Starting phenix.real_space_refine on Thu Jun 4 03:50:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.map" model { file = "/net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7f_49094/06_2026/9n7f_49094.cif" } resolution = 2.93 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= 0.031 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 Cl 2 4.86 5 C 6512 2.51 5 N 1788 2.21 5 O 1806 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10172 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2519 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain breaks: 2 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2488 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 17, 'TRANS': 297} Chain breaks: 3 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2519 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain breaks: 2 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2488 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 17, 'TRANS': 297} Chain breaks: 3 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'1SY': 1, '9IM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'9IM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.28 Number of scatterers: 10172 At special positions: 0 Unit cell: (90.468, 84.006, 104.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 52 16.00 P 4 15.00 F 8 9.00 O 1806 8.00 N 1788 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 473.9 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 65.3% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.621A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.635A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 116 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.664A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Proline residue: A 173 - end of helix removed outlier: 4.255A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.982A pdb=" N ALA A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 216' Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.762A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.599A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.573A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.619A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 117 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.674A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.397A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.643A pdb=" N ALA B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.634A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'C' and resid 16 through 37 removed outlier: 3.637A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.636A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.519A pdb=" N THR C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 116 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.646A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 186 Proline residue: C 173 - end of helix removed outlier: 4.252A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.963A pdb=" N ALA C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 216' Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.756A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.617A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 37 removed outlier: 3.621A pdb=" N GLY D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.526A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.786A pdb=" N THR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 109 Processing helix chain 'D' and resid 117 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 154 through 167 removed outlier: 3.690A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 186 Proline residue: D 173 - end of helix Processing helix chain 'D' and resid 211 through 216 removed outlier: 3.618A pdb=" N ALA D 215 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.660A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 4.032A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.952A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.383A pdb=" N GLN A 228 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 239 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY A 230 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A 237 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 224 removed outlier: 6.867A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER B 243 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL B 258 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.664A pdb=" N HIS B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 223 removed outlier: 6.943A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 255 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.431A pdb=" N GLN C 228 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL C 239 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY C 230 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C 237 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 224 removed outlier: 6.930A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER D 243 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 258 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR D 245 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR D 256 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.532A pdb=" N HIS D 232 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1920 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: 1.87 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1584 1.31 - 1.43: 2833 1.43 - 1.56: 5927 1.56 - 1.68: 8 1.68 - 1.81: 66 Bond restraints: 10418 Sorted by residual: bond pdb=" C38 1SY A 402 " pdb=" O43 1SY A 402 " ideal model delta sigma weight residual 1.225 1.400 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C38 1SY D 401 " pdb=" O43 1SY D 401 " ideal model delta sigma weight residual 1.225 1.399 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" C16 9IM C 401 " pdb=" N06 9IM C 401 " ideal model delta sigma weight residual 1.393 1.522 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C16 9IM A 401 " pdb=" N06 9IM A 401 " ideal model delta sigma weight residual 1.393 1.518 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C6 1SY D 401 " pdb=" N01 1SY D 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 14079 3.68 - 7.37: 89 7.37 - 11.05: 6 11.05 - 14.74: 4 14.74 - 18.42: 4 Bond angle restraints: 14182 Sorted by residual: angle pdb=" O19 1SY A 402 " pdb=" P18 1SY A 402 " pdb=" O44 1SY A 402 " ideal model delta sigma weight residual 123.21 104.79 18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" O29 1SY A 402 " pdb=" P27 1SY A 402 " pdb=" O30 1SY A 402 " ideal model delta sigma weight residual 123.47 105.08 18.39 3.00e+00 1.11e-01 3.76e+01 angle pdb=" O29 1SY D 401 " pdb=" P27 1SY D 401 " pdb=" O30 1SY D 401 " ideal model delta sigma weight residual 123.47 105.10 18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O19 1SY D 401 " pdb=" P18 1SY D 401 " pdb=" O44 1SY D 401 " ideal model delta sigma weight residual 123.21 104.94 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" O17 1SY A 402 " pdb=" P18 1SY A 402 " pdb=" O20 1SY A 402 " ideal model delta sigma weight residual 100.83 114.11 -13.28 3.00e+00 1.11e-01 1.96e+01 ... (remaining 14177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5671 17.70 - 35.41: 511 35.41 - 53.11: 84 53.11 - 70.82: 18 70.82 - 88.52: 12 Dihedral angle restraints: 6296 sinusoidal: 2612 harmonic: 3684 Sorted by residual: dihedral pdb=" CA ILE D 171 " pdb=" C ILE D 171 " pdb=" N LEU D 172 " pdb=" CA LEU D 172 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB GLU C 143 " pdb=" CG GLU C 143 " pdb=" CD GLU C 143 " pdb=" OE1 GLU C 143 " ideal model delta sinusoidal sigma weight residual 0.00 85.71 -85.71 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CB GLU A 143 " pdb=" CG GLU A 143 " pdb=" CD GLU A 143 " pdb=" OE1 GLU A 143 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 6293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1286 0.047 - 0.094: 234 0.094 - 0.141: 50 0.141 - 0.188: 6 0.188 - 0.235: 2 Chirality restraints: 1578 Sorted by residual: chirality pdb=" C22 1SY D 401 " pdb=" C21 1SY D 401 " pdb=" C24 1SY D 401 " pdb=" O23 1SY D 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.46 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C22 1SY A 402 " pdb=" C21 1SY A 402 " pdb=" C24 1SY A 402 " pdb=" O23 1SY A 402 " both_signs ideal model delta sigma weight residual False -2.70 -2.46 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU B 49 " pdb=" CB LEU B 49 " pdb=" CD1 LEU B 49 " pdb=" CD2 LEU B 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 1575 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 263 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 264 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 114 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 115 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 106 " -0.017 2.00e-02 2.50e+03 1.16e-02 2.68e+00 pdb=" CG TYR B 106 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 106 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 106 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 106 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 106 " -0.003 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 541 2.74 - 3.28: 10147 3.28 - 3.82: 17707 3.82 - 4.36: 20433 4.36 - 4.90: 35829 Nonbonded interactions: 84657 Sorted by model distance: nonbonded pdb=" OE1 GLU D 69 " pdb=" OH TYR D 77 " model vdw 2.195 3.040 nonbonded pdb=" NZ LYS B 224 " pdb=" OG SER B 243 " model vdw 2.277 3.120 nonbonded pdb=" O ILE D 171 " pdb=" N LEU D 175 " model vdw 2.279 3.120 nonbonded pdb=" NH2 ARG D 45 " pdb=" O PRO D 110 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR B 167 " pdb=" OE2 GLU B 260 " model vdw 2.281 3.040 ... (remaining 84652 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 5 through 110 or resid 116 through 334)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 110 or resid 116 through 334)) selection = (chain 'D' and resid 5 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.390 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.006 0.175 10418 Z= 0.314 Angle : 0.785 18.421 14182 Z= 0.338 Chirality : 0.039 0.235 1578 Planarity : 0.005 0.047 1792 Dihedral : 13.934 88.519 3936 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 are not related in a simple way. whole: 2.18 (0.25), residues: 1242 helix: 2.51 (0.18), residues: 736 sheet: -0.36 (0.44), residues: 142 loop : 0.01 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 281 TYR 0.028 0.001 TYR B 106 PHE 0.010 0.001 PHE C 279 TRP 0.012 0.002 TRP D 119 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.31 (10418) covalent geometry : angle 0.78527 / 0.34 (14182) hydrogen bonds : bond 0.10687 / 6.94 ( 646) hydrogen bonds : angle 6.50378 / 4.65 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: B 83 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7924 (mtp85) REVERT: D 108 SER cc_start: 0.8310 (m) cc_final: 0.8089 (m) REVERT: D 150 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8313 (ttpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.8208 time to fit residues: 122.9654 Evaluate side-chains 108 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 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 111 ASN A 218 ASN A 332 HIS B 176 GLN B 185 HIS B 227 GLN C 111 ASN C 228 GLN C 332 HIS D 154 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133855 restraints weight = 10012.149| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.94 r_work: 0.3247 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10418 Z= 0.170 Angle : 0.562 5.722 14182 Z= 0.281 Chirality : 0.039 0.152 1578 Planarity : 0.005 0.050 1792 Dihedral : 5.438 32.509 1580 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.21 % Allowed : 7.76 % Favored : 91.03 % 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 are not related in a simple way. whole: 2.02 (0.24), residues: 1242 helix: 2.35 (0.18), residues: 750 sheet: -0.15 (0.44), residues: 136 loop : -0.23 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 281 TYR 0.026 0.002 TYR C 106 PHE 0.011 0.002 PHE C 279 TRP 0.016 0.002 TRP D 119 HIS 0.006 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (10418) covalent geometry : angle 0.56187 / 0.28 (14182) hydrogen bonds : bond 0.04153 / 2.90 ( 646) hydrogen bonds : angle 5.01202 / 3.56 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7475 (tpp-160) REVERT: B 83 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8175 (mtp85) REVERT: B 286 GLU cc_start: 0.7840 (tp30) cc_final: 0.7356 (pt0) REVERT: C 310 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7418 (tpp-160) REVERT: D 150 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8422 (ttpt) outliers start: 13 outliers final: 6 residues processed: 120 average time/residue: 0.7328 time to fit residues: 93.4071 Evaluate side-chains 116 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 261 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 154 ASN B 176 GLN C 332 HIS D 154 ASN D 232 HIS D 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137957 restraints weight = 9913.617| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.89 r_work: 0.3283 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10418 Z= 0.126 Angle : 0.500 4.852 14182 Z= 0.252 Chirality : 0.037 0.147 1578 Planarity : 0.005 0.051 1792 Dihedral : 5.098 32.114 1580 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.50 % Allowed : 9.72 % Favored : 88.79 % 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 are not related in a simple way. whole: 2.27 (0.24), residues: 1242 helix: 2.66 (0.18), residues: 744 sheet: -0.25 (0.44), residues: 140 loop : -0.24 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 281 TYR 0.014 0.001 TYR C 106 PHE 0.009 0.002 PHE C 279 TRP 0.012 0.002 TRP D 119 HIS 0.004 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10418) covalent geometry : angle 0.49973 / 0.25 (14182) hydrogen bonds : bond 0.03639 / 2.54 ( 646) hydrogen bonds : angle 4.64498 / 3.30 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LEU cc_start: 0.8186 (mt) cc_final: 0.7980 (mt) REVERT: B 83 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8116 (mtp85) REVERT: B 328 GLU cc_start: 0.7928 (tp30) cc_final: 0.7588 (tp30) REVERT: D 120 MET cc_start: 0.6736 (mtp) cc_final: 0.6461 (mtp) REVERT: D 150 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8407 (ttpt) REVERT: D 218 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7493 (t0) REVERT: D 310 ARG cc_start: 0.8051 (tpt90) cc_final: 0.7325 (tpt-90) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 0.6700 time to fit residues: 88.7504 Evaluate side-chains 117 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 261 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 176 GLN C 266 GLN C 332 HIS D 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140576 restraints weight = 10054.698| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.86 r_work: 0.3297 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10418 Z= 0.107 Angle : 0.471 4.916 14182 Z= 0.239 Chirality : 0.036 0.146 1578 Planarity : 0.005 0.050 1792 Dihedral : 4.948 39.067 1580 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.96 % Allowed : 10.28 % Favored : 87.76 % 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 are not related in a simple way. whole: 2.51 (0.24), residues: 1242 helix: 2.90 (0.18), residues: 744 sheet: -0.36 (0.44), residues: 142 loop : -0.18 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 281 TYR 0.015 0.001 TYR C 106 PHE 0.008 0.001 PHE C 279 TRP 0.010 0.001 TRP D 161 HIS 0.004 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10418) covalent geometry : angle 0.47109 / 0.24 (14182) hydrogen bonds : bond 0.03322 / 2.33 ( 646) hydrogen bonds : angle 4.41865 / 3.13 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8030 (mtp85) REVERT: B 106 TYR cc_start: 0.7292 (m-80) cc_final: 0.6982 (m-80) REVERT: B 328 GLU cc_start: 0.7843 (tp30) cc_final: 0.7306 (tp30) REVERT: C 258 VAL cc_start: 0.8654 (t) cc_final: 0.8436 (t) REVERT: C 266 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 150 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8347 (ttpt) REVERT: D 310 ARG cc_start: 0.7988 (tpt90) cc_final: 0.7395 (tpt-90) outliers start: 21 outliers final: 7 residues processed: 138 average time/residue: 0.6104 time to fit residues: 90.0249 Evaluate side-chains 123 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain D residue 261 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 176 GLN B 227 GLN C 266 GLN D 131 ASN D 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124371 restraints weight = 10237.750| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.99 r_work: 0.3217 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10418 Z= 0.312 Angle : 0.699 7.327 14182 Z= 0.342 Chirality : 0.045 0.164 1578 Planarity : 0.006 0.050 1792 Dihedral : 5.823 32.939 1580 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.15 % Allowed : 12.15 % Favored : 85.70 % 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 are not related in a simple way. whole: 1.35 (0.24), residues: 1242 helix: 1.79 (0.18), residues: 748 sheet: -0.20 (0.46), residues: 130 loop : -0.50 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.041 0.002 TYR A 106 PHE 0.013 0.003 PHE B 105 TRP 0.021 0.004 TRP D 119 HIS 0.006 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.31 (10418) covalent geometry : angle 0.69880 / 0.34 (14182) hydrogen bonds : bond 0.05028 / 3.53 ( 646) hydrogen bonds : angle 5.22977 / 3.73 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8412 (mt) cc_final: 0.7928 (mp) REVERT: B 83 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8215 (mtp85) REVERT: B 106 TYR cc_start: 0.7639 (m-80) cc_final: 0.6845 (m-80) REVERT: B 286 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: B 331 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7368 (ttm170) REVERT: D 127 SER cc_start: 0.8848 (t) cc_final: 0.8400 (m) REVERT: D 150 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8351 (ttpt) REVERT: D 328 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7745 (tp30) outliers start: 23 outliers final: 10 residues processed: 138 average time/residue: 0.6730 time to fit residues: 98.8988 Evaluate side-chains 142 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 154 ASN B 176 GLN C 266 GLN D 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131625 restraints weight = 10188.907| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.84 r_work: 0.3230 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10418 Z= 0.120 Angle : 0.492 4.948 14182 Z= 0.251 Chirality : 0.037 0.148 1578 Planarity : 0.005 0.049 1792 Dihedral : 5.284 45.253 1580 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.34 % Allowed : 12.15 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.24), residues: 1242 helix: 2.53 (0.18), residues: 746 sheet: -0.29 (0.45), residues: 140 loop : -0.28 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 281 TYR 0.017 0.001 TYR A 106 PHE 0.009 0.002 PHE A 279 TRP 0.011 0.002 TRP D 161 HIS 0.004 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10418) covalent geometry : angle 0.49249 / 0.25 (14182) hydrogen bonds : bond 0.03533 / 2.48 ( 646) hydrogen bonds : angle 4.56626 / 3.25 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.7672 (t80) cc_final: 0.7385 (t80) REVERT: A 310 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7454 (tpp-160) REVERT: B 83 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8080 (mtp85) REVERT: B 106 TYR cc_start: 0.7470 (m-80) cc_final: 0.6705 (m-80) REVERT: B 331 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7169 (ttp80) REVERT: C 258 VAL cc_start: 0.8706 (t) cc_final: 0.8486 (t) outliers start: 25 outliers final: 8 residues processed: 131 average time/residue: 0.6210 time to fit residues: 87.1632 Evaluate side-chains 122 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 176 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.173617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134191 restraints weight = 10087.964| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.86 r_work: 0.3222 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10418 Z= 0.130 Angle : 0.499 4.899 14182 Z= 0.253 Chirality : 0.037 0.148 1578 Planarity : 0.005 0.049 1792 Dihedral : 5.161 42.684 1580 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.24 % Allowed : 12.52 % Favored : 85.23 % 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 are not related in a simple way. whole: 2.26 (0.24), residues: 1242 helix: 2.68 (0.18), residues: 744 sheet: -0.41 (0.45), residues: 142 loop : -0.22 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 281 TYR 0.024 0.001 TYR A 106 PHE 0.008 0.002 PHE C 279 TRP 0.012 0.002 TRP D 161 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10418) covalent geometry : angle 0.49888 / 0.25 (14182) hydrogen bonds : bond 0.03591 / 2.53 ( 646) hydrogen bonds : angle 4.54317 / 3.23 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 VAL cc_start: 0.8760 (t) cc_final: 0.8542 (t) REVERT: B 83 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8120 (mtp85) REVERT: B 106 TYR cc_start: 0.7452 (m-80) cc_final: 0.6632 (m-80) REVERT: B 324 SER cc_start: 0.6378 (OUTLIER) cc_final: 0.6004 (t) REVERT: C 310 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7532 (tpp-160) REVERT: D 328 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7518 (tp30) outliers start: 24 outliers final: 10 residues processed: 135 average time/residue: 0.6437 time to fit residues: 93.0451 Evaluate side-chains 131 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 154 ASN B 176 GLN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.174319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132243 restraints weight = 10050.883| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.83 r_work: 0.3228 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10418 Z= 0.125 Angle : 0.494 5.448 14182 Z= 0.251 Chirality : 0.037 0.147 1578 Planarity : 0.005 0.050 1792 Dihedral : 5.149 46.426 1580 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.59 % Allowed : 13.93 % Favored : 84.49 % 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 are not related in a simple way. whole: 2.36 (0.24), residues: 1242 helix: 2.76 (0.18), residues: 744 sheet: -0.39 (0.45), residues: 142 loop : -0.19 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 281 TYR 0.028 0.001 TYR A 106 PHE 0.008 0.002 PHE C 279 TRP 0.011 0.002 TRP D 161 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10418) covalent geometry : angle 0.49436 / 0.25 (14182) hydrogen bonds : bond 0.03499 / 2.46 ( 646) hydrogen bonds : angle 4.47781 / 3.18 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 VAL cc_start: 0.8759 (t) cc_final: 0.8546 (t) REVERT: B 83 ARG cc_start: 0.8384 (mtp85) cc_final: 0.8048 (mtp85) REVERT: B 106 TYR cc_start: 0.7404 (m-80) cc_final: 0.6574 (m-80) REVERT: B 324 SER cc_start: 0.6321 (OUTLIER) cc_final: 0.5959 (t) REVERT: C 258 VAL cc_start: 0.8745 (t) cc_final: 0.8533 (t) REVERT: C 310 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7476 (tpp-160) REVERT: D 310 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7561 (tpt-90) REVERT: D 328 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7480 (tp30) outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.6383 time to fit residues: 86.7054 Evaluate side-chains 127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 154 ASN B 176 GLN D 131 ASN D 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133783 restraints weight = 10084.674| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.83 r_work: 0.3233 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10418 Z= 0.114 Angle : 0.481 5.963 14182 Z= 0.245 Chirality : 0.036 0.146 1578 Planarity : 0.005 0.049 1792 Dihedral : 5.033 46.093 1580 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.68 % Allowed : 14.02 % Favored : 84.30 % 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 are not related in a simple way. whole: 2.48 (0.24), residues: 1242 helix: 2.87 (0.18), residues: 744 sheet: -0.38 (0.45), residues: 142 loop : -0.16 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 281 TYR 0.032 0.001 TYR A 106 PHE 0.009 0.001 PHE D 105 TRP 0.011 0.002 TRP B 82 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10418) covalent geometry : angle 0.48112 / 0.25 (14182) hydrogen bonds : bond 0.03358 / 2.36 ( 646) hydrogen bonds : angle 4.38318 / 3.11 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.6195 (ptp90) REVERT: A 258 VAL cc_start: 0.8740 (t) cc_final: 0.8523 (t) REVERT: B 83 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8043 (mtp85) REVERT: B 106 TYR cc_start: 0.7446 (m-80) cc_final: 0.6723 (m-80) REVERT: B 324 SER cc_start: 0.6373 (OUTLIER) cc_final: 0.6020 (t) REVERT: C 258 VAL cc_start: 0.8707 (t) cc_final: 0.8502 (t) REVERT: C 310 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7456 (tpp-160) REVERT: D 310 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7593 (tpt-90) REVERT: D 328 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7511 (tp30) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.6969 time to fit residues: 97.3306 Evaluate side-chains 127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 176 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130334 restraints weight = 10065.468| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.84 r_work: 0.3227 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10418 Z= 0.139 Angle : 0.509 6.353 14182 Z= 0.258 Chirality : 0.037 0.147 1578 Planarity : 0.005 0.050 1792 Dihedral : 5.109 43.407 1580 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.68 % Allowed : 13.93 % Favored : 84.39 % 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 are not related in a simple way. whole: 2.36 (0.24), residues: 1242 helix: 2.75 (0.18), residues: 744 sheet: -0.39 (0.45), residues: 142 loop : -0.16 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.028 0.001 TYR A 106 PHE 0.010 0.002 PHE D 105 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10418) covalent geometry : angle 0.50921 / 0.26 (14182) hydrogen bonds : bond 0.03604 / 2.53 ( 646) hydrogen bonds : angle 4.50553 / 3.21 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8001 (tmt) cc_final: 0.7756 (tmt) REVERT: A 258 VAL cc_start: 0.8750 (t) cc_final: 0.8542 (t) REVERT: B 83 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8049 (mtp85) REVERT: B 106 TYR cc_start: 0.7449 (m-80) cc_final: 0.6628 (m-80) REVERT: B 324 SER cc_start: 0.6403 (OUTLIER) cc_final: 0.6012 (t) REVERT: B 328 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: C 258 VAL cc_start: 0.8749 (t) cc_final: 0.8539 (t) REVERT: D 197 ARG cc_start: 0.6637 (mtp180) cc_final: 0.6402 (mtp180) REVERT: D 310 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7411 (tpt-90) REVERT: D 328 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7584 (tp30) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.6899 time to fit residues: 90.6378 Evaluate side-chains 129 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 176 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133721 restraints weight = 10198.085| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.93 r_work: 0.3230 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10418 Z= 0.121 Angle : 0.496 6.082 14182 Z= 0.252 Chirality : 0.037 0.147 1578 Planarity : 0.005 0.050 1792 Dihedral : 5.063 44.830 1580 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.78 % Allowed : 14.11 % Favored : 84.11 % 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 are not related in a simple way. whole: 2.43 (0.24), residues: 1242 helix: 2.81 (0.18), residues: 744 sheet: -0.39 (0.45), residues: 142 loop : -0.16 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 281 TYR 0.025 0.001 TYR A 106 PHE 0.008 0.002 PHE D 105 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10418) covalent geometry : angle 0.49591 / 0.25 (14182) hydrogen bonds : bond 0.03451 / 2.42 ( 646) hydrogen bonds : angle 4.42749 / 3.15 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.77 seconds wall clock time: 65 minutes 5.03 seconds (3905.03 seconds total)