Starting phenix.real_space_refine on Wed Feb 4 17:31:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.map" model { file = "/net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d0y_46466/02_2026/9d0y_46466.cif" } resolution = 3.1 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7338 2.51 5 N 2043 2.21 5 O 2346 1.98 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11781 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294} Chain: "D" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'TRANS': 163} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, E, F Time building chain proxies: 2.03, per 1000 atoms: 0.17 Number of scatterers: 11781 At special positions: 0 Unit cell: (88.55, 86.25, 149.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2346 8.00 N 2043 7.00 C 7338 6.00 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 D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.08 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.07 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS E 137 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.08 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.08 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.07 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.07 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 401 " - " ASN A 38 " " NAG A 402 " - " ASN A 63 " " NAG A 403 " - " ASN A 126 " " NAG A 404 " - " ASN A 133 " " NAG A 405 " - " ASN A 158 " " NAG A 406 " - " ASN A 165 " " NAG A 407 " - " ASN A 246 " " NAG A 408 " - " ASN A 285 " " NAG A 409 " - " ASN A 45 " " NAG B 401 " - " ASN B 38 " " NAG B 402 " - " ASN B 63 " " NAG B 403 " - " ASN B 126 " " NAG B 404 " - " ASN B 133 " " NAG B 405 " - " ASN B 158 " " NAG B 406 " - " ASN B 165 " " NAG B 407 " - " ASN B 246 " " NAG B 408 " - " ASN B 285 " " NAG B 409 " - " ASN B 45 " " NAG C 401 " - " ASN C 38 " " NAG C 402 " - " ASN C 63 " " NAG C 403 " - " ASN C 126 " " NAG C 404 " - " ASN C 133 " " NAG C 405 " - " ASN C 158 " " NAG C 406 " - " ASN C 165 " " NAG C 407 " - " ASN C 246 " " NAG C 408 " - " ASN C 285 " " NAG C 409 " - " ASN C 45 " " NAG D 501 " - " ASN D 154 " " NAG E 501 " - " ASN E 154 " " NAG F 501 " - " ASN F 154 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 460.4 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.8% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.810A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 158 through 167 removed outlier: 4.077A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASP D 164 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.810A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'E' and resid 37 through 54 Processing helix chain 'E' and resid 75 through 126 Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 158 through 167 removed outlier: 4.077A pdb=" N TYR E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.810A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 54 Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 158 through 167 removed outlier: 4.077A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP F 164 " --> pdb=" O ASN F 160 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU F 165 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 170 No H-bonds generated for 'chain 'F' and resid 168 through 170' Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.108A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.834A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.687A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.351A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 305 removed outlier: 3.661A pdb=" N CYS A 305 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN D 60 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 32 through 36 Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.108A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.834A pdb=" N ILE 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: 4.686A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.351A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 305 removed outlier: 3.660A pdb=" N CYS B 305 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN E 60 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AC6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.108A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.834A pdb=" N ILE 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: 4.687A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (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 281 through 283 removed outlier: 4.351A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 303 through 305 removed outlier: 3.661A pdb=" N CYS C 305 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN F 60 " --> pdb=" O CYS C 305 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2530 1.32 - 1.45: 3955 1.45 - 1.59: 5431 1.59 - 1.73: 27 1.73 - 1.87: 72 Bond restraints: 12015 Sorted by residual: bond pdb=" CB ILE E 173 " pdb=" CG1 ILE E 173 " ideal model delta sigma weight residual 1.530 1.673 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" CB ILE D 173 " pdb=" CG1 ILE D 173 " ideal model delta sigma weight residual 1.530 1.673 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" CB ILE F 173 " pdb=" CG1 ILE F 173 " ideal model delta sigma weight residual 1.530 1.673 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" CB ILE C 267 " pdb=" CG1 ILE C 267 " ideal model delta sigma weight residual 1.530 1.406 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CB ILE A 267 " pdb=" CG1 ILE A 267 " ideal model delta sigma weight residual 1.530 1.406 0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 12010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14158 2.53 - 5.07: 1839 5.07 - 7.60: 227 7.60 - 10.13: 33 10.13 - 12.66: 3 Bond angle restraints: 16260 Sorted by residual: angle pdb=" N ASN C 45 " pdb=" CA ASN C 45 " pdb=" C ASN C 45 " ideal model delta sigma weight residual 110.42 97.76 12.66 1.55e+00 4.16e-01 6.68e+01 angle pdb=" N ASN B 45 " pdb=" CA ASN B 45 " pdb=" C ASN B 45 " ideal model delta sigma weight residual 110.42 97.79 12.63 1.55e+00 4.16e-01 6.64e+01 angle pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" C ASN A 45 " ideal model delta sigma weight residual 110.42 97.79 12.63 1.55e+00 4.16e-01 6.64e+01 angle pdb=" C CYS A 305 " pdb=" N PRO A 306 " pdb=" CA PRO A 306 " ideal model delta sigma weight residual 119.78 127.64 -7.86 1.03e+00 9.43e-01 5.82e+01 angle pdb=" C CYS C 305 " pdb=" N PRO C 306 " pdb=" CA PRO C 306 " ideal model delta sigma weight residual 119.78 127.63 -7.85 1.03e+00 9.43e-01 5.81e+01 ... (remaining 16255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 7343 17.27 - 34.53: 199 34.53 - 51.80: 75 51.80 - 69.06: 33 69.06 - 86.33: 12 Dihedral angle restraints: 7662 sinusoidal: 3519 harmonic: 4143 Sorted by residual: dihedral pdb=" CB CYS B 52 " pdb=" SG CYS B 52 " pdb=" SG CYS B 277 " pdb=" CB CYS B 277 " ideal model delta sinusoidal sigma weight residual 93.00 55.29 37.71 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 55.30 37.70 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual 93.00 55.30 37.70 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 7659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1647 0.143 - 0.285: 191 0.285 - 0.428: 4 0.428 - 0.571: 9 0.571 - 0.713: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C1 NAG A 409 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 409 " pdb=" O5 NAG A 409 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG B 409 " pdb=" ND2 ASN B 45 " pdb=" C2 NAG B 409 " pdb=" O5 NAG B 409 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG C 409 " pdb=" ND2 ASN C 45 " pdb=" C2 NAG C 409 " pdb=" O5 NAG C 409 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 1851 not shown) Planarity restraints: 2115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C 403 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A 403 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 403 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 403 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 403 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG B 403 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG B 403 " -0.139 2.00e-02 2.50e+03 ... (remaining 2112 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 4092 2.86 - 3.37: 10684 3.37 - 3.88: 20293 3.88 - 4.39: 23674 4.39 - 4.90: 38571 Nonbonded interactions: 97314 Sorted by model distance: nonbonded pdb=" N ASN B 45 " pdb=" O ASN B 45 " model vdw 2.344 2.496 nonbonded pdb=" N ASN C 45 " pdb=" O ASN C 45 " model vdw 2.344 2.496 nonbonded pdb=" N ASN A 45 " pdb=" O ASN A 45 " model vdw 2.344 2.496 nonbonded pdb=" N ASP B 60 " pdb=" OD1 ASP B 60 " model vdw 2.391 3.120 nonbonded pdb=" N ASP C 60 " pdb=" OD1 ASP C 60 " model vdw 2.392 3.120 ... (remaining 97309 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.022 0.143 12063 Z= 1.183 Angle : 1.805 21.128 16386 Z= 1.180 Chirality : 0.102 0.713 1854 Planarity : 0.027 0.295 2085 Dihedral : 10.702 86.329 4944 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.33 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1419 helix: 0.47 (0.26), residues: 333 sheet: 1.02 (0.32), residues: 234 loop : -0.29 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 90 TYR 0.032 0.007 TYR B 105 PHE 0.029 0.005 PHE F 24 TRP 0.039 0.007 TRP E 14 HIS 0.014 0.003 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.02167 (12015) covalent geometry : angle 1.75838 (16260) SS BOND : bond 0.02501 ( 18) SS BOND : angle 4.14888 ( 36) hydrogen bonds : bond 0.14589 ( 477) hydrogen bonds : angle 8.20355 ( 1422) link_NAG-ASN : bond 0.01632 ( 30) link_NAG-ASN : angle 5.29055 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7170 (tppt) REVERT: D 115 MET cc_start: 0.8566 (tpp) cc_final: 0.8311 (tpp) REVERT: B 197 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7461 (mm-40) REVERT: B 214 ILE cc_start: 0.8640 (mm) cc_final: 0.8250 (mm) REVERT: B 276 LYS cc_start: 0.7411 (mmtt) cc_final: 0.6977 (tppt) REVERT: C 124 SER cc_start: 0.8284 (m) cc_final: 0.7987 (p) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1211 time to fit residues: 59.6457 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 80 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS E 142 HIS ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130664 restraints weight = 15342.994| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.65 r_work: 0.3390 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12063 Z= 0.181 Angle : 0.719 10.210 16386 Z= 0.365 Chirality : 0.049 0.265 1854 Planarity : 0.005 0.035 2085 Dihedral : 7.296 53.872 2184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.19 % Allowed : 7.70 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1419 helix: 1.64 (0.27), residues: 339 sheet: 0.65 (0.32), residues: 234 loop : -0.50 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.015 0.001 TYR D 141 PHE 0.013 0.002 PHE B 148 TRP 0.012 0.002 TRP A 84 HIS 0.008 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00403 (12015) covalent geometry : angle 0.69042 (16260) SS BOND : bond 0.00732 ( 18) SS BOND : angle 1.78865 ( 36) hydrogen bonds : bond 0.04963 ( 477) hydrogen bonds : angle 6.15225 ( 1422) link_NAG-ASN : bond 0.00357 ( 30) link_NAG-ASN : angle 2.60071 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7471 (mm-40) REVERT: D 86 ASP cc_start: 0.8730 (t0) cc_final: 0.8523 (t0) REVERT: B 119 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 276 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7237 (tppt) REVERT: C 35 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 124 SER cc_start: 0.8555 (m) cc_final: 0.8190 (p) REVERT: C 197 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7499 (tt0) outliers start: 15 outliers final: 8 residues processed: 252 average time/residue: 0.1135 time to fit residues: 39.7364 Evaluate side-chains 168 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 216 ASN ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128472 restraints weight = 15639.688| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.59 r_work: 0.3362 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12063 Z= 0.170 Angle : 0.632 9.495 16386 Z= 0.324 Chirality : 0.047 0.208 1854 Planarity : 0.005 0.038 2085 Dihedral : 7.281 53.420 2184 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.06 % Allowed : 9.84 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1419 helix: 1.63 (0.27), residues: 345 sheet: 0.41 (0.32), residues: 246 loop : -0.56 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 90 TYR 0.009 0.001 TYR D 141 PHE 0.012 0.002 PHE C 120 TRP 0.010 0.002 TRP D 92 HIS 0.006 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00388 (12015) covalent geometry : angle 0.61061 (16260) SS BOND : bond 0.00402 ( 18) SS BOND : angle 1.37862 ( 36) hydrogen bonds : bond 0.04546 ( 477) hydrogen bonds : angle 5.71288 ( 1422) link_NAG-ASN : bond 0.00437 ( 30) link_NAG-ASN : angle 2.16027 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7693 (mt-10) REVERT: D 65 GLN cc_start: 0.8551 (mt0) cc_final: 0.8158 (mt0) REVERT: B 119 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 197 GLN cc_start: 0.7942 (mm110) cc_final: 0.7713 (mm-40) REVERT: C 35 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 197 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7533 (mm-40) outliers start: 26 outliers final: 17 residues processed: 198 average time/residue: 0.1142 time to fit residues: 31.3874 Evaluate side-chains 170 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 142 HIS ** 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 = 0.3639 r_free = 0.3639 target = 0.142929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127923 restraints weight = 15683.636| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.59 r_work: 0.3355 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12063 Z= 0.151 Angle : 0.566 10.178 16386 Z= 0.294 Chirality : 0.046 0.248 1854 Planarity : 0.004 0.041 2085 Dihedral : 7.219 59.834 2184 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 11.67 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1419 helix: 1.49 (0.26), residues: 363 sheet: 0.41 (0.35), residues: 216 loop : -0.70 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 90 TYR 0.008 0.001 TYR E 22 PHE 0.012 0.001 PHE C 120 TRP 0.008 0.002 TRP D 92 HIS 0.005 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00346 (12015) covalent geometry : angle 0.54322 (16260) SS BOND : bond 0.00425 ( 18) SS BOND : angle 1.20570 ( 36) hydrogen bonds : bond 0.04175 ( 477) hydrogen bonds : angle 5.44133 ( 1422) link_NAG-ASN : bond 0.00290 ( 30) link_NAG-ASN : angle 2.08102 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 65 GLN cc_start: 0.8625 (mt0) cc_final: 0.8356 (mt0) REVERT: B 119 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7634 (mp0) REVERT: B 201 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7400 (ttp-170) REVERT: C 35 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 197 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7629 (mm-40) outliers start: 23 outliers final: 18 residues processed: 197 average time/residue: 0.1176 time to fit residues: 32.1715 Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.0270 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN E 142 HIS ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN C 22 ASN C 210 GLN ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123245 restraints weight = 15887.887| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.66 r_work: 0.3296 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12063 Z= 0.236 Angle : 0.644 10.920 16386 Z= 0.331 Chirality : 0.048 0.252 1854 Planarity : 0.005 0.046 2085 Dihedral : 7.103 58.110 2184 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.70 % Allowed : 12.14 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1419 helix: 1.27 (0.26), residues: 363 sheet: 0.18 (0.35), residues: 216 loop : -0.88 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.010 0.002 TYR D 141 PHE 0.015 0.002 PHE C 120 TRP 0.011 0.002 TRP B 234 HIS 0.006 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00565 (12015) covalent geometry : angle 0.62392 (16260) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.39550 ( 36) hydrogen bonds : bond 0.04550 ( 477) hydrogen bonds : angle 5.58494 ( 1422) link_NAG-ASN : bond 0.00320 ( 30) link_NAG-ASN : angle 2.11149 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7673 (tt0) REVERT: D 133 MET cc_start: 0.7547 (mtt) cc_final: 0.7184 (mtt) REVERT: C 35 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 197 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7676 (mm-40) REVERT: F 120 GLU cc_start: 0.7363 (mp0) cc_final: 0.7118 (mp0) outliers start: 34 outliers final: 23 residues processed: 185 average time/residue: 0.1227 time to fit residues: 31.0270 Evaluate side-chains 167 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN B 22 ASN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** F 159 HIS ** 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 = 0.3604 r_free = 0.3604 target = 0.140204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125184 restraints weight = 15760.916| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.63 r_work: 0.3318 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12063 Z= 0.165 Angle : 0.568 10.130 16386 Z= 0.295 Chirality : 0.046 0.216 1854 Planarity : 0.004 0.045 2085 Dihedral : 6.758 57.377 2184 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.38 % Allowed : 12.06 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1419 helix: 1.68 (0.27), residues: 345 sheet: -0.09 (0.33), residues: 240 loop : -0.66 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.013 0.001 TYR F 157 PHE 0.013 0.002 PHE C 120 TRP 0.010 0.002 TRP B 234 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00386 (12015) covalent geometry : angle 0.54654 (16260) SS BOND : bond 0.00387 ( 18) SS BOND : angle 1.11400 ( 36) hydrogen bonds : bond 0.04129 ( 477) hydrogen bonds : angle 5.42182 ( 1422) link_NAG-ASN : bond 0.00316 ( 30) link_NAG-ASN : angle 2.07412 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7686 (mtm110) REVERT: B 295 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.6989 (pt0) REVERT: C 35 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8284 (mt-10) outliers start: 30 outliers final: 20 residues processed: 180 average time/residue: 0.1189 time to fit residues: 29.5749 Evaluate side-chains 176 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN C 22 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** 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 = 0.3588 r_free = 0.3588 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123811 restraints weight = 15925.380| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.67 r_work: 0.3302 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12063 Z= 0.191 Angle : 0.612 10.869 16386 Z= 0.316 Chirality : 0.047 0.225 1854 Planarity : 0.005 0.045 2085 Dihedral : 6.725 52.170 2184 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.30 % Allowed : 11.98 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1419 helix: 1.39 (0.26), residues: 363 sheet: -0.05 (0.34), residues: 228 loop : -0.87 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 150 TYR 0.009 0.001 TYR D 141 PHE 0.013 0.002 PHE C 120 TRP 0.010 0.002 TRP B 234 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00452 (12015) covalent geometry : angle 0.58331 (16260) SS BOND : bond 0.00434 ( 18) SS BOND : angle 2.48841 ( 36) hydrogen bonds : bond 0.04225 ( 477) hydrogen bonds : angle 5.40505 ( 1422) link_NAG-ASN : bond 0.00305 ( 30) link_NAG-ASN : angle 2.04337 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 208 ARG cc_start: 0.7510 (mtm110) cc_final: 0.6748 (mtm-85) REVERT: B 208 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7608 (mtm110) REVERT: B 295 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7132 (pt0) REVERT: C 35 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8329 (mt-10) outliers start: 29 outliers final: 24 residues processed: 177 average time/residue: 0.1166 time to fit residues: 28.2891 Evaluate side-chains 170 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125317 restraints weight = 15911.856| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.66 r_work: 0.3319 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12063 Z= 0.153 Angle : 0.565 10.166 16386 Z= 0.293 Chirality : 0.045 0.203 1854 Planarity : 0.004 0.045 2085 Dihedral : 6.505 52.577 2184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.30 % Allowed : 11.90 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1419 helix: 1.83 (0.27), residues: 345 sheet: -0.20 (0.34), residues: 228 loop : -0.78 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.008 0.001 TYR D 141 PHE 0.013 0.001 PHE C 120 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00357 (12015) covalent geometry : angle 0.53823 (16260) SS BOND : bond 0.00354 ( 18) SS BOND : angle 2.08703 ( 36) hydrogen bonds : bond 0.04000 ( 477) hydrogen bonds : angle 5.27382 ( 1422) link_NAG-ASN : bond 0.00320 ( 30) link_NAG-ASN : angle 2.02814 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.8369 (m) cc_final: 0.7705 (p) REVERT: A 119 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 197 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7676 (mm-40) REVERT: B 208 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7614 (mtm110) REVERT: B 295 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 35 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8329 (mt-10) outliers start: 29 outliers final: 25 residues processed: 188 average time/residue: 0.1153 time to fit residues: 29.7908 Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 95 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN F 34 GLN ** F 159 HIS ** 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 = 0.3623 r_free = 0.3623 target = 0.141813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126798 restraints weight = 15785.215| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.64 r_work: 0.3348 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12063 Z= 0.126 Angle : 0.539 9.637 16386 Z= 0.279 Chirality : 0.045 0.204 1854 Planarity : 0.004 0.044 2085 Dihedral : 6.294 52.714 2184 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.06 % Allowed : 12.54 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1419 helix: 1.99 (0.27), residues: 345 sheet: -0.32 (0.33), residues: 234 loop : -0.83 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.011 0.001 TYR E 157 PHE 0.012 0.001 PHE C 120 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00287 (12015) covalent geometry : angle 0.51474 (16260) SS BOND : bond 0.00292 ( 18) SS BOND : angle 1.72576 ( 36) hydrogen bonds : bond 0.03803 ( 477) hydrogen bonds : angle 5.08705 ( 1422) link_NAG-ASN : bond 0.00337 ( 30) link_NAG-ASN : angle 1.96070 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 SER cc_start: 0.8225 (m) cc_final: 0.7623 (p) REVERT: A 119 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 119 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7572 (mp0) REVERT: B 188 ASP cc_start: 0.7951 (m-30) cc_final: 0.7750 (t0) REVERT: B 197 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7662 (mm-40) REVERT: B 208 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7626 (mtm110) REVERT: B 295 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: C 114 SER cc_start: 0.8098 (m) cc_final: 0.7625 (p) REVERT: F 120 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6824 (mt-10) outliers start: 26 outliers final: 21 residues processed: 185 average time/residue: 0.1136 time to fit residues: 29.0528 Evaluate side-chains 175 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122885 restraints weight = 16151.740| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.66 r_work: 0.3291 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12063 Z= 0.222 Angle : 0.623 11.019 16386 Z= 0.321 Chirality : 0.047 0.220 1854 Planarity : 0.005 0.048 2085 Dihedral : 6.494 51.886 2184 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.62 % Allowed : 12.06 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1419 helix: 1.71 (0.27), residues: 345 sheet: -0.66 (0.29), residues: 270 loop : -0.79 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.018 0.002 TYR E 157 PHE 0.014 0.002 PHE F 138 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00532 (12015) covalent geometry : angle 0.59994 (16260) SS BOND : bond 0.00491 ( 18) SS BOND : angle 2.06872 ( 36) hydrogen bonds : bond 0.04214 ( 477) hydrogen bonds : angle 5.32112 ( 1422) link_NAG-ASN : bond 0.00291 ( 30) link_NAG-ASN : angle 1.98580 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 34 GLN cc_start: 0.7961 (tt0) cc_final: 0.7476 (tt0) REVERT: B 197 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7705 (mm-40) REVERT: B 208 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7609 (mtm110) REVERT: B 295 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7261 (pt0) outliers start: 33 outliers final: 30 residues processed: 181 average time/residue: 0.1183 time to fit residues: 29.2084 Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125652 restraints weight = 15900.909| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.56 r_work: 0.3328 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12063 Z= 0.144 Angle : 0.559 9.947 16386 Z= 0.290 Chirality : 0.045 0.201 1854 Planarity : 0.004 0.045 2085 Dihedral : 6.348 52.542 2184 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.46 % Allowed : 12.46 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1419 helix: 1.89 (0.27), residues: 345 sheet: -0.70 (0.29), residues: 270 loop : -0.75 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.011 0.001 TYR E 157 PHE 0.013 0.001 PHE D 24 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00334 (12015) covalent geometry : angle 0.53463 (16260) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.74721 ( 36) hydrogen bonds : bond 0.03891 ( 477) hydrogen bonds : angle 5.17395 ( 1422) link_NAG-ASN : bond 0.00325 ( 30) link_NAG-ASN : angle 1.98744 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.62 seconds wall clock time: 45 minutes 14.55 seconds (2714.55 seconds total)