1434) link_NAG-ASN : bond 0.00414 ( 9) link_NAG-ASN : angle 1.91818 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.8379 (ttm) cc_final: 0.7967 (ttm) REVERT: B 57 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.7359 (ttt-90) REVERT: C 57 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7258 (ttt-90) REVERT: C 368 LYS cc_start: 0.7367 (mppt) cc_final: 0.6428 (ttpp) REVERT: C 385 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6835 (mt) outliers start: 14 outliers final: 8 residues processed: 167 average time/residue: 0.9000 time to fit residues: 167.5934 Evaluate side-chains 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN A 498 ASN B 33 GLN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124436 restraints weight = 34470.634| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.55 r_work: 0.3475 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11910 Z= 0.228 Angle : 0.578 10.044 16179 Z= 0.299 Chirality : 0.044 0.146 1812 Planarity : 0.005 0.061 2094 Dihedral : 5.952 55.288 1878 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.63 % Allowed : 14.47 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1443 helix: 1.60 (0.26), residues: 339 sheet: -0.94 (0.32), residues: 270 loop : -1.13 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.015 0.002 TYR C 195 PHE 0.011 0.002 PHE B 120 TRP 0.005 0.001 TRP C 421 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00514 (11886) covalent geometry : angle 0.55690 (16122) SS BOND : bond 0.00384 ( 15) SS BOND : angle 3.18594 ( 30) hydrogen bonds : bond 0.03811 ( 492) hydrogen bonds : angle 5.53142 ( 1434) link_NAG-ASN : bond 0.00411 ( 9) link_NAG-ASN : angle 1.91887 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.8362 (ttm) cc_final: 0.7960 (ttm) REVERT: B 57 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7374 (ttt-90) REVERT: C 57 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7269 (ttt-90) REVERT: C 65 THR cc_start: 0.8476 (m) cc_final: 0.8273 (m) REVERT: C 385 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6874 (mt) outliers start: 8 outliers final: 8 residues processed: 164 average time/residue: 0.8898 time to fit residues: 161.9343 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 454 GLN B 33 GLN B 173 ASN B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126618 restraints weight = 34458.259| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.55 r_work: 0.3498 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11910 Z= 0.162 Angle : 0.546 9.235 16179 Z= 0.283 Chirality : 0.043 0.147 1812 Planarity : 0.004 0.041 2094 Dihedral : 5.671 53.927 1878 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.71 % Allowed : 14.62 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1443 helix: 1.76 (0.26), residues: 339 sheet: -0.95 (0.30), residues: 291 loop : -1.10 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.013 0.001 TYR C 195 PHE 0.010 0.001 PHE B 120 TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00361 (11886) covalent geometry : angle 0.52252 (16122) SS BOND : bond 0.00379 ( 15) SS BOND : angle 3.41006 ( 30) hydrogen bonds : bond 0.03618 ( 492) hydrogen bonds : angle 5.42109 ( 1434) link_NAG-ASN : bond 0.00222 ( 9) link_NAG-ASN : angle 1.71427 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7182 (ttt-90) REVERT: A 346 MET cc_start: 0.8282 (ttm) cc_final: 0.7892 (ttm) REVERT: B 57 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7347 (ttt-90) REVERT: B 346 MET cc_start: 0.8211 (ttm) cc_final: 0.7871 (ttm) REVERT: B 452 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7669 (ttp-170) REVERT: C 57 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7250 (ttt-90) REVERT: C 368 LYS cc_start: 0.7291 (mppt) cc_final: 0.6363 (ttpp) REVERT: C 385 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6851 (mt) outliers start: 9 outliers final: 6 residues processed: 167 average time/residue: 0.8563 time to fit residues: 159.3771 Evaluate side-chains 160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN B 33 GLN B 173 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126536 restraints weight = 34394.634| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.54 r_work: 0.3494 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11910 Z= 0.175 Angle : 0.552 10.028 16179 Z= 0.285 Chirality : 0.043 0.146 1812 Planarity : 0.004 0.048 2094 Dihedral : 5.625 54.373 1878 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.55 % Allowed : 14.86 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1443 helix: 1.79 (0.25), residues: 339 sheet: -0.81 (0.32), residues: 264 loop : -1.15 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.013 0.001 TYR C 195 PHE 0.010 0.001 PHE B 120 TRP 0.005 0.001 TRP B 127 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00393 (11886) covalent geometry : angle 0.52822 (16122) SS BOND : bond 0.00346 ( 15) SS BOND : angle 3.39484 ( 30) hydrogen bonds : bond 0.03624 ( 492) hydrogen bonds : angle 5.39342 ( 1434) link_NAG-ASN : bond 0.00269 ( 9) link_NAG-ASN : angle 1.73108 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6727.84 seconds wall clock time: 114 minutes 49.65 seconds (6889.65 seconds total)