Starting phenix.real_space_refine on Sat May 10 09:17:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj4_38393/05_2025/8xj4_38393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj4_38393/05_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_38393/05_2025/8xj4_38393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj4_38393/05_2025/8xj4_38393.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj4_38393/05_2025/8xj4_38393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj4_38393/05_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-5687/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: 1.62 Conformation dependent library (CDL) restraints added in 859.8 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: 0.67 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: 1.62 Time building geometry restraints manager: 1.85 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: 0.350 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- 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 : 0.682 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: 0.1810 time to fit residues: 20.7124 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 : 0.680 ------------------------------------------------------------------------------- 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 = 0.100652 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 2.43137 ( 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 : 0.692 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: 0.5908 (p90) cc_final: 0.5627 (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: 0.1755 time to fit residues: 14.9963 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 : 0.643 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.136032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100718 restraints weight = 8706.076| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.24 r_work: 0.3155 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5999 Z= 0.151 Angle : 0.698 10.602 8172 Z= 0.332 Chirality : 0.046 0.272 913 Planarity : 0.006 0.055 1019 Dihedral : 17.228 111.874 1025 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: 1.42 (0.33), residues: 689 helix: 2.50 (0.30), residues: 316 sheet: 0.84 (0.56), residues: 76 loop : -0.80 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS A 78 PHE 0.012 0.001 PHE A 158 TYR 0.027 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 1.83353 ( 18) link_BETA1-4 : bond 0.01035 ( 2) link_BETA1-4 : angle 1.67998 ( 6) link_ALPHA1-2 : bond 0.01228 ( 1) link_ALPHA1-2 : angle 2.35486 ( 3) link_ALPHA1-3 : bond 0.02042 ( 2) link_ALPHA1-3 : angle 4.70502 ( 6) hydrogen bonds : bond 0.04853 ( 247) hydrogen bonds : angle 3.77303 ( 774) SS BOND : bond 0.00693 ( 4) SS BOND : angle 2.23022 ( 8) covalent geometry : bond 0.00355 ( 5984) covalent geometry : angle 0.67598 ( 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: 12 poor density : 52 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 170 GLU cc_start: 0.7863 (tp30) cc_final: 0.7392 (tm-30) REVERT: B 373 MET cc_start: 0.6851 (tmm) cc_final: 0.6533 (tmm) REVERT: A 156 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5482 (tm) REVERT: A 161 CYS cc_start: 0.6175 (p) cc_final: 0.5970 (p) outliers start: 12 outliers final: 4 residues processed: 61 average time/residue: 0.1666 time to fit residues: 13.9924 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 : 0.636 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** ** A 337 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 = 0.3736 r_free = 0.3736 target = 0.136545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101585 restraints weight = 8793.270| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.19 r_work: 0.3170 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5999 Z= 0.133 Angle : 0.664 8.376 8172 Z= 0.314 Chirality : 0.045 0.296 913 Planarity : 0.006 0.053 1019 Dihedral : 16.297 110.736 1021 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.73 % Allowed : 12.60 % Favored : 85.67 % 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: 1.49 (0.33), residues: 689 helix: 2.63 (0.30), residues: 315 sheet: 0.75 (0.56), residues: 76 loop : -0.80 (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 0.00294 ( 6) link_NAG-ASN : angle 2.07846 ( 18) link_BETA1-4 : bond 0.01079 ( 2) link_BETA1-4 : angle 1.79506 ( 6) link_ALPHA1-2 : bond 0.01123 ( 1) link_ALPHA1-2 : angle 2.16559 ( 3) link_ALPHA1-3 : bond 0.01975 ( 2) link_ALPHA1-3 : angle 4.89519 ( 6) hydrogen bonds : bond 0.04076 ( 247) hydrogen bonds : angle 3.61862 ( 774) SS BOND : bond 0.00567 ( 4) SS BOND : angle 1.67218 ( 8) covalent geometry : bond 0.00314 ( 5984) covalent geometry : angle 0.64004 ( 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 64 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8376 (mtmt) REVERT: B 156 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6664 (mm) REVERT: B 170 GLU cc_start: 0.7901 (tp30) cc_final: 0.7424 (tm-30) REVERT: A 156 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5474 (tm) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.1818 time to fit residues: 15.0445 Evaluate side-chains 51 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 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: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.134676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099849 restraints weight = 8695.084| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.15 r_work: 0.3144 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5999 Z= 0.150 Angle : 0.685 8.530 8172 Z= 0.322 Chirality : 0.045 0.305 913 Planarity : 0.006 0.051 1019 Dihedral : 15.807 111.679 1021 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.20 % Allowed : 13.70 % Favored : 84.09 % 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: 1.49 (0.33), residues: 689 helix: 2.65 (0.30), residues: 315 sheet: 0.67 (0.56), residues: 76 loop : -0.81 (0.36), 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 0.028 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 6) link_NAG-ASN : angle 2.08984 ( 18) link_BETA1-4 : bond 0.01077 ( 2) link_BETA1-4 : angle 2.01583 ( 6) link_ALPHA1-2 : bond 0.01156 ( 1) link_ALPHA1-2 : angle 2.01927 ( 3) link_ALPHA1-3 : bond 0.01971 ( 2) link_ALPHA1-3 : angle 4.93599 ( 6) hydrogen bonds : bond 0.04519 ( 247) hydrogen bonds : angle 3.62342 ( 774) SS BOND : bond 0.00322 ( 4) SS BOND : angle 2.12140 ( 8) covalent geometry : bond 0.00364 ( 5984) covalent geometry : angle 0.65915 ( 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 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8390 (mtmt) REVERT: B 156 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6806 (mm) REVERT: B 170 GLU cc_start: 0.7948 (tp30) cc_final: 0.7478 (tm-30) REVERT: A 156 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.5611 (tm) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 0.1638 time to fit residues: 12.5590 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 343 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103787 restraints weight = 8637.710| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.15 r_work: 0.3200 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5999 Z= 0.107 Angle : 0.636 8.257 8172 Z= 0.296 Chirality : 0.043 0.290 913 Planarity : 0.006 0.048 1019 Dihedral : 15.335 112.779 1021 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.94 % Allowed : 15.12 % 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: 1.67 (0.34), residues: 689 helix: 2.70 (0.31), residues: 317 sheet: 0.86 (0.56), residues: 76 loop : -0.64 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 226 HIS 0.003 0.001 HIS A 78 PHE 0.009 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 0.00394 ( 6) link_NAG-ASN : angle 1.88208 ( 18) link_BETA1-4 : bond 0.01047 ( 2) link_BETA1-4 : angle 1.74197 ( 6) link_ALPHA1-2 : bond 0.01232 ( 1) link_ALPHA1-2 : angle 1.87483 ( 3) link_ALPHA1-3 : bond 0.01642 ( 2) link_ALPHA1-3 : angle 5.10955 ( 6) hydrogen bonds : bond 0.03014 ( 247) hydrogen bonds : angle 3.42001 ( 774) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.61420 ( 8) covalent geometry : bond 0.00233 ( 5984) covalent geometry : angle 0.61131 ( 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 61 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8395 (mtmt) REVERT: B 170 GLU cc_start: 0.8061 (tp30) cc_final: 0.7579 (tm-30) REVERT: A 170 GLU cc_start: 0.6905 (tp30) cc_final: 0.6446 (tm-30) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.1816 time to fit residues: 14.2329 Evaluate side-chains 51 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.0060 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103414 restraints weight = 8722.146| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.15 r_work: 0.3193 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2200 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= 0.112 Angle : 0.657 8.239 8172 Z= 0.302 Chirality : 0.043 0.280 913 Planarity : 0.005 0.047 1019 Dihedral : 14.885 113.237 1021 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 1.77 (0.34), residues: 689 helix: 2.72 (0.31), residues: 319 sheet: 1.03 (0.57), residues: 76 loop : -0.57 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.003 0.001 HIS A 78 PHE 0.007 0.001 PHE A 53 TYR 0.024 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 6) link_NAG-ASN : angle 1.84163 ( 18) link_BETA1-4 : bond 0.01026 ( 2) link_BETA1-4 : angle 1.78654 ( 6) link_ALPHA1-2 : bond 0.01200 ( 1) link_ALPHA1-2 : angle 1.78058 ( 3) link_ALPHA1-3 : bond 0.01521 ( 2) link_ALPHA1-3 : angle 5.06183 ( 6) hydrogen bonds : bond 0.03147 ( 247) hydrogen bonds : angle 3.41048 ( 774) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.70201 ( 8) covalent geometry : bond 0.00253 ( 5984) covalent geometry : angle 0.63349 ( 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 : 0.628 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (mtmt) REVERT: B 156 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6635 (mm) REVERT: B 166 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7847 (pt0) REVERT: B 170 GLU cc_start: 0.8079 (tp30) cc_final: 0.7594 (tm-30) REVERT: A 170 GLU cc_start: 0.6908 (tp30) cc_final: 0.6441 (tm-30) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.1777 time to fit residues: 13.5199 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.136764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102208 restraints weight = 8616.954| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.14 r_work: 0.3177 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5999 Z= 0.121 Angle : 0.669 8.772 8172 Z= 0.306 Chirality : 0.044 0.281 913 Planarity : 0.006 0.049 1019 Dihedral : 14.861 118.148 1021 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.57 % Allowed : 16.06 % 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: 1.71 (0.34), residues: 689 helix: 2.69 (0.31), residues: 319 sheet: 0.98 (0.57), residues: 76 loop : -0.62 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.011 0.001 PHE A 356 TYR 0.023 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 2.52848 ( 18) link_BETA1-4 : bond 0.00944 ( 2) link_BETA1-4 : angle 1.90526 ( 6) link_ALPHA1-2 : bond 0.01136 ( 1) link_ALPHA1-2 : angle 1.66003 ( 3) link_ALPHA1-3 : bond 0.01483 ( 2) link_ALPHA1-3 : angle 4.99201 ( 6) hydrogen bonds : bond 0.03523 ( 247) hydrogen bonds : angle 3.40066 ( 774) SS BOND : bond 0.00388 ( 4) SS BOND : angle 1.64980 ( 8) covalent geometry : bond 0.00286 ( 5984) covalent geometry : angle 0.64134 ( 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 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8405 (mtmt) REVERT: B 156 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6703 (mm) REVERT: B 166 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7845 (pt0) REVERT: B 170 GLU cc_start: 0.8075 (tp30) cc_final: 0.7589 (tm-30) REVERT: A 170 GLU cc_start: 0.6919 (tp30) cc_final: 0.6449 (tm-30) REVERT: A 178 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7903 (mm-40) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.1903 time to fit residues: 14.7229 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 : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR 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 275 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 66 optimal weight: 0.0970 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101702 restraints weight = 8714.629| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.15 r_work: 0.3169 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5999 Z= 0.128 Angle : 0.685 12.076 8172 Z= 0.314 Chirality : 0.045 0.420 913 Planarity : 0.006 0.050 1019 Dihedral : 13.100 113.083 1021 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.26 % Allowed : 16.38 % 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: 1.68 (0.34), residues: 689 helix: 2.66 (0.31), residues: 319 sheet: 0.98 (0.57), residues: 76 loop : -0.64 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.008 0.001 PHE A 164 TYR 0.023 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 6) link_NAG-ASN : angle 3.35222 ( 18) link_BETA1-4 : bond 0.00906 ( 2) link_BETA1-4 : angle 1.94045 ( 6) link_ALPHA1-2 : bond 0.01076 ( 1) link_ALPHA1-2 : angle 1.57632 ( 3) link_ALPHA1-3 : bond 0.01423 ( 2) link_ALPHA1-3 : angle 4.97654 ( 6) hydrogen bonds : bond 0.03669 ( 247) hydrogen bonds : angle 3.41307 ( 774) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.58565 ( 8) covalent geometry : bond 0.00308 ( 5984) covalent geometry : angle 0.65032 ( 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 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (mtmt) REVERT: B 156 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6723 (mm) REVERT: B 166 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7848 (pt0) REVERT: B 170 GLU cc_start: 0.8073 (tp30) cc_final: 0.7587 (tm-30) REVERT: A 170 GLU cc_start: 0.6843 (tp30) cc_final: 0.6393 (tm-30) REVERT: A 178 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7909 (mm-40) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1851 time to fit residues: 14.0704 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR 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 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 48 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.136724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102207 restraints weight = 8719.859| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.15 r_work: 0.3167 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2408 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= 0.121 Angle : 0.688 10.851 8172 Z= 0.313 Chirality : 0.045 0.423 913 Planarity : 0.005 0.050 1019 Dihedral : 12.862 112.952 1021 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.94 % Allowed : 16.69 % 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: 1.69 (0.34), residues: 689 helix: 2.66 (0.31), residues: 319 sheet: 1.01 (0.57), residues: 76 loop : -0.63 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.008 0.001 PHE A 164 TYR 0.023 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 6) link_NAG-ASN : angle 3.33441 ( 18) link_BETA1-4 : bond 0.00898 ( 2) link_BETA1-4 : angle 1.86657 ( 6) link_ALPHA1-2 : bond 0.01066 ( 1) link_ALPHA1-2 : angle 1.51797 ( 3) link_ALPHA1-3 : bond 0.01399 ( 2) link_ALPHA1-3 : angle 5.01416 ( 6) hydrogen bonds : bond 0.03480 ( 247) hydrogen bonds : angle 3.39122 ( 774) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.51516 ( 8) covalent geometry : bond 0.00286 ( 5984) covalent geometry : angle 0.65305 ( 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 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6630 (mm) REVERT: B 166 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7847 (pt0) REVERT: B 170 GLU cc_start: 0.8076 (tp30) cc_final: 0.7590 (tm-30) REVERT: A 170 GLU cc_start: 0.6838 (tp30) cc_final: 0.6390 (tm-30) REVERT: A 178 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7910 (mm-40) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1566 time to fit residues: 11.9574 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR 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 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: 3.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.137004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102607 restraints weight = 8787.419| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.16 r_work: 0.3182 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5999 Z= 0.118 Angle : 0.678 10.238 8172 Z= 0.310 Chirality : 0.044 0.407 913 Planarity : 0.005 0.053 1019 Dihedral : 12.282 112.612 1017 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 16.38 % 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: 1.71 (0.34), residues: 689 helix: 2.68 (0.31), residues: 319 sheet: 1.09 (0.58), residues: 76 loop : -0.65 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.008 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 0.00528 ( 6) link_NAG-ASN : angle 3.07180 ( 18) link_BETA1-4 : bond 0.00848 ( 2) link_BETA1-4 : angle 1.77803 ( 6) link_ALPHA1-2 : bond 0.01071 ( 1) link_ALPHA1-2 : angle 1.45513 ( 3) link_ALPHA1-3 : bond 0.01366 ( 2) link_ALPHA1-3 : angle 5.07118 ( 6) hydrogen bonds : bond 0.03336 ( 247) hydrogen bonds : angle 3.37258 ( 774) SS BOND : bond 0.00418 ( 4) SS BOND : angle 1.47436 ( 8) covalent geometry : bond 0.00278 ( 5984) covalent geometry : angle 0.64558 ( 8131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.36 seconds wall clock time: 46 minutes 26.46 seconds (2786.46 seconds total)