Starting phenix.real_space_refine on Tue Jan 14 05:48:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj4_38393/01_2025/8xj4_38393.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 32 5.16 5 C 3736 2.51 5 N 941 2.21 5 O 1111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5820 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2834 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 25, 'TRANS': 321} Chain: "A" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2826 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.92, per 1000 atoms: 0.67 Number of scatterers: 5820 At special positions: 0 Unit cell: (89.1, 106.7, 74.8, 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 32 16.00 O 1111 8.00 N 941 7.00 C 3736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 3 " - " MAN D 4 " ALPHA1-3 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 401 " - " ASN A 94 " " NAG A 402 " - " ASN A 220 " " NAG B 401 " - " ASN B 94 " " NAG B 403 " - " ASN B 220 " " NAG C 1 " - " ASN B 333 " " NAG D 1 " - " ASN A 333 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 777.8 milliseconds 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 50.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 59 through 63 removed outlier: 3.502A pdb=" N SER B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.588A pdb=" N MET B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 removed outlier: 3.508A pdb=" N LEU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.911A pdb=" N ILE B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.536A pdb=" N GLN B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.615A pdb=" N GLN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.636A pdb=" N ALA B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.061A pdb=" N TYR B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.691A pdb=" N VAL B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 301 removed outlier: 3.561A pdb=" N VAL B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 124 removed outlier: 3.508A pdb=" N LEU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.521A pdb=" N SER A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 131 " --> pdb=" O GLY A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.918A pdb=" N GLN A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 3.581A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.701A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 228 through 248 removed outlier: 4.068A pdb=" N TYR A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.684A pdb=" N VAL A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.524A pdb=" N VAL A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.535A pdb=" N GLU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.539A pdb=" N HIS B 144 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 103 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER B 287 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 105 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE B 284 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 38 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 286 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 40 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 318 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 38 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 316 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 40 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS B 314 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.539A pdb=" N HIS B 144 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 103 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER B 287 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 105 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE B 284 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 38 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 286 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 40 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 318 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 38 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 316 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 40 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS B 314 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 327 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS B 351 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.684A pdb=" N TYR A 103 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A 287 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG A 105 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE A 284 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 38 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 286 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 40 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 318 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 38 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 316 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 40 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS A 314 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET A 329 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.684A pdb=" N TYR A 103 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A 287 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG A 105 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE A 284 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 38 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 286 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 40 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 318 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 38 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 316 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 40 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS A 314 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 327 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS A 351 " --> pdb=" O VAL A 327 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 774 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: 1.66 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1366 1.33 - 1.45: 1337 1.45 - 1.58: 3229 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 5984 Sorted by residual: bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LEU A 156 " pdb=" CA LEU A 156 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.30e+00 bond pdb=" N LEU A 153 " pdb=" CA LEU A 153 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.24e+00 bond pdb=" N GLN B 101 " pdb=" CA GLN B 101 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.92e+00 ... (remaining 5979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 7818 1.93 - 3.87: 262 3.87 - 5.80: 43 5.80 - 7.74: 6 7.74 - 9.67: 2 Bond angle restraints: 8131 Sorted by residual: angle pdb=" N GLY B 248 " pdb=" CA GLY B 248 " pdb=" C GLY B 248 " ideal model delta sigma weight residual 113.18 122.85 -9.67 2.37e+00 1.78e-01 1.67e+01 angle pdb=" C PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 112.62 106.12 6.50 1.65e+00 3.67e-01 1.55e+01 angle pdb=" C CYS A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta sigma weight residual 119.05 123.25 -4.20 1.11e+00 8.12e-01 1.43e+01 angle pdb=" N GLY A 248 " pdb=" CA GLY A 248 " pdb=" C GLY A 248 " ideal model delta sigma weight residual 113.18 122.02 -8.84 2.37e+00 1.78e-01 1.39e+01 angle pdb=" CA SER B 96 " pdb=" C SER B 96 " pdb=" O SER B 96 " ideal model delta sigma weight residual 121.87 117.66 4.21 1.16e+00 7.43e-01 1.32e+01 ... (remaining 8126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 3437 24.58 - 49.16: 236 49.16 - 73.75: 53 73.75 - 98.33: 24 98.33 - 122.91: 17 Dihedral angle restraints: 3767 sinusoidal: 1724 harmonic: 2043 Sorted by residual: dihedral pdb=" CD ARG A 159 " pdb=" NE ARG A 159 " pdb=" CZ ARG A 159 " pdb=" NH1 ARG A 159 " ideal model delta sinusoidal sigma weight residual 0.00 -75.83 75.83 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS B 347 " pdb=" SG CYS B 347 " pdb=" SG CYS B 351 " pdb=" CB CYS B 351 " ideal model delta sinusoidal sigma weight residual 93.00 140.40 -47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N ASN B 220 " pdb=" CA ASN B 220 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 3764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 794 0.064 - 0.129: 101 0.129 - 0.193: 15 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 913 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG B 403 " pdb=" ND2 ASN B 220 " pdb=" C2 NAG B 403 " pdb=" O5 NAG B 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2 MAN D 3 " pdb=" C1 MAN D 3 " pdb=" C3 MAN D 3 " pdb=" O2 MAN D 3 " both_signs ideal model delta sigma weight residual False 2.52 2.71 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 910 not shown) Planarity restraints: 1025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 159 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG A 159 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 159 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 159 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 159 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 163 " 0.551 9.50e-02 1.11e+02 2.47e-01 3.73e+01 pdb=" NE ARG A 163 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 163 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 163 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 163 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 223 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 224 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " -0.036 5.00e-02 4.00e+02 ... (remaining 1022 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 890 2.76 - 3.29: 5531 3.29 - 3.83: 8992 3.83 - 4.36: 9947 4.36 - 4.90: 17912 Nonbonded interactions: 43272 Sorted by model distance: nonbonded pdb=" OH TYR B 89 " pdb=" OE2 GLU B 317 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 89 " pdb=" OE2 GLU A 317 " model vdw 2.357 3.040 nonbonded pdb=" O GLU B 166 " pdb=" OG SER B 169 " model vdw 2.380 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG SER A 169 " model vdw 2.396 3.040 nonbonded pdb=" O GLU A 168 " pdb=" OG1 THR A 171 " model vdw 2.408 3.040 ... (remaining 43267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 377 or resid 401)) selection = (chain 'B' and (resid 32 through 377 or resid 401)) } 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: 0.380 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.005 0.079 5984 Z= 0.324 Angle : 0.797 9.674 8131 Z= 0.445 Chirality : 0.047 0.322 913 Planarity : 0.018 0.478 1019 Dihedral : 19.960 122.909 2441 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.57 % Allowed : 1.42 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.33), residues: 689 helix: 2.28 (0.31), residues: 307 sheet: 0.85 (0.53), residues: 76 loop : -0.77 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 206 HIS 0.005 0.001 HIS A 337 PHE 0.012 0.002 PHE A 356 TYR 0.016 0.001 TYR A 319 ARG 0.005 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: B 170 GLU cc_start: 0.7675 (tp30) cc_final: 0.7308 (tp30) REVERT: B 184 TYR cc_start: 0.6229 (p90) cc_final: 0.5922 (p90) outliers start: 10 outliers final: 3 residues processed: 87 average time/residue: 0.1939 time to fit residues: 22.2112 Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN B 304 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099820 restraints weight = 8686.669| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.23 r_work: 0.3138 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5984 Z= 0.306 Angle : 0.710 9.358 8131 Z= 0.348 Chirality : 0.047 0.186 913 Planarity : 0.006 0.061 1019 Dihedral : 17.886 110.842 1025 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 8.03 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.33), residues: 689 helix: 2.27 (0.30), residues: 315 sheet: 0.73 (0.54), residues: 76 loop : -0.87 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS A 314 PHE 0.018 0.002 PHE A 158 TYR 0.019 0.002 TYR A 184 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.693 Fit side-chains REVERT: B 170 GLU cc_start: 0.7867 (tp30) cc_final: 0.7402 (tm-30) REVERT: A 170 GLU cc_start: 0.6956 (tp30) cc_final: 0.6566 (tm-30) REVERT: A 336 GLN cc_start: 0.7967 (pm20) cc_final: 0.7709 (pp30) outliers start: 8 outliers final: 2 residues processed: 60 average time/residue: 0.1825 time to fit residues: 14.9433 Evaluate side-chains 47 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099741 restraints weight = 8729.717| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.25 r_work: 0.3141 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5984 Z= 0.247 Angle : 0.690 11.482 8131 Z= 0.333 Chirality : 0.047 0.297 913 Planarity : 0.006 0.057 1019 Dihedral : 17.170 112.934 1019 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.89 % Allowed : 11.18 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.33), residues: 689 helix: 2.45 (0.30), residues: 316 sheet: 0.70 (0.56), residues: 76 loop : -0.84 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS B 314 PHE 0.014 0.001 PHE A 158 TYR 0.027 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 170 GLU cc_start: 0.7895 (tp30) cc_final: 0.7403 (tm-30) REVERT: B 373 MET cc_start: 0.6801 (tmm) cc_final: 0.6481 (tmm) REVERT: A 161 CYS cc_start: 0.6251 (p) cc_final: 0.6045 (p) outliers start: 12 outliers final: 4 residues processed: 61 average time/residue: 0.1703 time to fit residues: 14.2724 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102625 restraints weight = 8784.957| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.20 r_work: 0.3185 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5984 Z= 0.173 Angle : 0.624 8.069 8131 Z= 0.299 Chirality : 0.044 0.292 913 Planarity : 0.006 0.052 1019 Dihedral : 16.224 110.802 1019 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.57 % Allowed : 12.91 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 689 helix: 2.63 (0.30), residues: 315 sheet: 0.76 (0.55), residues: 76 loop : -0.74 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.003 0.001 HIS A 78 PHE 0.012 0.001 PHE A 53 TYR 0.029 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8390 (mtmt) REVERT: B 156 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6766 (mm) REVERT: B 170 GLU cc_start: 0.7911 (tp30) cc_final: 0.7435 (tm-30) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 0.1707 time to fit residues: 15.0503 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 HIS ** A 250 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 = 0.3722 r_free = 0.3722 target = 0.135124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100150 restraints weight = 8689.053| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.16 r_work: 0.3149 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5984 Z= 0.233 Angle : 0.663 8.401 8131 Z= 0.317 Chirality : 0.045 0.296 913 Planarity : 0.006 0.051 1019 Dihedral : 15.801 111.705 1019 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.42 % Allowed : 14.65 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.33), residues: 689 helix: 2.63 (0.30), residues: 315 sheet: 0.65 (0.55), residues: 76 loop : -0.73 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 226 HIS 0.003 0.001 HIS B 219 PHE 0.011 0.001 PHE A 53 TYR 0.024 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8415 (mtmt) REVERT: B 156 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6797 (mm) REVERT: B 170 GLU cc_start: 0.7980 (tp30) cc_final: 0.7511 (tm-30) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.1838 time to fit residues: 13.9641 Evaluate side-chains 51 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100540 restraints weight = 8705.831| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.16 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5984 Z= 0.208 Angle : 0.645 8.201 8131 Z= 0.307 Chirality : 0.045 0.291 913 Planarity : 0.006 0.067 1019 Dihedral : 15.373 112.273 1019 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.10 % Allowed : 15.75 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 689 helix: 2.63 (0.30), residues: 315 sheet: 0.61 (0.55), residues: 76 loop : -0.72 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.010 0.001 PHE A 53 TYR 0.027 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mtmt) REVERT: B 156 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6816 (mm) REVERT: B 170 GLU cc_start: 0.8040 (tp30) cc_final: 0.7551 (tm-30) REVERT: A 170 GLU cc_start: 0.6884 (tp30) cc_final: 0.6429 (tm-30) REVERT: A 336 GLN cc_start: 0.8371 (pm20) cc_final: 0.7801 (pp30) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.1716 time to fit residues: 12.6961 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097111 restraints weight = 8816.466| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.16 r_work: 0.3098 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5984 Z= 0.305 Angle : 0.706 8.985 8131 Z= 0.339 Chirality : 0.046 0.284 913 Planarity : 0.006 0.065 1019 Dihedral : 15.183 112.058 1019 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.73 % Allowed : 16.06 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.33), residues: 689 helix: 2.52 (0.30), residues: 315 sheet: 0.31 (0.55), residues: 76 loop : -0.94 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 226 HIS 0.003 0.001 HIS B 219 PHE 0.013 0.002 PHE A 158 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7041 (mm) REVERT: A 156 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 170 GLU cc_start: 0.6928 (tp30) cc_final: 0.6346 (tm-30) REVERT: A 336 GLN cc_start: 0.8485 (pm20) cc_final: 0.7892 (pp30) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 0.1784 time to fit residues: 13.1495 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.0030 chunk 43 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 250 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 = 0.3744 r_free = 0.3744 target = 0.137043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102744 restraints weight = 8595.095| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.13 r_work: 0.3183 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5984 Z= 0.156 Angle : 0.632 7.602 8131 Z= 0.299 Chirality : 0.043 0.284 913 Planarity : 0.006 0.054 1019 Dihedral : 14.938 112.974 1015 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.79 % Allowed : 16.85 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 689 helix: 2.63 (0.30), residues: 317 sheet: 0.58 (0.56), residues: 76 loop : -0.70 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 226 HIS 0.003 0.001 HIS A 78 PHE 0.009 0.001 PHE A 164 TYR 0.023 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7844 (pt0) REVERT: B 170 GLU cc_start: 0.7886 (tp30) cc_final: 0.7416 (tm-30) REVERT: A 170 GLU cc_start: 0.6895 (tp30) cc_final: 0.6435 (tm-30) REVERT: A 336 GLN cc_start: 0.8486 (pm20) cc_final: 0.7861 (pp30) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.1782 time to fit residues: 13.0773 Evaluate side-chains 49 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102215 restraints weight = 8688.898| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.18 r_work: 0.3178 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5984 Z= 0.162 Angle : 0.649 10.875 8131 Z= 0.302 Chirality : 0.043 0.271 913 Planarity : 0.006 0.052 1019 Dihedral : 14.547 113.352 1015 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.26 % Allowed : 17.17 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.34), residues: 689 helix: 2.66 (0.30), residues: 319 sheet: 0.73 (0.56), residues: 76 loop : -0.60 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 226 HIS 0.003 0.001 HIS B 182 PHE 0.008 0.001 PHE A 164 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7833 (pt0) REVERT: B 170 GLU cc_start: 0.7963 (tp30) cc_final: 0.7504 (tm-30) REVERT: A 170 GLU cc_start: 0.6890 (tp30) cc_final: 0.6428 (tm-30) REVERT: A 336 GLN cc_start: 0.8508 (pm20) cc_final: 0.7860 (pp30) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.1670 time to fit residues: 12.7053 Evaluate side-chains 52 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100882 restraints weight = 8718.549| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.17 r_work: 0.3157 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5984 Z= 0.194 Angle : 0.654 8.809 8131 Z= 0.307 Chirality : 0.043 0.265 913 Planarity : 0.006 0.053 1019 Dihedral : 14.142 112.905 1015 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.94 % Allowed : 17.32 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.34), residues: 689 helix: 2.70 (0.31), residues: 317 sheet: 0.73 (0.56), residues: 76 loop : -0.73 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.009 0.001 PHE B 158 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7824 (pt0) REVERT: B 170 GLU cc_start: 0.7915 (tp30) cc_final: 0.7499 (tp30) REVERT: A 170 GLU cc_start: 0.6893 (tp30) cc_final: 0.6431 (tm-30) REVERT: A 336 GLN cc_start: 0.8560 (pm20) cc_final: 0.7891 (pp30) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1730 time to fit residues: 12.2546 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 373 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 61 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103192 restraints weight = 8795.995| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.21 r_work: 0.3190 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5984 Z= 0.163 Angle : 0.650 11.803 8131 Z= 0.299 Chirality : 0.042 0.257 913 Planarity : 0.006 0.052 1019 Dihedral : 13.229 112.539 1015 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.94 % Allowed : 17.64 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 689 helix: 2.68 (0.30), residues: 319 sheet: 0.91 (0.57), residues: 76 loop : -0.61 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 226 HIS 0.004 0.001 HIS B 182 PHE 0.008 0.001 PHE A 164 TYR 0.026 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.08 seconds wall clock time: 45 minutes 51.45 seconds (2751.45 seconds total)