Starting phenix.real_space_refine on Sun Apr 27 13:22:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj4_38393/04_2025/8xj4_38393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj4_38393/04_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_38393/04_2025/8xj4_38393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj4_38393/04_2025/8xj4_38393.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj4_38393/04_2025/8xj4_38393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj4_38393/04_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-5669/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: 4.01, per 1000 atoms: 0.69 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: 1.81 Conformation dependent library (CDL) restraints added in 806.6 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: 0.84 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: 1.44 Time building geometry restraints manager: 1.92 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.210 Find NCS groups from input model: 0.380 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- 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 5999 Z= 0.272 Angle : 0.824 9.674 8172 Z= 0.451 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 3.29910 ( 18) link_BETA1-4 : bond 0.01666 ( 2) link_BETA1-4 : angle 2.76796 ( 6) link_ALPHA1-2 : bond 0.00508 ( 1) link_ALPHA1-2 : angle 1.98471 ( 3) link_ALPHA1-3 : bond 0.01328 ( 2) link_ALPHA1-3 : angle 2.09342 ( 6) hydrogen bonds : bond 0.17343 ( 247) hydrogen bonds : angle 5.02086 ( 774) SS BOND : bond 0.00221 ( 4) SS BOND : angle 3.60370 ( 8) covalent geometry : bond 0.00493 ( 5984) covalent geometry : angle 0.79706 ( 8131) *********************** 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 : 0.678 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: 0.1836 time to fit residues: 21.0941 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 : 0.809 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100651 restraints weight = 8674.245| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.23 r_work: 0.3152 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5999 Z= 0.182 Angle : 0.717 9.313 8172 Z= 0.346 Chirality : 0.046 0.175 913 Planarity : 0.006 0.067 1019 Dihedral : 18.115 111.241 1025 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.60 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: 1.27 (0.33), residues: 689 helix: 2.33 (0.30), residues: 315 sheet: 0.81 (0.54), residues: 76 loop : -0.81 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS B 314 PHE 0.014 0.002 PHE A 158 TYR 0.020 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 2.45560 ( 18) link_BETA1-4 : bond 0.01034 ( 2) link_BETA1-4 : angle 1.68641 ( 6) link_ALPHA1-2 : bond 0.01121 ( 1) link_ALPHA1-2 : angle 2.43136 ( 3) link_ALPHA1-3 : bond 0.01997 ( 2) link_ALPHA1-3 : angle 4.91339 ( 6) hydrogen bonds : bond 0.05870 ( 247) hydrogen bonds : angle 4.02619 ( 774) SS BOND : bond 0.00362 ( 4) SS BOND : angle 2.05876 ( 8) covalent geometry : bond 0.00438 ( 5984) covalent geometry : angle 0.69117 ( 8131) *********************** 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 62 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.752 Fit side-chains REVERT: B 91 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (mtpt) REVERT: B 170 GLU cc_start: 0.7862 (tp30) cc_final: 0.7396 (tm-30) REVERT: B 184 TYR cc_start: 0.5907 (p90) cc_final: 0.5626 (p90) REVERT: A 156 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5519 (tm) REVERT: A 170 GLU cc_start: 0.6920 (tp30) cc_final: 0.6520 (tm-30) outliers start: 8 outliers final: 3 residues processed: 62 average time/residue: 0.1740 time to fit residues: 14.8326 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 : 0.662 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 37 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102348 restraints weight = 8683.382| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.23 r_work: 0.3179 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5999 Z= 0.130 Angle : 0.673 8.617 8172 Z= 0.318 Chirality : 0.045 0.265 913 Planarity : 0.006 0.054 1019 Dihedral : 17.344 112.096 1025 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.57 % Allowed : 11.02 % Favored : 87.40 % 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: 1.51 (0.33), residues: 689 helix: 2.53 (0.30), residues: 316 sheet: 0.95 (0.56), residues: 76 loop : -0.73 (0.36), residues: 297 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 0.011 0.001 PHE A 53 TYR 0.028 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 6) link_NAG-ASN : angle 2.00460 ( 18) link_BETA1-4 : bond 0.01072 ( 2) link_BETA1-4 : angle 1.54002 ( 6) link_ALPHA1-2 : bond 0.01294 ( 1) link_ALPHA1-2 : angle 2.37642 ( 3) link_ALPHA1-3 : bond 0.02047 ( 2) link_ALPHA1-3 : angle 4.75558 ( 6) hydrogen bonds : bond 0.04351 ( 247) hydrogen bonds : angle 3.71578 ( 774) SS BOND : bond 0.01016 ( 4) SS BOND : angle 1.99826 ( 8) covalent geometry : bond 0.00286 ( 5984) covalent geometry : angle 0.64907 ( 8131) *********************** 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 64 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8405 (mtmt) REVERT: B 170 GLU cc_start: 0.7861 (tp30) cc_final: 0.7390 (tm-30) REVERT: B 184 TYR cc_start: 0.5892 (p90) cc_final: 0.5591 (p90) REVERT: A 156 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5443 (tm) REVERT: A 161 CYS cc_start: 0.6564 (p) cc_final: 0.6228 (p) outliers start: 10 outliers final: 2 residues processed: 61 average time/residue: 0.2132 time to fit residues: 17.5593 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 : 0.640 ------------------------------------------------------------------------------- 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 343 MET Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** ** A 337 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 = 0.3756 r_free = 0.3756 target = 0.138282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103649 restraints weight = 8758.271| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.17 r_work: 0.3200 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5999 Z= 0.117 Angle : 0.647 8.256 8172 Z= 0.304 Chirality : 0.044 0.258 913 Planarity : 0.006 0.052 1019 Dihedral : 16.429 111.310 1021 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.42 % Allowed : 12.60 % Favored : 85.98 % 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: 1.67 (0.33), residues: 689 helix: 2.68 (0.30), residues: 315 sheet: 1.07 (0.56), residues: 76 loop : -0.66 (0.36), 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 0.011 0.001 PHE A 53 TYR 0.029 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 6) link_NAG-ASN : angle 2.03266 ( 18) link_BETA1-4 : bond 0.01076 ( 2) link_BETA1-4 : angle 1.59431 ( 6) link_ALPHA1-2 : bond 0.01253 ( 1) link_ALPHA1-2 : angle 2.22057 ( 3) link_ALPHA1-3 : bond 0.01942 ( 2) link_ALPHA1-3 : angle 4.89458 ( 6) hydrogen bonds : bond 0.03589 ( 247) hydrogen bonds : angle 3.56522 ( 774) SS BOND : bond 0.00521 ( 4) SS BOND : angle 1.58664 ( 8) covalent geometry : bond 0.00263 ( 5984) covalent geometry : angle 0.62249 ( 8131) *********************** 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 62 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8409 (mtmt) REVERT: B 156 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6689 (mm) REVERT: B 170 GLU cc_start: 0.7896 (tp30) cc_final: 0.7426 (tm-30) REVERT: B 184 TYR cc_start: 0.6054 (p90) cc_final: 0.5756 (p90) REVERT: B 373 MET cc_start: 0.6555 (tmm) cc_final: 0.6272 (tmm) REVERT: A 156 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5529 (tm) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.2024 time to fit residues: 16.7817 Evaluate side-chains 51 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 343 MET Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.137414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102868 restraints weight = 8675.288| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.15 r_work: 0.3189 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5999 Z= 0.122 Angle : 0.657 8.224 8172 Z= 0.307 Chirality : 0.044 0.300 913 Planarity : 0.006 0.051 1019 Dihedral : 15.811 112.451 1021 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.42 % Allowed : 14.02 % Favored : 84.57 % 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: 1.75 (0.33), residues: 689 helix: 2.71 (0.30), residues: 317 sheet: 1.08 (0.56), residues: 76 loop : -0.58 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS B 219 PHE 0.010 0.001 PHE A 53 TYR 0.029 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 2.05028 ( 18) link_BETA1-4 : bond 0.01030 ( 2) link_BETA1-4 : angle 1.74113 ( 6) link_ALPHA1-2 : bond 0.01177 ( 1) link_ALPHA1-2 : angle 2.04205 ( 3) link_ALPHA1-3 : bond 0.01859 ( 2) link_ALPHA1-3 : angle 4.94304 ( 6) hydrogen bonds : bond 0.03677 ( 247) hydrogen bonds : angle 3.51698 ( 774) SS BOND : bond 0.00476 ( 4) SS BOND : angle 2.15847 ( 8) covalent geometry : bond 0.00285 ( 5984) covalent geometry : angle 0.63050 ( 8131) *********************** 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 : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (mtmt) REVERT: B 156 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6698 (mm) REVERT: B 170 GLU cc_start: 0.8030 (tp30) cc_final: 0.7547 (tm-30) REVERT: B 373 MET cc_start: 0.6691 (tmm) cc_final: 0.6396 (tmm) REVERT: A 170 GLU cc_start: 0.6817 (tp30) cc_final: 0.6374 (tm-30) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.1725 time to fit residues: 13.1426 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 94 ASN Chi-restraints excluded: chain A residue 156 LEU 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: 1.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100750 restraints weight = 8706.805| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.15 r_work: 0.3159 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5999 Z= 0.139 Angle : 0.667 8.259 8172 Z= 0.312 Chirality : 0.044 0.285 913 Planarity : 0.006 0.066 1019 Dihedral : 15.249 112.638 1021 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 14.33 % 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: 1.64 (0.34), residues: 689 helix: 2.67 (0.30), residues: 317 sheet: 0.89 (0.56), residues: 76 loop : -0.65 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.002 0.001 HIS A 314 PHE 0.010 0.001 PHE A 356 TYR 0.028 0.001 TYR A 184 ARG 0.002 0.000 ARG A 332 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 6) link_NAG-ASN : angle 1.89874 ( 18) link_BETA1-4 : bond 0.01036 ( 2) link_BETA1-4 : angle 2.00408 ( 6) link_ALPHA1-2 : bond 0.01163 ( 1) link_ALPHA1-2 : angle 1.88764 ( 3) link_ALPHA1-3 : bond 0.01756 ( 2) link_ALPHA1-3 : angle 4.98378 ( 6) hydrogen bonds : bond 0.04252 ( 247) hydrogen bonds : angle 3.53717 ( 774) SS BOND : bond 0.00534 ( 4) SS BOND : angle 1.96241 ( 8) covalent geometry : bond 0.00334 ( 5984) covalent geometry : angle 0.64210 ( 8131) *********************** 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 63 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8373 (mtmt) REVERT: B 156 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6800 (mm) REVERT: B 170 GLU cc_start: 0.8037 (tp30) cc_final: 0.7550 (tm-30) REVERT: B 347 CYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5453 (t) REVERT: B 373 MET cc_start: 0.6655 (tmm) cc_final: 0.6449 (tmm) REVERT: A 170 GLU cc_start: 0.6824 (tp30) cc_final: 0.6376 (tm-30) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.1799 time to fit residues: 14.8677 Evaluate side-chains 52 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 B residue 347 CYS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.3749 r_free = 0.3749 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102990 restraints weight = 8727.509| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.15 r_work: 0.3189 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5999 Z= 0.115 Angle : 0.658 8.212 8172 Z= 0.304 Chirality : 0.043 0.284 913 Planarity : 0.006 0.058 1019 Dihedral : 14.948 112.952 1021 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.57 % Allowed : 15.43 % Favored : 82.99 % 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: 1.71 (0.34), residues: 689 helix: 2.69 (0.30), residues: 317 sheet: 1.02 (0.56), residues: 76 loop : -0.62 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.003 0.001 HIS B 337 PHE 0.009 0.001 PHE A 164 TYR 0.024 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 6) link_NAG-ASN : angle 1.79753 ( 18) link_BETA1-4 : bond 0.01014 ( 2) link_BETA1-4 : angle 1.83956 ( 6) link_ALPHA1-2 : bond 0.01264 ( 1) link_ALPHA1-2 : angle 1.78337 ( 3) link_ALPHA1-3 : bond 0.01601 ( 2) link_ALPHA1-3 : angle 5.06115 ( 6) hydrogen bonds : bond 0.03363 ( 247) hydrogen bonds : angle 3.46257 ( 774) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.45887 ( 8) covalent geometry : bond 0.00263 ( 5984) covalent geometry : angle 0.63477 ( 8131) *********************** 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 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8345 (mtmt) REVERT: B 156 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6727 (mm) REVERT: B 166 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7822 (pt0) REVERT: B 170 GLU cc_start: 0.8057 (tp30) cc_final: 0.7578 (tm-30) REVERT: B 347 CYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5367 (t) REVERT: A 170 GLU cc_start: 0.6919 (tp30) cc_final: 0.6445 (tm-30) REVERT: A 178 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7901 (mm-40) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.1847 time to fit residues: 14.1507 Evaluate side-chains 56 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 B residue 347 CYS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.3737 r_free = 0.3737 target = 0.136477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101496 restraints weight = 8647.778| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.20 r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5999 Z= 0.125 Angle : 0.669 8.804 8172 Z= 0.308 Chirality : 0.044 0.274 913 Planarity : 0.006 0.055 1019 Dihedral : 14.659 113.191 1021 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 15.28 % Favored : 82.99 % 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: 2.71 (0.30), residues: 317 sheet: 0.98 (0.57), residues: 76 loop : -0.64 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.003 0.001 HIS B 270 PHE 0.010 0.001 PHE A 356 TYR 0.021 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 1.77082 ( 18) link_BETA1-4 : bond 0.00924 ( 2) link_BETA1-4 : angle 1.91221 ( 6) link_ALPHA1-2 : bond 0.01110 ( 1) link_ALPHA1-2 : angle 1.65982 ( 3) link_ALPHA1-3 : bond 0.01518 ( 2) link_ALPHA1-3 : angle 4.99038 ( 6) hydrogen bonds : bond 0.03714 ( 247) hydrogen bonds : angle 3.43505 ( 774) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.55761 ( 8) covalent geometry : bond 0.00296 ( 5984) covalent geometry : angle 0.64697 ( 8131) *********************** 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 61 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8293 (mtmt) REVERT: B 156 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6780 (mm) REVERT: B 166 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7838 (pt0) REVERT: B 170 GLU cc_start: 0.8070 (tp30) cc_final: 0.7587 (tm-30) REVERT: A 170 GLU cc_start: 0.6847 (tp30) cc_final: 0.6391 (tm-30) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.1806 time to fit residues: 13.9486 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 : 0.684 ------------------------------------------------------------------------------- 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 B residue 347 CYS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.135221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100352 restraints weight = 8735.214| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.16 r_work: 0.3147 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5999 Z= 0.142 Angle : 0.690 8.181 8172 Z= 0.322 Chirality : 0.044 0.269 913 Planarity : 0.006 0.055 1019 Dihedral : 14.335 113.059 1021 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.42 % Allowed : 15.28 % Favored : 83.31 % 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: 1.59 (0.34), residues: 689 helix: 2.68 (0.30), residues: 315 sheet: 0.86 (0.57), residues: 76 loop : -0.74 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 226 HIS 0.003 0.001 HIS B 219 PHE 0.010 0.001 PHE B 158 TYR 0.021 0.001 TYR A 184 ARG 0.002 0.000 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 1.70578 ( 18) link_BETA1-4 : bond 0.00907 ( 2) link_BETA1-4 : angle 2.05195 ( 6) link_ALPHA1-2 : bond 0.01065 ( 1) link_ALPHA1-2 : angle 1.52800 ( 3) link_ALPHA1-3 : bond 0.01438 ( 2) link_ALPHA1-3 : angle 4.88891 ( 6) hydrogen bonds : bond 0.04223 ( 247) hydrogen bonds : angle 3.49620 ( 774) SS BOND : bond 0.00436 ( 4) SS BOND : angle 1.66410 ( 8) covalent geometry : bond 0.00344 ( 5984) covalent geometry : angle 0.66943 ( 8131) *********************** 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 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (mtmt) REVERT: B 156 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6999 (mm) REVERT: B 166 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7851 (pt0) REVERT: B 170 GLU cc_start: 0.8077 (tp30) cc_final: 0.7592 (tm-30) REVERT: A 170 GLU cc_start: 0.6900 (tp30) cc_final: 0.6436 (tm-30) REVERT: A 178 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7919 (mm-40) REVERT: A 184 TYR cc_start: 0.5340 (p90) cc_final: 0.5006 (p90) REVERT: A 373 MET cc_start: 0.7050 (tmm) cc_final: 0.6720 (tmm) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.1723 time to fit residues: 13.2879 Evaluate side-chains 56 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 B residue 347 CYS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.3740 r_free = 0.3740 target = 0.136857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102238 restraints weight = 8724.431| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.14 r_work: 0.3179 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5999 Z= 0.119 Angle : 0.678 11.417 8172 Z= 0.310 Chirality : 0.043 0.265 913 Planarity : 0.006 0.054 1019 Dihedral : 13.978 112.750 1021 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.10 % Allowed : 15.59 % Favored : 83.31 % 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: 2.69 (0.30), residues: 317 sheet: 1.00 (0.57), residues: 76 loop : -0.62 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.007 0.001 PHE A 164 TYR 0.018 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 6) link_NAG-ASN : angle 1.69874 ( 18) link_BETA1-4 : bond 0.00800 ( 2) link_BETA1-4 : angle 1.84812 ( 6) link_ALPHA1-2 : bond 0.01081 ( 1) link_ALPHA1-2 : angle 1.47535 ( 3) link_ALPHA1-3 : bond 0.01365 ( 2) link_ALPHA1-3 : angle 5.04867 ( 6) hydrogen bonds : bond 0.03368 ( 247) hydrogen bonds : angle 3.36759 ( 774) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.37872 ( 8) covalent geometry : bond 0.00279 ( 5984) covalent geometry : angle 0.65711 ( 8131) ********************** 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 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6754 (mm) REVERT: B 166 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7842 (pt0) REVERT: B 170 GLU cc_start: 0.8075 (tp30) cc_final: 0.7590 (tm-30) REVERT: A 170 GLU cc_start: 0.6884 (tp30) cc_final: 0.6425 (tm-30) REVERT: A 178 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 184 TYR cc_start: 0.5683 (p90) cc_final: 0.5372 (p90) REVERT: A 373 MET cc_start: 0.7058 (tmm) cc_final: 0.6753 (tmm) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.1752 time to fit residues: 13.8417 Evaluate side-chains 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 275 THR 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: 0.9980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099458 restraints weight = 8816.771| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.17 r_work: 0.3135 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5999 Z= 0.161 Angle : 0.715 10.596 8172 Z= 0.331 Chirality : 0.044 0.257 913 Planarity : 0.006 0.057 1019 Dihedral : 13.748 115.714 1017 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.26 % Allowed : 15.75 % Favored : 82.99 % 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 (0.34), residues: 689 helix: 2.65 (0.31), residues: 315 sheet: 0.79 (0.57), residues: 76 loop : -0.79 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 226 HIS 0.003 0.001 HIS B 219 PHE 0.011 0.001 PHE A 356 TYR 0.018 0.001 TYR A 184 ARG 0.001 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 6) link_NAG-ASN : angle 2.51717 ( 18) link_BETA1-4 : bond 0.00838 ( 2) link_BETA1-4 : angle 2.02639 ( 6) link_ALPHA1-2 : bond 0.01015 ( 1) link_ALPHA1-2 : angle 1.43274 ( 3) link_ALPHA1-3 : bond 0.01485 ( 2) link_ALPHA1-3 : angle 5.04546 ( 6) hydrogen bonds : bond 0.04550 ( 247) hydrogen bonds : angle 3.51524 ( 774) SS BOND : bond 0.00424 ( 4) SS BOND : angle 1.77138 ( 8) covalent geometry : bond 0.00397 ( 5984) covalent geometry : angle 0.68825 ( 8131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.55 seconds wall clock time: 51 minutes 32.98 seconds (3092.98 seconds total)