Starting phenix.real_space_refine on Wed Sep 17 06:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj4_38393/09_2025/8xj4_38393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj4_38393/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xj4_38393/09_2025/8xj4_38393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj4_38393/09_2025/8xj4_38393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xj4_38393/09_2025/8xj4_38393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj4_38393/09_2025/8xj4_38393.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.85, per 1000 atoms: 0.32 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: 0.40 Conformation dependent library (CDL) restraints added in 196.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 0.72 Time building geometry restraints manager: 0.53 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 401) selection = (chain 'B' and resid 32 through 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: 0.520 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 105 TYR 0.016 0.001 TYR A 319 PHE 0.012 0.002 PHE A 356 TRP 0.022 0.002 TRP B 206 HIS 0.005 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 5984) covalent geometry : angle 0.79706 ( 8131) SS BOND : bond 0.00221 ( 4) SS BOND : angle 3.60370 ( 8) hydrogen bonds : bond 0.17343 ( 247) hydrogen bonds : angle 5.02086 ( 774) 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) link_BETA1-4 : bond 0.01666 ( 2) link_BETA1-4 : angle 2.76796 ( 6) link_NAG-ASN : bond 0.00426 ( 6) link_NAG-ASN : angle 3.29910 ( 18) *********************** 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 : 0.237 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: 0.0832 time to fit residues: 9.4581 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 : 0.231 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102104 restraints weight = 8653.157| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.23 r_work: 0.3173 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1160 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= 0.155 Angle : 0.701 8.996 8172 Z= 0.335 Chirality : 0.045 0.177 913 Planarity : 0.006 0.061 1019 Dihedral : 17.855 110.795 1025 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.26 % Allowed : 7.87 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.33), residues: 689 helix: 2.35 (0.30), residues: 315 sheet: 0.91 (0.54), residues: 76 loop : -0.78 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.021 0.001 TYR A 184 PHE 0.013 0.002 PHE A 124 TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5984) covalent geometry : angle 0.67297 ( 8131) SS BOND : bond 0.00461 ( 4) SS BOND : angle 2.08134 ( 8) hydrogen bonds : bond 0.05135 ( 247) hydrogen bonds : angle 3.92683 ( 774) link_ALPHA1-2 : bond 0.01390 ( 1) link_ALPHA1-2 : angle 2.53599 ( 3) link_ALPHA1-3 : bond 0.02021 ( 2) link_ALPHA1-3 : angle 5.06840 ( 6) link_BETA1-4 : bond 0.00910 ( 2) link_BETA1-4 : angle 1.52952 ( 6) link_NAG-ASN : bond 0.00296 ( 6) link_NAG-ASN : angle 2.42903 ( 18) *********************** 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 67 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.245 Fit side-chains REVERT: B 91 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8546 (mtpt) REVERT: B 170 GLU cc_start: 0.7842 (tp30) cc_final: 0.7372 (tm-30) REVERT: B 184 TYR cc_start: 0.6073 (p90) cc_final: 0.5772 (p90) REVERT: A 156 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5298 (tm) REVERT: A 170 GLU cc_start: 0.6943 (tp30) cc_final: 0.6553 (tm-30) outliers start: 8 outliers final: 2 residues processed: 66 average time/residue: 0.0694 time to fit residues: 6.2756 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS 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 50 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.137414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102616 restraints weight = 8657.974| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.23 r_work: 0.3184 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1476 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= 0.132 Angle : 0.677 9.280 8172 Z= 0.320 Chirality : 0.045 0.267 913 Planarity : 0.006 0.055 1019 Dihedral : 17.114 112.381 1023 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 11.34 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.33), residues: 689 helix: 2.61 (0.30), residues: 316 sheet: 1.08 (0.56), residues: 76 loop : -0.70 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.028 0.001 TYR A 184 PHE 0.011 0.001 PHE A 53 TRP 0.013 0.001 TRP A 368 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5984) covalent geometry : angle 0.65304 ( 8131) SS BOND : bond 0.01029 ( 4) SS BOND : angle 2.14867 ( 8) hydrogen bonds : bond 0.04240 ( 247) hydrogen bonds : angle 3.67146 ( 774) link_ALPHA1-2 : bond 0.01230 ( 1) link_ALPHA1-2 : angle 2.28177 ( 3) link_ALPHA1-3 : bond 0.02028 ( 2) link_ALPHA1-3 : angle 4.70017 ( 6) link_BETA1-4 : bond 0.01045 ( 2) link_BETA1-4 : angle 1.54284 ( 6) link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 2.10354 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8375 (mtmt) REVERT: B 170 GLU cc_start: 0.7858 (tp30) cc_final: 0.7387 (tm-30) REVERT: B 184 TYR cc_start: 0.5815 (p90) cc_final: 0.5505 (p90) REVERT: B 373 MET cc_start: 0.6728 (tmm) cc_final: 0.6376 (tmm) REVERT: A 156 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5453 (tm) outliers start: 10 outliers final: 2 residues processed: 60 average time/residue: 0.0797 time to fit residues: 6.4903 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 : 0.229 ------------------------------------------------------------------------------- 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 21 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.131450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096198 restraints weight = 8787.166| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.16 r_work: 0.3086 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5999 Z= 0.240 Angle : 0.771 9.476 8172 Z= 0.371 Chirality : 0.049 0.282 913 Planarity : 0.007 0.065 1019 Dihedral : 16.381 110.734 1021 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.33), residues: 689 helix: 2.40 (0.30), residues: 316 sheet: 0.49 (0.55), residues: 76 loop : -1.00 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.027 0.002 TYR A 184 PHE 0.019 0.002 PHE A 158 TRP 0.010 0.001 TRP B 206 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 5984) covalent geometry : angle 0.74700 ( 8131) SS BOND : bond 0.00712 ( 4) SS BOND : angle 2.34342 ( 8) hydrogen bonds : bond 0.06512 ( 247) hydrogen bonds : angle 3.98054 ( 774) link_ALPHA1-2 : bond 0.01133 ( 1) link_ALPHA1-2 : angle 2.25282 ( 3) link_ALPHA1-3 : bond 0.02165 ( 2) link_ALPHA1-3 : angle 4.78875 ( 6) link_BETA1-4 : bond 0.01185 ( 2) link_BETA1-4 : angle 2.28814 ( 6) link_NAG-ASN : bond 0.00553 ( 6) link_NAG-ASN : angle 2.30589 ( 18) *********************** 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 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.7928 (tp30) cc_final: 0.7430 (tm-30) REVERT: A 170 GLU cc_start: 0.6853 (tp30) cc_final: 0.6420 (tm-30) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.0804 time to fit residues: 6.2284 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.133801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098786 restraints weight = 8846.236| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.18 r_work: 0.3125 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2030 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= 0.156 Angle : 0.690 8.682 8172 Z= 0.326 Chirality : 0.046 0.318 913 Planarity : 0.006 0.054 1019 Dihedral : 16.007 110.915 1021 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 14.49 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.33), residues: 689 helix: 2.53 (0.30), residues: 315 sheet: 0.39 (0.55), residues: 76 loop : -0.93 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.028 0.001 TYR A 184 PHE 0.012 0.001 PHE A 53 TRP 0.009 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5984) covalent geometry : angle 0.66480 ( 8131) SS BOND : bond 0.00492 ( 4) SS BOND : angle 1.84333 ( 8) hydrogen bonds : bond 0.04642 ( 247) hydrogen bonds : angle 3.71484 ( 774) link_ALPHA1-2 : bond 0.01048 ( 1) link_ALPHA1-2 : angle 1.99121 ( 3) link_ALPHA1-3 : bond 0.02097 ( 2) link_ALPHA1-3 : angle 4.98617 ( 6) link_BETA1-4 : bond 0.01090 ( 2) link_BETA1-4 : angle 2.09180 ( 6) link_NAG-ASN : bond 0.00313 ( 6) link_NAG-ASN : angle 2.07110 ( 18) *********************** 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: 12 poor density : 47 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7010 (mm) REVERT: B 170 GLU cc_start: 0.7914 (tp30) cc_final: 0.7430 (tm-30) REVERT: A 156 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.5640 (tm) REVERT: A 170 GLU cc_start: 0.6851 (tp30) cc_final: 0.6368 (tm-30) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.0844 time to fit residues: 6.1122 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 181 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 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.0020 chunk 12 optimal weight: 0.0000 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.138688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104254 restraints weight = 8709.430| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.16 r_work: 0.3208 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5999 Z= 0.108 Angle : 0.646 8.269 8172 Z= 0.301 Chirality : 0.043 0.292 913 Planarity : 0.006 0.048 1019 Dihedral : 15.410 113.001 1021 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 16.22 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.34), residues: 689 helix: 2.67 (0.31), residues: 317 sheet: 0.82 (0.56), residues: 76 loop : -0.66 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.029 0.001 TYR A 184 PHE 0.009 0.001 PHE A 53 TRP 0.011 0.001 TRP B 226 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 5984) covalent geometry : angle 0.62167 ( 8131) SS BOND : bond 0.00542 ( 4) SS BOND : angle 1.47869 ( 8) hydrogen bonds : bond 0.02781 ( 247) hydrogen bonds : angle 3.46933 ( 774) link_ALPHA1-2 : bond 0.01188 ( 1) link_ALPHA1-2 : angle 1.85232 ( 3) link_ALPHA1-3 : bond 0.01675 ( 2) link_ALPHA1-3 : angle 5.16750 ( 6) link_BETA1-4 : bond 0.01010 ( 2) link_BETA1-4 : angle 1.69696 ( 6) link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 1.93334 ( 18) *********************** 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 60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8072 (tp30) cc_final: 0.7586 (tm-30) REVERT: A 170 GLU cc_start: 0.6852 (tp30) cc_final: 0.6402 (tm-30) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.0798 time to fit residues: 6.1939 Evaluate side-chains 48 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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** 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 = 0.3736 r_free = 0.3736 target = 0.136416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101760 restraints weight = 8783.541| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.18 r_work: 0.3171 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5999 Z= 0.120 Angle : 0.660 8.276 8172 Z= 0.305 Chirality : 0.044 0.283 913 Planarity : 0.006 0.049 1019 Dihedral : 15.017 113.211 1017 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.42 % Allowed : 16.54 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.34), residues: 689 helix: 2.67 (0.31), residues: 317 sheet: 0.90 (0.57), residues: 76 loop : -0.63 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.026 0.001 TYR A 184 PHE 0.009 0.001 PHE B 158 TRP 0.010 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5984) covalent geometry : angle 0.63581 ( 8131) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.70505 ( 8) hydrogen bonds : bond 0.03488 ( 247) hydrogen bonds : angle 3.45430 ( 774) link_ALPHA1-2 : bond 0.01001 ( 1) link_ALPHA1-2 : angle 1.73113 ( 3) link_ALPHA1-3 : bond 0.01590 ( 2) link_ALPHA1-3 : angle 5.09150 ( 6) link_BETA1-4 : bond 0.01025 ( 2) link_BETA1-4 : angle 1.87895 ( 6) link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 1.87065 ( 18) *********************** 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 61 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6539 (mm) REVERT: B 166 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7820 (pt0) REVERT: B 170 GLU cc_start: 0.8067 (tp30) cc_final: 0.7577 (tm-30) REVERT: A 170 GLU cc_start: 0.6865 (tp30) cc_final: 0.6407 (tm-30) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.0677 time to fit residues: 5.4541 Evaluate side-chains 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain A residue 275 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN A 160 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098383 restraints weight = 8745.616| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.14 r_work: 0.3120 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2354 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= 0.163 Angle : 0.717 8.864 8172 Z= 0.335 Chirality : 0.045 0.278 913 Planarity : 0.006 0.055 1019 Dihedral : 14.805 112.436 1017 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.57 % Allowed : 16.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.34), residues: 689 helix: 2.60 (0.31), residues: 315 sheet: 0.62 (0.56), residues: 76 loop : -0.86 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.024 0.001 TYR A 184 PHE 0.014 0.002 PHE A 356 TRP 0.016 0.001 TRP B 226 HIS 0.003 0.001 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5984) covalent geometry : angle 0.69492 ( 8131) SS BOND : bond 0.00414 ( 4) SS BOND : angle 1.93309 ( 8) hydrogen bonds : bond 0.04812 ( 247) hydrogen bonds : angle 3.60270 ( 774) link_ALPHA1-2 : bond 0.01123 ( 1) link_ALPHA1-2 : angle 1.68904 ( 3) link_ALPHA1-3 : bond 0.01528 ( 2) link_ALPHA1-3 : angle 4.96591 ( 6) link_BETA1-4 : bond 0.00974 ( 2) link_BETA1-4 : angle 2.22612 ( 6) link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 1.79950 ( 18) *********************** 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 60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6806 (mm) REVERT: B 166 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7823 (pt0) REVERT: B 170 GLU cc_start: 0.8048 (tp30) cc_final: 0.7547 (tm-30) REVERT: A 170 GLU cc_start: 0.6902 (tp30) cc_final: 0.6435 (tm-30) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0799 time to fit residues: 6.3181 Evaluate side-chains 56 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.134568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099877 restraints weight = 8764.140| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.14 r_work: 0.3141 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.037 5999 Z= 0.135 Angle : 0.689 8.149 8172 Z= 0.322 Chirality : 0.044 0.278 913 Planarity : 0.006 0.056 1019 Dihedral : 14.678 112.761 1017 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.89 % Allowed : 16.69 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.34), residues: 689 helix: 2.62 (0.30), residues: 315 sheet: 0.66 (0.56), residues: 76 loop : -0.82 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.023 0.001 TYR A 184 PHE 0.009 0.001 PHE A 356 TRP 0.013 0.001 TRP B 226 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5984) covalent geometry : angle 0.66686 ( 8131) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.62301 ( 8) hydrogen bonds : bond 0.04070 ( 247) hydrogen bonds : angle 3.50876 ( 774) link_ALPHA1-2 : bond 0.00906 ( 1) link_ALPHA1-2 : angle 1.57613 ( 3) link_ALPHA1-3 : bond 0.01545 ( 2) link_ALPHA1-3 : angle 5.00393 ( 6) link_BETA1-4 : bond 0.01062 ( 2) link_BETA1-4 : angle 2.03368 ( 6) link_NAG-ASN : bond 0.00346 ( 6) link_NAG-ASN : angle 1.82613 ( 18) *********************** 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 60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6644 (mm) REVERT: B 166 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7821 (pt0) REVERT: B 170 GLU cc_start: 0.8070 (tp30) cc_final: 0.7576 (tm-30) REVERT: A 170 GLU cc_start: 0.6895 (tp30) cc_final: 0.6425 (tm-30) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.0708 time to fit residues: 5.6539 Evaluate side-chains 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 373 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.135165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100309 restraints weight = 8889.486| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.18 r_work: 0.3144 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5999 Z= 0.127 Angle : 0.692 10.939 8172 Z= 0.320 Chirality : 0.044 0.274 913 Planarity : 0.006 0.055 1019 Dihedral : 14.511 113.008 1017 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.89 % Allowed : 16.69 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.34), residues: 689 helix: 2.64 (0.30), residues: 315 sheet: 0.73 (0.57), residues: 76 loop : -0.81 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.024 0.001 TYR A 184 PHE 0.008 0.001 PHE A 356 TRP 0.013 0.001 TRP B 226 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5984) covalent geometry : angle 0.67088 ( 8131) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.54233 ( 8) hydrogen bonds : bond 0.03813 ( 247) hydrogen bonds : angle 3.45436 ( 774) link_ALPHA1-2 : bond 0.01065 ( 1) link_ALPHA1-2 : angle 1.55020 ( 3) link_ALPHA1-3 : bond 0.01453 ( 2) link_ALPHA1-3 : angle 5.01836 ( 6) link_BETA1-4 : bond 0.00976 ( 2) link_BETA1-4 : angle 2.00452 ( 6) link_NAG-ASN : bond 0.00357 ( 6) link_NAG-ASN : angle 1.76128 ( 18) ********************** 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 60 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6546 (mm) REVERT: B 166 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7841 (pt0) REVERT: B 170 GLU cc_start: 0.8065 (tp30) cc_final: 0.7570 (tm-30) REVERT: A 170 GLU cc_start: 0.6885 (tp30) cc_final: 0.6418 (tm-30) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.0728 time to fit residues: 5.8847 Evaluate side-chains 59 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 373 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.0170 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101600 restraints weight = 8690.833| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.14 r_work: 0.3165 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5999 Z= 0.118 Angle : 0.694 11.286 8172 Z= 0.319 Chirality : 0.046 0.555 913 Planarity : 0.006 0.053 1019 Dihedral : 12.952 112.986 1017 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 16.22 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.34), residues: 689 helix: 2.72 (0.31), residues: 311 sheet: 0.83 (0.57), residues: 76 loop : -0.73 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.025 0.001 TYR A 184 PHE 0.008 0.001 PHE A 92 TRP 0.031 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5984) covalent geometry : angle 0.65668 ( 8131) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.45596 ( 8) hydrogen bonds : bond 0.03430 ( 247) hydrogen bonds : angle 3.38628 ( 774) link_ALPHA1-2 : bond 0.01094 ( 1) link_ALPHA1-2 : angle 1.50741 ( 3) link_ALPHA1-3 : bond 0.01323 ( 2) link_ALPHA1-3 : angle 5.07427 ( 6) link_BETA1-4 : bond 0.00894 ( 2) link_BETA1-4 : angle 1.85419 ( 6) link_NAG-ASN : bond 0.00396 ( 6) link_NAG-ASN : angle 3.59329 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.13 seconds wall clock time: 25 minutes 8.40 seconds (1508.40 seconds total)