Starting phenix.real_space_refine on Thu Mar 5 16:19:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796.map" model { file = "/net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pr3_71796/03_2026/9pr3_71796_neut_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 75 5.16 5 C 7305 2.51 5 N 1977 2.21 5 O 2250 1.98 5 H 10959 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 22566 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7452 Classifications: {'peptide': 475} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain breaks: 1 Chain: "B" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7452 Classifications: {'peptide': 475} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain breaks: 1 Chain: "C" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7452 Classifications: {'peptide': 475} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 455} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 3.75, per 1000 atoms: 0.17 Number of scatterers: 22566 At special positions: 0 Unit cell: (93.573, 91.887, 134.037, 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 75 16.00 O 2250 8.00 N 1977 7.00 C 7305 6.00 H 10959 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.01 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.02 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 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 169 " " NAG A 604 " - " ASN A 289 " " NAG A 605 " - " ASN A 483 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 169 " " NAG B 604 " - " ASN B 289 " " NAG B 605 " - " ASN B 483 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 169 " " NAG C 604 " - " ASN C 289 " " NAG C 605 " - " ASN C 483 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 554.0 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 27.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.552A pdb=" N TRP A 127 " --> pdb=" O LYS A 125a" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 388 removed outlier: 4.268A pdb=" N GLN A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.691A pdb=" N TYR A 491 " --> pdb=" O TYR A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 71 removed outlier: 3.940A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 4.917A pdb=" N GLU B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.673A pdb=" N TRP B 127 " --> pdb=" O LYS B 125a" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 388 removed outlier: 3.522A pdb=" N GLN B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 456 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.540A pdb=" N GLN B 490 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 491 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 492 " --> pdb=" O PRO B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'C' and resid 65 through 71 removed outlier: 3.915A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 removed outlier: 4.904A pdb=" N GLU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 3.586A pdb=" N TRP C 127 " --> pdb=" O LYS C 125a" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 388 removed outlier: 3.567A pdb=" N GLN C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 456 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.540A pdb=" N GLN C 490 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 491 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 3.714A pdb=" N GLY A 16 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 352 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 355 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.824A pdb=" N LEU A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.720A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.968A pdb=" N VAL A 261 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS A 117 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 262a" --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 115 " --> pdb=" O LYS A 262a" (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 102 removed outlier: 8.190A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.610A pdb=" N ILE A 243 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB1, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 460 Processing sheet with id=AB3, first strand: chain 'B' and resid 12 through 17 removed outlier: 3.614A pdb=" N GLY B 16 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 352 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.746A pdb=" N LEU B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.719A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.826A pdb=" N VAL B 261 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS B 117 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS B 262a" --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 115 " --> pdb=" O LYS B 262a" (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 8.002A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 3.676A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA B 138 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ALA B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.573A pdb=" N ILE B 243 " --> pdb=" O TYR B 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC4, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AC5, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.806A pdb=" N GLY C 16 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY C 352 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AC8, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.711A pdb=" N LEU C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.724A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.129A pdb=" N VAL C 261 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS C 117 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 262a" --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 115 " --> pdb=" O LYS C 262a" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 8.127A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 3.723A pdb=" N SER C 146 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA C 138 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N ALA C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AD6, first strand: chain 'C' and resid 294 through 295 474 hydrogen bonds defined for protein. 1269 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: 5.57 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10959 1.03 - 1.23: 268 1.23 - 1.43: 4880 1.43 - 1.63: 6612 1.63 - 1.82: 114 Bond restraints: 22833 Sorted by residual: bond pdb=" CG1 ILE C 384 " pdb=" CD1 ILE C 384 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 bond pdb=" C TYR A 201 " pdb=" N ILE A 202 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.42e-02 4.96e+03 1.89e+00 bond pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.67e+00 bond pdb=" CB CYS C 281 " pdb=" SG CYS C 281 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 ... (remaining 22828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 38243 1.32 - 2.64: 2468 2.64 - 3.96: 276 3.96 - 5.28: 60 5.28 - 6.60: 8 Bond angle restraints: 41055 Sorted by residual: angle pdb=" C ASP B 95 " pdb=" CA ASP B 95 " pdb=" CB ASP B 95 " ideal model delta sigma weight residual 116.54 111.45 5.09 1.15e+00 7.56e-01 1.96e+01 angle pdb=" C ASP C 95 " pdb=" CA ASP C 95 " pdb=" CB ASP C 95 " ideal model delta sigma weight residual 116.54 111.48 5.06 1.15e+00 7.56e-01 1.93e+01 angle pdb=" N GLN B 211 " pdb=" CA GLN B 211 " pdb=" C GLN B 211 " ideal model delta sigma weight residual 110.35 114.07 -3.72 1.36e+00 5.41e-01 7.47e+00 angle pdb=" N PRO B 239 " pdb=" CA PRO B 239 " pdb=" C PRO B 239 " ideal model delta sigma weight residual 112.47 117.90 -5.43 2.06e+00 2.36e-01 6.94e+00 angle pdb=" CA ASP B 95 " pdb=" C ASP B 95 " pdb=" N LEU B 96 " ideal model delta sigma weight residual 119.52 117.45 2.07 7.90e-01 1.60e+00 6.87e+00 ... (remaining 41050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 9946 16.41 - 32.82: 701 32.82 - 49.23: 210 49.23 - 65.64: 171 65.64 - 82.05: 24 Dihedral angle restraints: 11052 sinusoidal: 6093 harmonic: 4959 Sorted by residual: dihedral pdb=" CA LEU A 176 " pdb=" C LEU A 176 " pdb=" N LEU A 177 " pdb=" CA LEU A 177 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA TYR B 256 " pdb=" C TYR B 256 " pdb=" N ALA B 257 " pdb=" CA ALA B 257 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 304 " pdb=" C GLU B 304 " pdb=" N CYS B 305 " pdb=" CA CYS B 305 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 11049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1556 0.078 - 0.156: 167 0.156 - 0.234: 20 0.234 - 0.312: 9 0.312 - 0.390: 9 Chirality restraints: 1761 Sorted by residual: chirality pdb=" C2 NAG B 605 " pdb=" C1 NAG B 605 " pdb=" C3 NAG B 605 " pdb=" N2 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C2 NAG C 605 " pdb=" C1 NAG C 605 " pdb=" C3 NAG C 605 " pdb=" N2 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C2 NAG C 602 " pdb=" C1 NAG C 602 " pdb=" C3 NAG C 602 " pdb=" N2 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1758 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 458 " -0.046 2.00e-02 2.50e+03 5.56e-02 4.64e+01 pdb=" CG ASN B 458 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 458 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 458 " 0.087 2.00e-02 2.50e+03 pdb="HD21 ASN B 458 " 0.003 2.00e-02 2.50e+03 pdb="HD22 ASN B 458 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 458 " -0.042 2.00e-02 2.50e+03 5.22e-02 4.09e+01 pdb=" CG ASN C 458 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 458 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 458 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN C 458 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN C 458 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 458 " -0.042 2.00e-02 2.50e+03 5.18e-02 4.02e+01 pdb=" CG ASN A 458 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 458 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 458 " 0.081 2.00e-02 2.50e+03 pdb="HD21 ASN A 458 " 0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 458 " -0.079 2.00e-02 2.50e+03 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 466 2.05 - 2.69: 35656 2.69 - 3.33: 65742 3.33 - 3.96: 83462 3.96 - 4.60: 133756 Nonbonded interactions: 319082 Sorted by model distance: nonbonded pdb=" H ALA B 19 " pdb=" O TRP B 343 " model vdw 1.415 2.450 nonbonded pdb=" H ALA C 19 " pdb=" O TRP C 343 " model vdw 1.423 2.450 nonbonded pdb=" HE2 HIS B 184 " pdb=" OD2 ASP B 231 " model vdw 1.468 2.450 nonbonded pdb=" O PHE C 439 " pdb="HD21 ASN C 443 " model vdw 1.468 2.450 nonbonded pdb=" HE2 HIS C 184 " pdb=" OD2 ASP C 231 " model vdw 1.469 2.450 ... (remaining 319077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.020 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: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.290 Find NCS groups from input model: 0.270 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 0.056 11907 Z= 0.301 Angle : 0.881 11.965 16167 Z= 0.475 Chirality : 0.059 0.390 1761 Planarity : 0.007 0.076 2082 Dihedral : 12.635 82.045 4608 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.28 % Favored : 91.58 % Rotamer: Outliers : 0.48 % Allowed : 3.25 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.81 (0.19), residues: 1413 helix: -2.10 (0.22), residues: 330 sheet: -1.58 (0.40), residues: 153 loop : -1.91 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG C 405 TYR 0.033 0.006 TYR C 161 PHE 0.020 0.003 PHE C 294 TRP 0.022 0.005 TRP B 421 HIS 0.012 0.003 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00666 (11874) covalent geometry : angle 0.83829 (16086) SS BOND : bond 0.00897 ( 18) SS BOND : angle 2.09958 ( 36) hydrogen bonds : bond 0.29216 ( 438) hydrogen bonds : angle 9.71491 ( 1269) link_NAG-ASN : bond 0.00628 ( 15) link_NAG-ASN : angle 4.90346 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 268 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6899 (mt0) cc_final: 0.6579 (mt0) REVERT: A 147 PHE cc_start: 0.7746 (t80) cc_final: 0.7259 (t80) REVERT: A 173 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7394 (ttp80) REVERT: A 231 ASP cc_start: 0.5892 (m-30) cc_final: 0.5678 (m-30) REVERT: A 307 LYS cc_start: 0.5756 (mmtt) cc_final: 0.4648 (mmtt) REVERT: A 312 ASN cc_start: 0.8344 (m-40) cc_final: 0.7878 (p0) REVERT: A 426 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 12 GLN cc_start: 0.6822 (mt0) cc_final: 0.6568 (mt0) REVERT: B 23 THR cc_start: 0.8531 (p) cc_final: 0.8312 (t) REVERT: B 30 MET cc_start: 0.6907 (mtm) cc_final: 0.6686 (mtp) REVERT: B 173 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7120 (ttp80) REVERT: B 231 ASP cc_start: 0.5367 (m-30) cc_final: 0.4712 (m-30) REVERT: B 312 ASN cc_start: 0.8463 (m-40) cc_final: 0.8003 (p0) REVERT: B 321 ARG cc_start: 0.6672 (ttm-80) cc_final: 0.6416 (mtt90) REVERT: B 426 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 438 ASP cc_start: 0.8751 (m-30) cc_final: 0.8307 (t0) REVERT: C 15 ILE cc_start: 0.7277 (mt) cc_final: 0.7006 (mt) REVERT: C 23 THR cc_start: 0.8629 (p) cc_final: 0.8415 (t) REVERT: C 70 LEU cc_start: 0.8724 (mt) cc_final: 0.8517 (mt) REVERT: C 79 PHE cc_start: 0.7088 (m-80) cc_final: 0.6797 (m-80) REVERT: C 173 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6675 (tpt90) REVERT: C 174 GLU cc_start: 0.6958 (mp0) cc_final: 0.6740 (mp0) REVERT: C 231 ASP cc_start: 0.5690 (m-30) cc_final: 0.5060 (m-30) REVERT: C 307 LYS cc_start: 0.5388 (mmtt) cc_final: 0.4270 (mmtt) REVERT: C 321 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6650 (mtt90) REVERT: C 455 LEU cc_start: 0.6007 (mt) cc_final: 0.5491 (pp) outliers start: 6 outliers final: 4 residues processed: 274 average time/residue: 0.2359 time to fit residues: 91.4858 Evaluate side-chains 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 351 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 94 ASN C 40 GLN C 94 ASN C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144264 restraints weight = 51808.336| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.17 r_work: 0.3846 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11907 Z= 0.183 Angle : 0.684 5.594 16167 Z= 0.374 Chirality : 0.044 0.170 1761 Planarity : 0.004 0.032 2082 Dihedral : 7.200 59.210 1853 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.95 % Allowed : 9.29 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -2.18 (0.20), residues: 1413 helix: -0.83 (0.26), residues: 354 sheet: -1.10 (0.42), residues: 141 loop : -1.84 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 435 TYR 0.017 0.002 TYR C 363 PHE 0.016 0.002 PHE C 118 TRP 0.013 0.001 TRP A 69 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00370 (11874) covalent geometry : angle 0.66650 (16086) SS BOND : bond 0.00905 ( 18) SS BOND : angle 2.09993 ( 36) hydrogen bonds : bond 0.09615 ( 438) hydrogen bonds : angle 7.63393 ( 1269) link_NAG-ASN : bond 0.00284 ( 15) link_NAG-ASN : angle 2.35832 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7297 (ttp80) REVERT: A 307 LYS cc_start: 0.5328 (mmtt) cc_final: 0.4247 (mmtt) REVERT: A 312 ASN cc_start: 0.8241 (m-40) cc_final: 0.7861 (p0) REVERT: A 426 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 173 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7192 (ttp80) REVERT: B 312 ASN cc_start: 0.8373 (m-40) cc_final: 0.7935 (p0) REVERT: B 321 ARG cc_start: 0.6438 (ttm-80) cc_final: 0.6077 (ptp-170) REVERT: B 426 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 174 GLU cc_start: 0.6586 (mp0) cc_final: 0.6138 (mm-30) REVERT: C 321 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6214 (ptp-170) REVERT: C 435 ARG cc_start: 0.8260 (mtt90) cc_final: 0.8039 (mtt-85) outliers start: 12 outliers final: 11 residues processed: 237 average time/residue: 0.2407 time to fit residues: 79.5641 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 197 ASN C 94 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.162580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137902 restraints weight = 52623.447| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.11 r_work: 0.3759 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11907 Z= 0.276 Angle : 0.725 12.042 16167 Z= 0.390 Chirality : 0.044 0.169 1761 Planarity : 0.005 0.041 2082 Dihedral : 7.149 54.684 1851 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.75 % Allowed : 12.46 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: -2.50 (0.20), residues: 1413 helix: -0.80 (0.26), residues: 342 sheet: -1.59 (0.40), residues: 141 loop : -2.13 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 405 TYR 0.011 0.002 TYR C 488 PHE 0.021 0.002 PHE B 148 TRP 0.010 0.002 TRP C 69 HIS 0.007 0.002 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00598 (11874) covalent geometry : angle 0.69817 (16086) SS BOND : bond 0.00904 ( 18) SS BOND : angle 2.58306 ( 36) hydrogen bonds : bond 0.08895 ( 438) hydrogen bonds : angle 7.55214 ( 1269) link_NAG-ASN : bond 0.00492 ( 15) link_NAG-ASN : angle 3.02501 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8599 (m-30) cc_final: 0.8394 (m-30) REVERT: A 173 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7346 (ttp80) REVERT: A 307 LYS cc_start: 0.5364 (mmtt) cc_final: 0.4232 (mmtt) REVERT: A 312 ASN cc_start: 0.8402 (m-40) cc_final: 0.7931 (p0) REVERT: A 426 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 173 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7373 (ttp80) REVERT: B 426 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7376 (mm-30) REVERT: C 172 ASN cc_start: 0.7880 (t0) cc_final: 0.7413 (t0) REVERT: C 321 ARG cc_start: 0.6868 (ttm-80) cc_final: 0.6620 (mtt180) REVERT: C 426 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7244 (mm-30) outliers start: 22 outliers final: 18 residues processed: 212 average time/residue: 0.2331 time to fit residues: 70.5067 Evaluate side-chains 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN B 197 ASN C 40 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141103 restraints weight = 52216.473| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.13 r_work: 0.3786 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11907 Z= 0.199 Angle : 0.672 12.077 16167 Z= 0.358 Chirality : 0.043 0.149 1761 Planarity : 0.004 0.042 2082 Dihedral : 6.877 52.927 1851 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.90 % Allowed : 13.81 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.20), residues: 1413 helix: -0.80 (0.27), residues: 339 sheet: -1.14 (0.39), residues: 156 loop : -2.20 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 405 TYR 0.012 0.001 TYR A 363 PHE 0.024 0.002 PHE B 147 TRP 0.007 0.001 TRP C 69 HIS 0.007 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00424 (11874) covalent geometry : angle 0.64633 (16086) SS BOND : bond 0.00921 ( 18) SS BOND : angle 2.70101 ( 36) hydrogen bonds : bond 0.07833 ( 438) hydrogen bonds : angle 7.53003 ( 1269) link_NAG-ASN : bond 0.00272 ( 15) link_NAG-ASN : angle 2.64803 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8598 (m-30) cc_final: 0.8360 (m-30) REVERT: A 173 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7333 (ttp80) REVERT: A 307 LYS cc_start: 0.5272 (mmtt) cc_final: 0.4182 (mmtt) REVERT: A 312 ASN cc_start: 0.8397 (m-40) cc_final: 0.7960 (p0) REVERT: A 426 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 173 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7511 (ttp80) REVERT: B 426 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 426 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 446 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8840 (m110) outliers start: 24 outliers final: 19 residues processed: 214 average time/residue: 0.2435 time to fit residues: 74.0091 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 92 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.144079 restraints weight = 51868.805| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.15 r_work: 0.3815 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11907 Z= 0.157 Angle : 0.617 11.795 16167 Z= 0.326 Chirality : 0.043 0.153 1761 Planarity : 0.004 0.038 2082 Dihedral : 6.387 51.715 1851 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.83 % Allowed : 13.65 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.20), residues: 1413 helix: -0.66 (0.27), residues: 339 sheet: -0.98 (0.40), residues: 156 loop : -2.09 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.013 0.001 TYR A 363 PHE 0.015 0.002 PHE B 147 TRP 0.013 0.001 TRP A 69 HIS 0.006 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00338 (11874) covalent geometry : angle 0.59470 (16086) SS BOND : bond 0.00755 ( 18) SS BOND : angle 2.53703 ( 36) hydrogen bonds : bond 0.07030 ( 438) hydrogen bonds : angle 7.15850 ( 1269) link_NAG-ASN : bond 0.00236 ( 15) link_NAG-ASN : angle 2.23159 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7260 (ttp80) REVERT: A 312 ASN cc_start: 0.8351 (m-40) cc_final: 0.7994 (p0) REVERT: A 426 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 312 ASN cc_start: 0.8354 (m-40) cc_final: 0.7898 (p0) REVERT: B 354 HIS cc_start: 0.8177 (t70) cc_final: 0.7905 (t70) REVERT: B 426 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7328 (mm-30) REVERT: C 77 ASP cc_start: 0.6423 (m-30) cc_final: 0.6168 (m-30) REVERT: C 446 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8802 (m110) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.2053 time to fit residues: 64.5246 Evaluate side-chains 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN B 94 ASN B 197 ASN C 40 GLN C 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141094 restraints weight = 52178.072| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.12 r_work: 0.3782 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11907 Z= 0.210 Angle : 0.650 10.193 16167 Z= 0.346 Chirality : 0.043 0.150 1761 Planarity : 0.004 0.046 2082 Dihedral : 6.577 50.860 1851 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.14 % Allowed : 14.60 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.20), residues: 1413 helix: -0.60 (0.27), residues: 339 sheet: -1.16 (0.40), residues: 156 loop : -2.23 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.008 0.001 TYR A 195 PHE 0.028 0.002 PHE B 147 TRP 0.010 0.001 TRP A 69 HIS 0.006 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00456 (11874) covalent geometry : angle 0.62739 (16086) SS BOND : bond 0.00805 ( 18) SS BOND : angle 2.40422 ( 36) hydrogen bonds : bond 0.07247 ( 438) hydrogen bonds : angle 7.10415 ( 1269) link_NAG-ASN : bond 0.00378 ( 15) link_NAG-ASN : angle 2.55108 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7254 (ttp80) REVERT: A 307 LYS cc_start: 0.5271 (mmtt) cc_final: 0.4190 (mmtt) REVERT: A 426 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 173 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7342 (ttp80) REVERT: B 354 HIS cc_start: 0.8237 (t70) cc_final: 0.7932 (t70) REVERT: B 426 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7323 (mm-30) REVERT: C 426 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7162 (mm-30) REVERT: C 446 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8810 (m110) outliers start: 27 outliers final: 22 residues processed: 206 average time/residue: 0.2272 time to fit residues: 67.4949 Evaluate side-chains 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 410 ASN C 40 GLN C 94 ASN C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.163214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138917 restraints weight = 52308.344| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.08 r_work: 0.3790 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11907 Z= 0.238 Angle : 0.668 9.556 16167 Z= 0.356 Chirality : 0.043 0.150 1761 Planarity : 0.004 0.050 2082 Dihedral : 6.817 49.957 1851 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.62 % Allowed : 14.84 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.58 (0.20), residues: 1413 helix: -0.45 (0.27), residues: 321 sheet: -1.35 (0.40), residues: 156 loop : -2.39 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.010 0.002 TYR B 353 PHE 0.019 0.002 PHE C 147 TRP 0.011 0.001 TRP C 153 HIS 0.010 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00517 (11874) covalent geometry : angle 0.64446 (16086) SS BOND : bond 0.00919 ( 18) SS BOND : angle 2.38954 ( 36) hydrogen bonds : bond 0.07406 ( 438) hydrogen bonds : angle 7.07290 ( 1269) link_NAG-ASN : bond 0.00388 ( 15) link_NAG-ASN : angle 2.71509 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7256 (ttp80) REVERT: A 307 LYS cc_start: 0.5294 (mmtt) cc_final: 0.4172 (mmtt) REVERT: A 426 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 173 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7396 (ttp80) REVERT: B 354 HIS cc_start: 0.8257 (t70) cc_final: 0.8016 (t70) REVERT: B 426 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 426 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 446 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8829 (m110) outliers start: 33 outliers final: 27 residues processed: 198 average time/residue: 0.2096 time to fit residues: 61.6687 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0010 chunk 126 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 197 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141812 restraints weight = 51852.755| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.08 r_work: 0.3822 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11907 Z= 0.162 Angle : 0.603 8.741 16167 Z= 0.320 Chirality : 0.043 0.144 1761 Planarity : 0.004 0.050 2082 Dihedral : 6.600 50.695 1851 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.06 % Allowed : 15.63 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.20), residues: 1413 helix: -0.24 (0.27), residues: 336 sheet: -1.23 (0.41), residues: 156 loop : -2.32 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.011 0.001 TYR B 363 PHE 0.015 0.002 PHE C 147 TRP 0.010 0.001 TRP A 69 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00340 (11874) covalent geometry : angle 0.58416 (16086) SS BOND : bond 0.00625 ( 18) SS BOND : angle 2.04381 ( 36) hydrogen bonds : bond 0.06801 ( 438) hydrogen bonds : angle 6.90448 ( 1269) link_NAG-ASN : bond 0.00214 ( 15) link_NAG-ASN : angle 2.28671 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7229 (ttp80) REVERT: A 307 LYS cc_start: 0.5286 (mmtt) cc_final: 0.4152 (mmtt) REVERT: B 77 ASP cc_start: 0.7026 (m-30) cc_final: 0.6794 (m-30) REVERT: B 173 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7378 (ttp80) REVERT: B 268 MET cc_start: 0.5082 (ttp) cc_final: 0.4853 (mtp) REVERT: B 354 HIS cc_start: 0.8190 (t70) cc_final: 0.7953 (t70) REVERT: B 426 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7278 (mm-30) REVERT: C 105 TYR cc_start: 0.8398 (t80) cc_final: 0.7738 (t80) outliers start: 26 outliers final: 22 residues processed: 201 average time/residue: 0.2058 time to fit residues: 61.0995 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 94 ASN C 197 ASN C 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.166324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141853 restraints weight = 52248.851| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.11 r_work: 0.3820 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11907 Z= 0.162 Angle : 0.598 8.354 16167 Z= 0.318 Chirality : 0.043 0.144 1761 Planarity : 0.004 0.049 2082 Dihedral : 6.574 50.665 1851 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.98 % Allowed : 15.79 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.21), residues: 1413 helix: -0.15 (0.27), residues: 336 sheet: -1.14 (0.41), residues: 156 loop : -2.28 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 452 TYR 0.009 0.001 TYR B 363 PHE 0.026 0.002 PHE C 148 TRP 0.021 0.001 TRP C 69 HIS 0.009 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00344 (11874) covalent geometry : angle 0.58066 (16086) SS BOND : bond 0.00617 ( 18) SS BOND : angle 1.98440 ( 36) hydrogen bonds : bond 0.06651 ( 438) hydrogen bonds : angle 6.79984 ( 1269) link_NAG-ASN : bond 0.00222 ( 15) link_NAG-ASN : angle 2.20528 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7209 (ttp80) REVERT: A 307 LYS cc_start: 0.5237 (mmtt) cc_final: 0.4126 (mmtt) REVERT: B 77 ASP cc_start: 0.7009 (m-30) cc_final: 0.6796 (m-30) REVERT: B 173 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7375 (ttp80) REVERT: B 354 HIS cc_start: 0.8169 (t70) cc_final: 0.7956 (t70) REVERT: C 105 TYR cc_start: 0.8390 (t80) cc_final: 0.7730 (t80) outliers start: 25 outliers final: 23 residues processed: 199 average time/residue: 0.2053 time to fit residues: 60.0016 Evaluate side-chains 194 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 197 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141717 restraints weight = 52306.167| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.12 r_work: 0.3811 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11907 Z= 0.184 Angle : 0.617 8.255 16167 Z= 0.329 Chirality : 0.043 0.143 1761 Planarity : 0.004 0.051 2082 Dihedral : 6.779 56.493 1851 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.98 % Allowed : 16.19 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.21), residues: 1413 helix: -0.11 (0.27), residues: 336 sheet: -1.20 (0.41), residues: 156 loop : -2.34 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.008 0.001 TYR B 363 PHE 0.020 0.002 PHE C 148 TRP 0.013 0.001 TRP B 69 HIS 0.009 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00395 (11874) covalent geometry : angle 0.59866 (16086) SS BOND : bond 0.00658 ( 18) SS BOND : angle 2.10932 ( 36) hydrogen bonds : bond 0.06789 ( 438) hydrogen bonds : angle 6.78648 ( 1269) link_NAG-ASN : bond 0.00266 ( 15) link_NAG-ASN : angle 2.30586 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7222 (ttp80) REVERT: A 307 LYS cc_start: 0.5243 (mmtt) cc_final: 0.4134 (mmtt) REVERT: B 173 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7395 (ttp80) REVERT: B 354 HIS cc_start: 0.8189 (t70) cc_final: 0.7977 (t70) REVERT: C 426 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7129 (mm-30) outliers start: 25 outliers final: 24 residues processed: 185 average time/residue: 0.2068 time to fit residues: 56.7335 Evaluate side-chains 190 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.167828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143262 restraints weight = 52299.111| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.13 r_work: 0.3838 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11907 Z= 0.145 Angle : 0.586 8.036 16167 Z= 0.311 Chirality : 0.043 0.143 1761 Planarity : 0.004 0.049 2082 Dihedral : 6.566 53.262 1851 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.83 % Allowed : 16.43 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.21), residues: 1413 helix: 0.07 (0.27), residues: 333 sheet: -1.02 (0.41), residues: 156 loop : -2.26 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.009 0.001 TYR B 363 PHE 0.020 0.002 PHE C 148 TRP 0.018 0.001 TRP C 69 HIS 0.008 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00305 (11874) covalent geometry : angle 0.56970 (16086) SS BOND : bond 0.00545 ( 18) SS BOND : angle 1.99088 ( 36) hydrogen bonds : bond 0.06378 ( 438) hydrogen bonds : angle 6.64056 ( 1269) link_NAG-ASN : bond 0.00200 ( 15) link_NAG-ASN : angle 2.01648 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.80 seconds wall clock time: 80 minutes 24.91 seconds (4824.91 seconds total)