Starting phenix.real_space_refine on Wed Mar 4 04:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqq_21354/03_2026/6vqq_21354.cif" } resolution = 2.56 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.298 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 70 5.16 5 C 7324 2.51 5 N 1715 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10987 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2190 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "B" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2216 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 3, 'TRANS': 278} Chain: "C" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2183 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 3, 'TRANS': 274} Chain: "D" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2221 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2177 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 3, 'TRANS': 273} Time building chain proxies: 2.79, per 1000 atoms: 0.25 Number of scatterers: 10987 At special positions: 0 Unit cell: (87.48, 100.44, 98.28, 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 70 16.00 O 1878 8.00 N 1715 7.00 C 7324 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: 0.88 Conformation dependent library (CDL) restraints added in 578.0 milliseconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 20 through 36 removed outlier: 3.573A pdb=" N SER A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 68 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.696A pdb=" N GLU A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.988A pdb=" N VAL A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.030A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.066A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.516A pdb=" N TYR A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 removed outlier: 4.135A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.627A pdb=" N CYS A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 4.111A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.541A pdb=" N ILE A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.506A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.767A pdb=" N ARG A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.683A pdb=" N CYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 69 Processing helix chain 'B' and resid 70 through 78 removed outlier: 4.028A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.592A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 178 removed outlier: 4.122A pdb=" N LEU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 3.762A pdb=" N LEU B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 removed outlier: 3.561A pdb=" N VAL B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 274 through 290 removed outlier: 3.552A pdb=" N TYR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 41 through 68 removed outlier: 3.886A pdb=" N ALA C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.065A pdb=" N GLU C 75 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.994A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.945A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 166 through 178 removed outlier: 3.864A pdb=" N LEU C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 210 through 227 removed outlier: 4.864A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.614A pdb=" N TYR C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 289 removed outlier: 5.576A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 289 " --> pdb=" O TYR C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 39 through 69 Processing helix chain 'D' and resid 70 through 78 removed outlier: 4.255A pdb=" N GLU D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 100 removed outlier: 3.958A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.811A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 147 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.090A pdb=" N PHE D 169 " --> pdb=" O HIS D 165 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 204 Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.696A pdb=" N VAL D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.793A pdb=" N TYR D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.726A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.801A pdb=" N TYR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.586A pdb=" N LEU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 4.122A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.565A pdb=" N CYS E 96 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 101 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.706A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 removed outlier: 3.537A pdb=" N TYR E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.786A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 170 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 208 through 226 removed outlier: 4.186A pdb=" N PHE E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 281 removed outlier: 3.770A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 292 removed outlier: 3.929A pdb=" N TYR E 285 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1848 1.33 - 1.45: 3240 1.45 - 1.57: 6087 1.57 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11275 Sorted by residual: bond pdb=" CA THR A 113 " pdb=" C THR A 113 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.35e-02 5.49e+03 7.55e+00 bond pdb=" CA GLU D 229 " pdb=" C GLU D 229 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.18e-02 7.18e+03 6.99e+00 bond pdb=" C HIS D 230 " pdb=" O HIS D 230 " ideal model delta sigma weight residual 1.235 1.205 0.030 1.14e-02 7.69e+03 6.99e+00 bond pdb=" N HIS D 230 " pdb=" CA HIS D 230 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.24e-02 6.50e+03 6.95e+00 bond pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.76e+00 ... (remaining 11270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14981 2.28 - 4.57: 267 4.57 - 6.85: 22 6.85 - 9.14: 3 9.14 - 11.42: 5 Bond angle restraints: 15278 Sorted by residual: angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 113.57 124.99 -11.42 1.38e+00 5.25e-01 6.85e+01 angle pdb=" N ILE A 231 " pdb=" CA ILE A 231 " pdb=" C ILE A 231 " ideal model delta sigma weight residual 110.62 117.36 -6.74 1.02e+00 9.61e-01 4.37e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 110.62 118.10 -7.48 1.14e+00 7.69e-01 4.31e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 111.17 118.89 -7.72 1.38e+00 5.25e-01 3.13e+01 angle pdb=" N PHE E 105 " pdb=" CA PHE E 105 " pdb=" C PHE E 105 " ideal model delta sigma weight residual 111.11 117.65 -6.54 1.20e+00 6.94e-01 2.97e+01 ... (remaining 15273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 5637 16.31 - 32.63: 611 32.63 - 48.94: 135 48.94 - 65.25: 18 65.25 - 81.57: 5 Dihedral angle restraints: 6406 sinusoidal: 2324 harmonic: 4082 Sorted by residual: dihedral pdb=" CA HIS D 37 " pdb=" C HIS D 37 " pdb=" N TYR D 38 " pdb=" CA TYR D 38 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER C 39 " pdb=" C SER C 39 " pdb=" N ASN C 40 " pdb=" CA ASN C 40 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE A 280 " pdb=" C ILE A 280 " pdb=" N TYR A 281 " pdb=" CA TYR A 281 " ideal model delta harmonic sigma weight residual 180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 1741 0.357 - 0.714: 0 0.714 - 1.070: 0 1.070 - 1.427: 0 1.427 - 1.784: 2 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CG LEU B 73 " pdb=" CB LEU B 73 " pdb=" CD1 LEU B 73 " pdb=" CD2 LEU B 73 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.95e+01 chirality pdb=" CG LEU D 275 " pdb=" CB LEU D 275 " pdb=" CD1 LEU D 275 " pdb=" CD2 LEU D 275 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.78e+01 chirality pdb=" CA PHE D 90 " pdb=" N PHE D 90 " pdb=" C PHE D 90 " pdb=" CB PHE D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1740 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 229 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C GLU D 229 " 0.079 2.00e-02 2.50e+03 pdb=" O GLU D 229 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS D 230 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 196 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C VAL D 196 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 196 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS D 197 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C ASN A 171 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 172 " -0.015 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 74 2.51 - 3.11: 9057 3.11 - 3.71: 16858 3.71 - 4.30: 25630 4.30 - 4.90: 42328 Nonbonded interactions: 93947 Sorted by model distance: nonbonded pdb=" O CYS C 19 " pdb=" OG1 THR C 205 " model vdw 1.916 3.040 nonbonded pdb=" O ASN B 257 " pdb=" OG1 THR B 261 " model vdw 1.950 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O LYS E 207 " model vdw 1.974 3.040 nonbonded pdb=" O VAL C 148 " pdb=" OG SER C 152 " model vdw 1.981 3.040 nonbonded pdb=" O VAL A 148 " pdb=" OG SER A 152 " model vdw 2.014 3.040 ... (remaining 93942 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 16 through 290) selection = (chain 'B' and resid 16 through 290) selection = (chain 'C' and resid 16 through 290) selection = (chain 'D' and resid 16 through 290) selection = (chain 'E' and resid 16 through 290) } 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.820 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.063 11275 Z= 0.295 Angle : 0.767 11.422 15278 Z= 0.490 Chirality : 0.076 1.784 1743 Planarity : 0.005 0.054 1862 Dihedral : 13.928 81.568 3828 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % 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: -3.82 (0.18), residues: 1389 helix: -2.01 (0.13), residues: 1052 sheet: None (None), residues: 0 loop : -3.68 (0.26), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.027 0.002 TYR B 201 PHE 0.014 0.002 PHE A 223 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00551 (11275) covalent geometry : angle 0.76666 (15278) hydrogen bonds : bond 0.15280 ( 774) hydrogen bonds : angle 6.84828 ( 2316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.375 Fit side-chains REVERT: A 251 TYR cc_start: 0.8275 (t80) cc_final: 0.7903 (t80) REVERT: B 119 LYS cc_start: 0.6811 (mttp) cc_final: 0.6454 (mmmt) REVERT: B 279 PHE cc_start: 0.6214 (t80) cc_final: 0.5950 (t80) REVERT: C 35 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7164 (mtpm) REVERT: C 72 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7370 (mmtm) REVERT: D 33 LYS cc_start: 0.7294 (tttm) cc_final: 0.7076 (tptt) REVERT: D 200 VAL cc_start: 0.8632 (t) cc_final: 0.8093 (m) REVERT: E 202 PHE cc_start: 0.7404 (m-10) cc_final: 0.7197 (m-10) REVERT: E 282 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7499 (tmmt) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.3974 time to fit residues: 97.3994 Evaluate side-chains 187 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 265 ASN B 37 HIS B 239 ASN B 257 ASN D 193 ASN D 245 ASN D 257 ASN E 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.189505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.174971 restraints weight = 13124.572| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.56 r_work: 0.3984 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11275 Z= 0.154 Angle : 0.569 7.791 15278 Z= 0.322 Chirality : 0.043 0.153 1743 Planarity : 0.004 0.050 1862 Dihedral : 4.695 21.294 1525 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.74 % Allowed : 14.27 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.21), residues: 1389 helix: 0.17 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.027 0.002 TYR C 69 PHE 0.032 0.001 PHE A 223 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00336 (11275) covalent geometry : angle 0.56868 (15278) hydrogen bonds : bond 0.04766 ( 774) hydrogen bonds : angle 4.58727 ( 2316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.416 Fit side-chains REVERT: A 163 LYS cc_start: 0.7520 (tttm) cc_final: 0.6862 (mptt) REVERT: A 207 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6769 (mtmm) REVERT: A 251 TYR cc_start: 0.8273 (t80) cc_final: 0.7944 (t80) REVERT: B 52 MET cc_start: 0.5594 (tpp) cc_final: 0.5216 (tmt) REVERT: B 117 TYR cc_start: 0.8110 (m-10) cc_final: 0.7700 (m-10) REVERT: B 149 SER cc_start: 0.8933 (t) cc_final: 0.8574 (m) REVERT: B 204 LEU cc_start: 0.6896 (tm) cc_final: 0.6564 (mm) REVERT: C 119 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8121 (mttp) REVERT: C 267 ILE cc_start: 0.7238 (mt) cc_final: 0.7007 (mt) REVERT: D 200 VAL cc_start: 0.8447 (t) cc_final: 0.8240 (t) REVERT: E 81 MET cc_start: 0.7509 (mmm) cc_final: 0.7306 (mmm) REVERT: E 120 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7501 (mmmt) REVERT: E 122 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6869 (mttp) REVERT: E 163 LYS cc_start: 0.7074 (mttm) cc_final: 0.6587 (mtmt) REVERT: E 234 ASN cc_start: 0.8466 (m-40) cc_final: 0.7994 (m-40) REVERT: E 282 LYS cc_start: 0.7490 (tmtt) cc_final: 0.7147 (tmmt) outliers start: 20 outliers final: 9 residues processed: 238 average time/residue: 0.3655 time to fit residues: 97.4545 Evaluate side-chains 222 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 42 ASN E 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.185454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170286 restraints weight = 13330.139| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.60 r_work: 0.3917 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11275 Z= 0.154 Angle : 0.537 6.197 15278 Z= 0.303 Chirality : 0.042 0.151 1743 Planarity : 0.003 0.045 1862 Dihedral : 4.544 20.783 1525 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.96 % Allowed : 16.45 % Favored : 80.59 % 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: 0.15 (0.22), residues: 1389 helix: 0.86 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 27 TYR 0.029 0.002 TYR C 69 PHE 0.029 0.001 PHE A 223 HIS 0.004 0.001 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00341 (11275) covalent geometry : angle 0.53724 (15278) hydrogen bonds : bond 0.04894 ( 774) hydrogen bonds : angle 4.42150 ( 2316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.380 Fit side-chains REVERT: A 163 LYS cc_start: 0.7604 (tttm) cc_final: 0.7057 (mptt) REVERT: A 207 LYS cc_start: 0.7232 (mtpt) cc_final: 0.6996 (mtmm) REVERT: A 251 TYR cc_start: 0.8327 (t80) cc_final: 0.8110 (t80) REVERT: A 258 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 52 MET cc_start: 0.5470 (tpp) cc_final: 0.5122 (tmt) REVERT: B 149 SER cc_start: 0.9082 (t) cc_final: 0.8683 (m) REVERT: B 162 GLU cc_start: 0.8154 (mp0) cc_final: 0.7664 (mm-30) REVERT: C 119 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8120 (mttp) REVERT: C 146 PHE cc_start: 0.7640 (t80) cc_final: 0.7366 (t80) REVERT: D 195 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: D 200 VAL cc_start: 0.8534 (t) cc_final: 0.8320 (t) REVERT: D 223 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6740 (t80) REVERT: D 251 TYR cc_start: 0.6934 (t80) cc_final: 0.6693 (t80) REVERT: E 81 MET cc_start: 0.7568 (mmm) cc_final: 0.7311 (mmp) REVERT: E 122 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6861 (mtmm) REVERT: E 223 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6722 (t80) REVERT: E 282 LYS cc_start: 0.7378 (tmtt) cc_final: 0.7056 (tmmt) outliers start: 34 outliers final: 14 residues processed: 242 average time/residue: 0.3483 time to fit residues: 94.6716 Evaluate side-chains 237 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 108 optimal weight: 0.0370 chunk 43 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN C 37 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.186322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.170765 restraints weight = 13370.915| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.67 r_work: 0.3933 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11275 Z= 0.144 Angle : 0.524 7.583 15278 Z= 0.294 Chirality : 0.041 0.147 1743 Planarity : 0.003 0.043 1862 Dihedral : 4.442 20.579 1525 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.09 % Allowed : 18.36 % Favored : 77.55 % 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: 0.52 (0.22), residues: 1389 helix: 1.08 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : -2.37 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.022 0.001 TYR C 69 PHE 0.028 0.001 PHE A 223 HIS 0.004 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00316 (11275) covalent geometry : angle 0.52431 (15278) hydrogen bonds : bond 0.04612 ( 774) hydrogen bonds : angle 4.33089 ( 2316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7666 (tttm) cc_final: 0.7177 (mptt) REVERT: A 207 LYS cc_start: 0.7289 (mtpt) cc_final: 0.7039 (mtmm) REVERT: A 258 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 52 MET cc_start: 0.5605 (tpp) cc_final: 0.5144 (tmt) REVERT: B 134 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7842 (mt) REVERT: B 149 SER cc_start: 0.9087 (t) cc_final: 0.8662 (m) REVERT: B 234 ASN cc_start: 0.7887 (m110) cc_final: 0.7569 (m110) REVERT: C 56 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7577 (tp) REVERT: C 67 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7862 (tt) REVERT: C 69 TYR cc_start: 0.8375 (t80) cc_final: 0.7325 (t80) REVERT: C 119 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8099 (mttp) REVERT: C 146 PHE cc_start: 0.7644 (t80) cc_final: 0.7327 (t80) REVERT: C 216 VAL cc_start: 0.7697 (t) cc_final: 0.7420 (t) REVERT: C 267 ILE cc_start: 0.7084 (mt) cc_final: 0.6787 (mt) REVERT: D 33 LYS cc_start: 0.7349 (tttm) cc_final: 0.6936 (tppt) REVERT: D 195 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: D 200 VAL cc_start: 0.8542 (t) cc_final: 0.8322 (t) REVERT: D 223 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6837 (t80) REVERT: D 283 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5794 (pm20) REVERT: E 81 MET cc_start: 0.7700 (mmm) cc_final: 0.7443 (mmp) REVERT: E 122 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7003 (mtmm) REVERT: E 163 LYS cc_start: 0.7090 (mttm) cc_final: 0.6653 (mtmt) REVERT: E 223 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.6731 (t80) REVERT: E 282 LYS cc_start: 0.7546 (tmtt) cc_final: 0.7174 (tmmt) outliers start: 47 outliers final: 22 residues processed: 249 average time/residue: 0.3451 time to fit residues: 96.7013 Evaluate side-chains 251 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.187396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.171850 restraints weight = 13368.852| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.67 r_work: 0.3953 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11275 Z= 0.130 Angle : 0.505 6.571 15278 Z= 0.283 Chirality : 0.040 0.155 1743 Planarity : 0.003 0.041 1862 Dihedral : 4.338 20.408 1525 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.26 % Allowed : 19.32 % Favored : 76.41 % 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: 0.82 (0.22), residues: 1389 helix: 1.28 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.20 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.018 0.001 TYR C 69 PHE 0.027 0.001 PHE A 288 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00280 (11275) covalent geometry : angle 0.50499 (15278) hydrogen bonds : bond 0.04308 ( 774) hydrogen bonds : angle 4.25901 ( 2316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7643 (tttm) cc_final: 0.7179 (mptt) REVERT: A 258 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7979 (mm) REVERT: B 52 MET cc_start: 0.5528 (tpp) cc_final: 0.5094 (tmt) REVERT: B 134 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7794 (mt) REVERT: B 149 SER cc_start: 0.9097 (t) cc_final: 0.8645 (m) REVERT: B 223 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8010 (t80) REVERT: C 56 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7542 (tp) REVERT: C 67 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7637 (tt) REVERT: C 69 TYR cc_start: 0.8315 (t80) cc_final: 0.7250 (t80) REVERT: C 119 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8086 (mttp) REVERT: C 146 PHE cc_start: 0.7570 (t80) cc_final: 0.7323 (t80) REVERT: C 179 HIS cc_start: 0.7499 (m-70) cc_final: 0.7286 (t70) REVERT: C 267 ILE cc_start: 0.7071 (mt) cc_final: 0.6774 (mt) REVERT: D 33 LYS cc_start: 0.7330 (tttm) cc_final: 0.6889 (tppt) REVERT: D 195 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: D 200 VAL cc_start: 0.8483 (t) cc_final: 0.8253 (t) REVERT: D 283 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5734 (pm20) REVERT: E 81 MET cc_start: 0.7683 (mmm) cc_final: 0.7407 (mmp) REVERT: E 122 LYS cc_start: 0.7411 (mmtt) cc_final: 0.6967 (mtmm) REVERT: E 163 LYS cc_start: 0.7119 (mttm) cc_final: 0.6658 (mtmt) REVERT: E 223 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.6681 (t80) REVERT: E 282 LYS cc_start: 0.7491 (tmtt) cc_final: 0.7111 (tmmt) outliers start: 49 outliers final: 25 residues processed: 242 average time/residue: 0.3535 time to fit residues: 96.1235 Evaluate side-chains 246 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167597 restraints weight = 13445.600| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.68 r_work: 0.3910 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11275 Z= 0.172 Angle : 0.549 5.929 15278 Z= 0.308 Chirality : 0.042 0.155 1743 Planarity : 0.003 0.039 1862 Dihedral : 4.504 20.658 1525 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.92 % Allowed : 20.89 % Favored : 75.20 % 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 are not related in a simple way. whole: 0.63 (0.22), residues: 1389 helix: 1.11 (0.15), residues: 1096 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.018 0.002 TYR C 69 PHE 0.026 0.002 PHE A 223 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00384 (11275) covalent geometry : angle 0.54878 (15278) hydrogen bonds : bond 0.05110 ( 774) hydrogen bonds : angle 4.41025 ( 2316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7750 (tttm) cc_final: 0.7276 (mptp) REVERT: A 258 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 52 MET cc_start: 0.5561 (tpp) cc_final: 0.5097 (tmt) REVERT: B 134 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7906 (mt) REVERT: B 149 SER cc_start: 0.9123 (t) cc_final: 0.8649 (m) REVERT: C 56 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7631 (tp) REVERT: C 67 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7615 (tt) REVERT: C 69 TYR cc_start: 0.8401 (t80) cc_final: 0.7509 (t80) REVERT: C 119 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8067 (mttp) REVERT: C 146 PHE cc_start: 0.7707 (t80) cc_final: 0.7428 (t80) REVERT: D 33 LYS cc_start: 0.7379 (tttm) cc_final: 0.6963 (tppt) REVERT: D 195 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: D 200 VAL cc_start: 0.8544 (t) cc_final: 0.8316 (t) REVERT: D 223 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7075 (t80) REVERT: E 34 LYS cc_start: 0.6244 (mmmt) cc_final: 0.4421 (ptpt) REVERT: E 81 MET cc_start: 0.7798 (mmm) cc_final: 0.7403 (mmp) REVERT: E 122 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7030 (mtmm) REVERT: E 193 ASN cc_start: 0.7944 (t0) cc_final: 0.7529 (t0) REVERT: E 223 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.6748 (t80) REVERT: E 234 ASN cc_start: 0.8570 (m-40) cc_final: 0.8079 (m-40) REVERT: E 282 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7256 (tmmt) outliers start: 45 outliers final: 23 residues processed: 249 average time/residue: 0.3616 time to fit residues: 100.7423 Evaluate side-chains 252 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 19 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** 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 = 0.4173 r_free = 0.4173 target = 0.184959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169412 restraints weight = 13367.278| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.67 r_work: 0.3904 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11275 Z= 0.146 Angle : 0.527 7.684 15278 Z= 0.294 Chirality : 0.041 0.192 1743 Planarity : 0.003 0.039 1862 Dihedral : 4.404 20.634 1525 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.26 % Allowed : 20.89 % Favored : 74.85 % 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: 0.78 (0.22), residues: 1389 helix: 1.23 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.016 0.002 TYR C 69 PHE 0.029 0.001 PHE A 288 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00324 (11275) covalent geometry : angle 0.52745 (15278) hydrogen bonds : bond 0.04634 ( 774) hydrogen bonds : angle 4.32918 ( 2316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7733 (tttm) cc_final: 0.7215 (mptt) REVERT: A 258 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 52 MET cc_start: 0.5532 (tpp) cc_final: 0.5085 (tmt) REVERT: B 134 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 149 SER cc_start: 0.9108 (t) cc_final: 0.8644 (m) REVERT: C 56 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7556 (tp) REVERT: C 67 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7734 (tt) REVERT: C 69 TYR cc_start: 0.8278 (t80) cc_final: 0.7423 (t80) REVERT: C 119 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8074 (mttp) REVERT: C 146 PHE cc_start: 0.7641 (t80) cc_final: 0.7372 (t80) REVERT: D 33 LYS cc_start: 0.7358 (tttm) cc_final: 0.6930 (tppt) REVERT: D 195 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: D 200 VAL cc_start: 0.8497 (t) cc_final: 0.8262 (t) REVERT: D 223 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7067 (t80) REVERT: D 283 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5706 (pm20) REVERT: E 34 LYS cc_start: 0.6217 (mmmt) cc_final: 0.4404 (ptpt) REVERT: E 81 MET cc_start: 0.7785 (mmm) cc_final: 0.7422 (mmp) REVERT: E 122 LYS cc_start: 0.7444 (mmtt) cc_final: 0.6986 (mtmm) REVERT: E 223 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.6460 (t80) REVERT: E 234 ASN cc_start: 0.8536 (m-40) cc_final: 0.8078 (m-40) REVERT: E 282 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7154 (tmmt) outliers start: 49 outliers final: 26 residues processed: 245 average time/residue: 0.3604 time to fit residues: 99.3277 Evaluate side-chains 249 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 9 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.184407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.168903 restraints weight = 13306.736| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.66 r_work: 0.3926 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11275 Z= 0.152 Angle : 0.540 9.497 15278 Z= 0.300 Chirality : 0.042 0.235 1743 Planarity : 0.003 0.039 1862 Dihedral : 4.420 20.341 1525 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.83 % Allowed : 21.15 % Favored : 75.02 % 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: 0.76 (0.22), residues: 1389 helix: 1.22 (0.16), residues: 1089 sheet: None (None), residues: 0 loop : -2.13 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.015 0.002 TYR C 69 PHE 0.031 0.001 PHE A 288 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00337 (11275) covalent geometry : angle 0.54042 (15278) hydrogen bonds : bond 0.04760 ( 774) hydrogen bonds : angle 4.35885 ( 2316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7588 (tttm) cc_final: 0.7262 (mptt) REVERT: A 258 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 52 MET cc_start: 0.5534 (tpp) cc_final: 0.5071 (tmt) REVERT: B 134 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7904 (mt) REVERT: B 223 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 252 GLN cc_start: 0.8304 (mt0) cc_final: 0.8087 (mt0) REVERT: C 35 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7455 (mtpp) REVERT: C 56 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7551 (tp) REVERT: C 67 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7700 (tt) REVERT: C 69 TYR cc_start: 0.8302 (t80) cc_final: 0.7486 (t80) REVERT: C 119 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8054 (mttp) REVERT: C 146 PHE cc_start: 0.7630 (t80) cc_final: 0.7364 (t80) REVERT: C 179 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7049 (t70) REVERT: D 33 LYS cc_start: 0.7361 (tttm) cc_final: 0.6949 (tppt) REVERT: D 195 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: D 200 VAL cc_start: 0.8489 (t) cc_final: 0.8245 (t) REVERT: D 223 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7047 (t80) REVERT: D 247 LYS cc_start: 0.6091 (ttpm) cc_final: 0.5811 (ttpm) REVERT: D 283 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5605 (pm20) REVERT: E 34 LYS cc_start: 0.6246 (mmmt) cc_final: 0.4417 (ptpt) REVERT: E 81 MET cc_start: 0.7785 (mmm) cc_final: 0.7412 (mmp) REVERT: E 122 LYS cc_start: 0.7442 (mmtt) cc_final: 0.6975 (mtmm) REVERT: E 223 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.6634 (t80) REVERT: E 234 ASN cc_start: 0.8532 (m-40) cc_final: 0.8067 (m-40) REVERT: E 282 LYS cc_start: 0.7523 (tmtt) cc_final: 0.7154 (tmmt) outliers start: 44 outliers final: 27 residues processed: 246 average time/residue: 0.3654 time to fit residues: 101.1471 Evaluate side-chains 257 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 81 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS E 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174650 restraints weight = 13150.423| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.66 r_work: 0.3973 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11275 Z= 0.111 Angle : 0.495 11.721 15278 Z= 0.273 Chirality : 0.039 0.254 1743 Planarity : 0.003 0.040 1862 Dihedral : 4.140 19.668 1525 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 22.11 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.16 (0.23), residues: 1389 helix: 1.52 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.017 0.001 TYR E 251 PHE 0.030 0.001 PHE A 288 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00225 (11275) covalent geometry : angle 0.49470 (15278) hydrogen bonds : bond 0.03715 ( 774) hydrogen bonds : angle 4.14666 ( 2316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7682 (tttm) cc_final: 0.7400 (mptp) REVERT: A 266 TYR cc_start: 0.6981 (t80) cc_final: 0.6729 (t80) REVERT: B 52 MET cc_start: 0.5551 (tpp) cc_final: 0.5096 (tmt) REVERT: B 134 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 149 SER cc_start: 0.9018 (t) cc_final: 0.8540 (m) REVERT: C 35 LYS cc_start: 0.8064 (mmtp) cc_final: 0.7496 (mtpp) REVERT: C 67 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7714 (tt) REVERT: C 69 TYR cc_start: 0.8136 (t80) cc_final: 0.7004 (t80) REVERT: C 119 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8039 (mttp) REVERT: D 33 LYS cc_start: 0.7293 (tttm) cc_final: 0.6882 (tppt) REVERT: D 195 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5807 (m-80) REVERT: D 200 VAL cc_start: 0.8427 (t) cc_final: 0.8161 (t) REVERT: D 223 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7136 (t80) REVERT: D 283 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: E 81 MET cc_start: 0.7692 (mmm) cc_final: 0.7386 (mmp) REVERT: E 108 ASN cc_start: 0.7601 (p0) cc_final: 0.7354 (p0) REVERT: E 122 LYS cc_start: 0.7356 (mmtt) cc_final: 0.6878 (mtmm) REVERT: E 282 LYS cc_start: 0.7444 (tmtt) cc_final: 0.7093 (tmmt) outliers start: 37 outliers final: 21 residues processed: 249 average time/residue: 0.3570 time to fit residues: 100.0335 Evaluate side-chains 243 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.184643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169163 restraints weight = 13350.752| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.66 r_work: 0.3927 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11275 Z= 0.162 Angle : 0.567 11.878 15278 Z= 0.312 Chirality : 0.043 0.245 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.359 19.988 1525 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.96 % Allowed : 22.54 % Favored : 74.50 % 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: 0.84 (0.22), residues: 1389 helix: 1.27 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.018 0.002 TYR D 31 PHE 0.026 0.002 PHE A 288 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00365 (11275) covalent geometry : angle 0.56676 (15278) hydrogen bonds : bond 0.04832 ( 774) hydrogen bonds : angle 4.34261 ( 2316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7722 (tttm) cc_final: 0.7459 (mptp) REVERT: A 223 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.5451 (p90) REVERT: B 52 MET cc_start: 0.5601 (tpp) cc_final: 0.5141 (tmt) REVERT: B 149 SER cc_start: 0.9045 (t) cc_final: 0.8574 (m) REVERT: B 252 GLN cc_start: 0.8340 (mt0) cc_final: 0.8122 (mt0) REVERT: C 35 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7534 (mtpp) REVERT: C 67 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7549 (tt) REVERT: C 69 TYR cc_start: 0.8300 (t80) cc_final: 0.7429 (t80) REVERT: C 119 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8035 (mttp) REVERT: C 267 ILE cc_start: 0.7089 (mt) cc_final: 0.6764 (mt) REVERT: D 33 LYS cc_start: 0.7390 (tttm) cc_final: 0.6970 (tppt) REVERT: D 195 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: D 200 VAL cc_start: 0.8496 (t) cc_final: 0.8256 (t) REVERT: D 223 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7082 (t80) REVERT: D 247 LYS cc_start: 0.6096 (ttpm) cc_final: 0.5871 (ttpm) REVERT: D 283 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5574 (pm20) REVERT: E 34 LYS cc_start: 0.6204 (mmmt) cc_final: 0.4352 (ptpt) REVERT: E 81 MET cc_start: 0.7806 (mmm) cc_final: 0.7434 (mmp) REVERT: E 122 LYS cc_start: 0.7440 (mmtt) cc_final: 0.6999 (mtmm) REVERT: E 282 LYS cc_start: 0.7509 (tmtt) cc_final: 0.7151 (tmmt) outliers start: 34 outliers final: 23 residues processed: 234 average time/residue: 0.3609 time to fit residues: 94.7384 Evaluate side-chains 245 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 45 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 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 = 0.4176 r_free = 0.4176 target = 0.185218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169683 restraints weight = 13286.059| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.66 r_work: 0.3923 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11275 Z= 0.151 Angle : 0.557 11.987 15278 Z= 0.308 Chirality : 0.042 0.231 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.359 20.177 1525 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 22.89 % Favored : 74.06 % 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: 0.80 (0.22), residues: 1389 helix: 1.26 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -2.23 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 290 TYR 0.017 0.002 TYR A 286 PHE 0.032 0.002 PHE A 288 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00337 (11275) covalent geometry : angle 0.55688 (15278) hydrogen bonds : bond 0.04658 ( 774) hydrogen bonds : angle 4.33320 ( 2316) =============================================================================== Job complete usr+sys time: 3667.93 seconds wall clock time: 63 minutes 28.66 seconds (3808.66 seconds total)