Starting phenix.real_space_refine on Tue Jul 29 03:02:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqq_21354/07_2025/6vqq_21354.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqq_21354/07_2025/6vqq_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_21354/07_2025/6vqq_21354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqq_21354/07_2025/6vqq_21354.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqq_21354/07_2025/6vqq_21354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqq_21354/07_2025/6vqq_21354.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.80, per 1000 atoms: 0.62 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.95 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: 3.41 Time building geometry restraints manager: 3.38 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.710 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.006 0.001 HIS C 37 PHE 0.014 0.002 PHE A 223 TYR 0.027 0.002 TYR B 201 ARG 0.003 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.15280 ( 774) hydrogen bonds : angle 6.84828 ( 2316) covalent geometry : bond 0.00551 (11275) covalent geometry : angle 0.76666 (15278) *********************** 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 : 1.168 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: 0.8715 time to fit residues: 214.3605 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.0060 overall best weight: 3.6002 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.175657 restraints weight = 13007.125| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.55 r_work: 0.3991 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11275 Z= 0.151 Angle : 0.564 7.693 15278 Z= 0.319 Chirality : 0.043 0.164 1743 Planarity : 0.004 0.049 1862 Dihedral : 4.674 21.104 1525 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.83 % Allowed : 14.10 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1389 helix: 0.15 (0.15), residues: 1077 sheet: None (None), residues: 0 loop : -2.94 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 230 PHE 0.031 0.001 PHE A 223 TYR 0.027 0.002 TYR C 69 ARG 0.003 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 774) hydrogen bonds : angle 4.59674 ( 2316) covalent geometry : bond 0.00330 (11275) covalent geometry : angle 0.56394 (15278) *********************** 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 256 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 1.097 Fit side-chains REVERT: A 163 LYS cc_start: 0.7614 (tttm) cc_final: 0.6838 (mptt) REVERT: A 207 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6875 (mtmm) REVERT: A 251 TYR cc_start: 0.8257 (t80) cc_final: 0.7920 (t80) REVERT: B 52 MET cc_start: 0.5583 (tpp) cc_final: 0.5211 (tmt) REVERT: B 117 TYR cc_start: 0.8106 (m-10) cc_final: 0.7684 (m-10) REVERT: B 130 MET cc_start: 0.7869 (mmt) cc_final: 0.7648 (mmt) REVERT: B 149 SER cc_start: 0.8930 (t) cc_final: 0.8578 (m) REVERT: B 204 LEU cc_start: 0.6919 (tm) cc_final: 0.6580 (mm) REVERT: C 119 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8082 (mttp) REVERT: C 267 ILE cc_start: 0.7239 (mt) cc_final: 0.7005 (mt) REVERT: D 200 VAL cc_start: 0.8421 (t) cc_final: 0.8210 (t) REVERT: E 120 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7456 (mmmt) REVERT: E 234 ASN cc_start: 0.8412 (m-40) cc_final: 0.7935 (m-40) REVERT: E 282 LYS cc_start: 0.7486 (tmtt) cc_final: 0.7131 (tmmt) outliers start: 21 outliers final: 9 residues processed: 240 average time/residue: 0.7965 time to fit residues: 214.0757 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 : 1.104 ------------------------------------------------------------------------------- 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 126 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.183485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168002 restraints weight = 13351.573| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.66 r_work: 0.3923 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2946 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= 0.181 Angle : 0.571 6.523 15278 Z= 0.322 Chirality : 0.043 0.157 1743 Planarity : 0.004 0.045 1862 Dihedral : 4.700 21.034 1525 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.87 % Allowed : 16.97 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1389 helix: 0.69 (0.15), residues: 1084 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 165 PHE 0.029 0.002 PHE A 223 TYR 0.026 0.002 TYR C 69 ARG 0.002 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 774) hydrogen bonds : angle 4.54917 ( 2316) covalent geometry : bond 0.00408 (11275) covalent geometry : angle 0.57129 (15278) *********************** 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 264 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 1.093 Fit side-chains REVERT: A 163 LYS cc_start: 0.7600 (tttm) cc_final: 0.7132 (mptt) REVERT: A 207 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7111 (mtmm) REVERT: A 251 TYR cc_start: 0.8386 (t80) cc_final: 0.8182 (t80) REVERT: A 258 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7989 (mm) REVERT: B 52 MET cc_start: 0.5520 (tpp) cc_final: 0.5078 (tmt) REVERT: B 149 SER cc_start: 0.9111 (t) cc_final: 0.8708 (m) REVERT: B 195 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: C 67 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7768 (tt) REVERT: C 69 TYR cc_start: 0.8430 (t80) cc_final: 0.7681 (t80) REVERT: C 119 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8147 (mttp) REVERT: D 33 LYS cc_start: 0.7411 (tttm) cc_final: 0.7019 (tppt) REVERT: D 195 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.5933 (m-80) REVERT: D 200 VAL cc_start: 0.8608 (t) cc_final: 0.8396 (t) REVERT: D 223 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.6786 (t80) REVERT: D 251 TYR cc_start: 0.6902 (t80) cc_final: 0.6633 (t80) REVERT: E 223 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.6678 (t80) REVERT: E 282 LYS cc_start: 0.7405 (tmtt) cc_final: 0.7083 (tmmt) outliers start: 33 outliers final: 16 residues processed: 245 average time/residue: 0.7575 time to fit residues: 208.7571 Evaluate side-chains 236 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 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 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 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 272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 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 = 0.4168 r_free = 0.4168 target = 0.184579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169197 restraints weight = 13254.570| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.65 r_work: 0.3901 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11275 Z= 0.155 Angle : 0.538 7.103 15278 Z= 0.302 Chirality : 0.042 0.149 1743 Planarity : 0.003 0.044 1862 Dihedral : 4.540 20.987 1525 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.74 % Allowed : 19.15 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1389 helix: 0.96 (0.16), residues: 1090 sheet: None (None), residues: 0 loop : -2.41 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 37 PHE 0.029 0.001 PHE A 223 TYR 0.020 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 774) hydrogen bonds : angle 4.39460 ( 2316) covalent geometry : bond 0.00344 (11275) covalent geometry : angle 0.53843 (15278) *********************** 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 268 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 1.158 Fit side-chains REVERT: A 163 LYS cc_start: 0.7707 (tttm) cc_final: 0.7152 (mptt) REVERT: A 207 LYS cc_start: 0.7373 (mtpt) cc_final: 0.7004 (mtmm) REVERT: A 258 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (mm) REVERT: B 52 MET cc_start: 0.5607 (tpp) cc_final: 0.5131 (tmt) REVERT: B 134 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 149 SER cc_start: 0.9111 (t) cc_final: 0.8656 (m) REVERT: B 195 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: C 56 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7580 (tp) REVERT: C 67 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7747 (tt) REVERT: C 69 TYR cc_start: 0.8364 (t80) cc_final: 0.7489 (t80) REVERT: C 119 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8091 (mttp) REVERT: C 146 PHE cc_start: 0.7347 (t80) cc_final: 0.7129 (t80) REVERT: C 267 ILE cc_start: 0.7182 (mt) cc_final: 0.6861 (mt) REVERT: D 33 LYS cc_start: 0.7367 (tttm) cc_final: 0.6966 (tppt) REVERT: D 195 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: D 200 VAL cc_start: 0.8538 (t) cc_final: 0.8317 (t) REVERT: D 223 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.6892 (t80) REVERT: E 122 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7078 (mmtp) REVERT: E 163 LYS cc_start: 0.7066 (mttm) cc_final: 0.6622 (mtmt) REVERT: E 223 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.6771 (t80) REVERT: E 282 LYS cc_start: 0.7567 (tmtt) cc_final: 0.7200 (tmmt) outliers start: 43 outliers final: 19 residues processed: 246 average time/residue: 0.7678 time to fit residues: 212.6331 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 : 1.080 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU 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 231 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.183171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167599 restraints weight = 13345.830| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.66 r_work: 0.3903 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11275 Z= 0.169 Angle : 0.550 6.573 15278 Z= 0.309 Chirality : 0.042 0.164 1743 Planarity : 0.003 0.042 1862 Dihedral : 4.568 21.119 1525 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.09 % Allowed : 20.19 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1389 helix: 0.99 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 165 PHE 0.026 0.002 PHE A 223 TYR 0.018 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 774) hydrogen bonds : angle 4.45481 ( 2316) covalent geometry : bond 0.00379 (11275) covalent geometry : angle 0.55017 (15278) *********************** 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 272 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7699 (tttm) cc_final: 0.7192 (mptt) REVERT: A 207 LYS cc_start: 0.7234 (mtpt) cc_final: 0.7017 (mtmm) REVERT: A 258 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7992 (mm) REVERT: B 52 MET cc_start: 0.5581 (tpp) cc_final: 0.5091 (tmt) REVERT: B 134 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7947 (mt) REVERT: B 149 SER cc_start: 0.9107 (t) cc_final: 0.8642 (m) REVERT: B 195 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 223 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8273 (t80) REVERT: C 56 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7595 (tp) REVERT: C 67 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7605 (tt) REVERT: C 69 TYR cc_start: 0.8384 (t80) cc_final: 0.7583 (t80) REVERT: C 119 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8076 (mttp) REVERT: C 146 PHE cc_start: 0.7594 (t80) cc_final: 0.7341 (t80) REVERT: C 267 ILE cc_start: 0.7195 (mt) cc_final: 0.6869 (mt) REVERT: D 33 LYS cc_start: 0.7391 (tttm) cc_final: 0.6989 (tppt) REVERT: D 195 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: D 200 VAL cc_start: 0.8558 (t) cc_final: 0.8334 (t) REVERT: D 223 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.6979 (t80) REVERT: E 34 LYS cc_start: 0.6127 (mmmt) cc_final: 0.4334 (ptpt) REVERT: E 122 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7082 (mmtp) REVERT: E 223 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6769 (t80) REVERT: E 282 LYS cc_start: 0.7589 (tmtt) cc_final: 0.7223 (tmmt) outliers start: 47 outliers final: 24 residues processed: 245 average time/residue: 0.7403 time to fit residues: 205.1883 Evaluate side-chains 253 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 52 MET 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 52 MET 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 122 LYS 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 100 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS E 193 ASN E 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.180559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165028 restraints weight = 13378.354| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.67 r_work: 0.3886 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11275 Z= 0.204 Angle : 0.592 6.305 15278 Z= 0.331 Chirality : 0.044 0.173 1743 Planarity : 0.004 0.042 1862 Dihedral : 4.739 21.634 1525 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.87 % Allowed : 19.84 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1389 helix: 0.87 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -2.35 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 165 PHE 0.028 0.002 PHE A 288 TYR 0.018 0.002 TYR C 69 ARG 0.002 0.000 ARG C 128 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 774) hydrogen bonds : angle 4.56882 ( 2316) covalent geometry : bond 0.00464 (11275) covalent geometry : angle 0.59174 (15278) *********************** 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 285 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7768 (tttm) cc_final: 0.7265 (mptp) REVERT: A 207 LYS cc_start: 0.7266 (mtpt) cc_final: 0.6996 (mtmm) REVERT: A 258 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7987 (mm) REVERT: B 52 MET cc_start: 0.5545 (tpp) cc_final: 0.5041 (tmt) REVERT: B 195 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: B 223 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8318 (t80) REVERT: C 35 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7497 (mtpp) REVERT: C 56 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7603 (tp) REVERT: C 67 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7604 (tt) REVERT: C 69 TYR cc_start: 0.8393 (t80) cc_final: 0.7632 (t80) REVERT: C 119 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8066 (mttp) REVERT: C 146 PHE cc_start: 0.7655 (t80) cc_final: 0.7410 (t80) REVERT: C 267 ILE cc_start: 0.7181 (mt) cc_final: 0.6877 (mt) REVERT: D 33 LYS cc_start: 0.7367 (tttm) cc_final: 0.7060 (tppt) REVERT: D 195 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: D 200 VAL cc_start: 0.8574 (t) cc_final: 0.8344 (t) REVERT: D 223 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.6951 (t80) REVERT: E 122 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7124 (mmtp) REVERT: E 193 ASN cc_start: 0.8049 (t0) cc_final: 0.7678 (t0) REVERT: E 223 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.6852 (t80) REVERT: E 234 ASN cc_start: 0.8616 (m-40) cc_final: 0.8141 (m-40) REVERT: E 282 LYS cc_start: 0.7518 (tmtt) cc_final: 0.7186 (tmmt) outliers start: 56 outliers final: 30 residues processed: 258 average time/residue: 0.7377 time to fit residues: 215.6374 Evaluate side-chains 257 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 52 MET 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 40 ASN Chi-restraints excluded: chain D residue 52 MET 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 231 ILE 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 122 LYS Chi-restraints excluded: chain E residue 161 VAL 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 120 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 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 = 0.4157 r_free = 0.4157 target = 0.183380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167722 restraints weight = 13538.639| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.69 r_work: 0.3904 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11275 Z= 0.155 Angle : 0.546 7.199 15278 Z= 0.304 Chirality : 0.042 0.204 1743 Planarity : 0.003 0.042 1862 Dihedral : 4.552 21.415 1525 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.35 % Allowed : 21.06 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1389 helix: 1.04 (0.15), residues: 1096 sheet: None (None), residues: 0 loop : -2.23 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.031 0.001 PHE A 288 TYR 0.015 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 774) hydrogen bonds : angle 4.41259 ( 2316) covalent geometry : bond 0.00344 (11275) covalent geometry : angle 0.54612 (15278) *********************** 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 273 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7633 (tttm) cc_final: 0.7241 (mptt) REVERT: A 207 LYS cc_start: 0.7285 (mtpt) cc_final: 0.7014 (mtmm) REVERT: A 223 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.5593 (p90) REVERT: A 263 LEU cc_start: 0.8455 (tp) cc_final: 0.8136 (tp) REVERT: B 52 MET cc_start: 0.5560 (tpp) cc_final: 0.5073 (tmt) REVERT: B 195 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: C 35 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7483 (mtpp) REVERT: C 56 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7580 (tp) REVERT: C 67 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7687 (tt) REVERT: C 69 TYR cc_start: 0.8336 (t80) cc_final: 0.7420 (t80) REVERT: C 119 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8050 (mttp) REVERT: C 146 PHE cc_start: 0.7665 (t80) cc_final: 0.7377 (t80) REVERT: D 33 LYS cc_start: 0.7367 (tttm) cc_final: 0.7009 (tppt) REVERT: D 195 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: D 200 VAL cc_start: 0.8502 (t) cc_final: 0.8267 (t) REVERT: D 223 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7010 (t80) REVERT: E 223 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6492 (t80) REVERT: E 234 ASN cc_start: 0.8568 (m-40) cc_final: 0.8080 (m-40) REVERT: E 282 LYS cc_start: 0.7569 (tmtt) cc_final: 0.7194 (tmmt) outliers start: 50 outliers final: 32 residues processed: 247 average time/residue: 0.7763 time to fit residues: 217.0132 Evaluate side-chains 251 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 223 PHE 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 163 LYS Chi-restraints excluded: chain B residue 195 PHE 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 C residue 52 MET 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 52 MET 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 231 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4166 r_free = 0.4166 target = 0.184316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168764 restraints weight = 13303.767| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.67 r_work: 0.3932 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11275 Z= 0.146 Angle : 0.534 9.127 15278 Z= 0.298 Chirality : 0.042 0.215 1743 Planarity : 0.003 0.041 1862 Dihedral : 4.454 20.998 1525 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.09 % Allowed : 21.67 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1389 helix: 1.17 (0.16), residues: 1093 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.032 0.001 PHE A 288 TYR 0.015 0.001 TYR A 286 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 774) hydrogen bonds : angle 4.33940 ( 2316) covalent geometry : bond 0.00322 (11275) covalent geometry : angle 0.53447 (15278) *********************** 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 259 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7579 (tttm) cc_final: 0.7269 (mptt) REVERT: A 207 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6993 (mtmm) REVERT: A 223 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.5538 (p90) REVERT: A 263 LEU cc_start: 0.8456 (tp) cc_final: 0.8152 (tp) REVERT: B 52 MET cc_start: 0.5597 (tpp) cc_final: 0.5123 (tmt) REVERT: B 149 SER cc_start: 0.9051 (t) cc_final: 0.8598 (m) REVERT: C 35 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7471 (mtpp) REVERT: C 56 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 67 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7667 (tt) REVERT: C 69 TYR cc_start: 0.8309 (t80) cc_final: 0.7350 (t80) REVERT: C 119 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8065 (mttp) REVERT: C 146 PHE cc_start: 0.7663 (t80) cc_final: 0.7442 (t80) REVERT: D 33 LYS cc_start: 0.7351 (tttm) cc_final: 0.6966 (tppt) REVERT: D 195 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: D 200 VAL cc_start: 0.8483 (t) cc_final: 0.8242 (t) REVERT: D 223 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7064 (t80) REVERT: D 247 LYS cc_start: 0.6095 (ttpm) cc_final: 0.5810 (ttpm) REVERT: E 122 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7100 (mmtp) REVERT: E 234 ASN cc_start: 0.8534 (m-40) cc_final: 0.8091 (m-40) REVERT: E 282 LYS cc_start: 0.7546 (tmtt) cc_final: 0.7202 (tmmt) outliers start: 47 outliers final: 31 residues processed: 236 average time/residue: 0.7896 time to fit residues: 209.2601 Evaluate side-chains 246 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 223 PHE 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 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 52 MET 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 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 273 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.186323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170706 restraints weight = 13378.705| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.68 r_work: 0.3943 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11275 Z= 0.131 Angle : 0.526 11.064 15278 Z= 0.290 Chirality : 0.041 0.221 1743 Planarity : 0.003 0.041 1862 Dihedral : 4.338 20.736 1525 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.74 % Allowed : 22.45 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1389 helix: 1.31 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.032 0.001 PHE A 288 TYR 0.017 0.001 TYR A 286 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 774) hydrogen bonds : angle 4.24778 ( 2316) covalent geometry : bond 0.00284 (11275) covalent geometry : angle 0.52627 (15278) *********************** 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 257 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7571 (tttm) cc_final: 0.7266 (mptt) REVERT: A 207 LYS cc_start: 0.7208 (mtpt) cc_final: 0.6941 (mtmm) REVERT: A 223 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.5473 (p90) REVERT: A 263 LEU cc_start: 0.8429 (tp) cc_final: 0.8119 (tp) REVERT: B 52 MET cc_start: 0.5576 (tpp) cc_final: 0.5107 (tmt) REVERT: B 56 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 134 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 149 SER cc_start: 0.9025 (t) cc_final: 0.8593 (m) REVERT: C 35 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7491 (mtpp) REVERT: C 56 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7564 (tp) REVERT: C 67 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 69 TYR cc_start: 0.8253 (t80) cc_final: 0.7064 (t80) REVERT: C 119 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8045 (mttp) REVERT: C 267 ILE cc_start: 0.7065 (mt) cc_final: 0.6757 (mt) REVERT: D 33 LYS cc_start: 0.7369 (tttm) cc_final: 0.6964 (tppt) REVERT: D 195 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: D 200 VAL cc_start: 0.8445 (t) cc_final: 0.8198 (t) REVERT: D 247 LYS cc_start: 0.6084 (ttpm) cc_final: 0.5854 (ttpm) REVERT: E 108 ASN cc_start: 0.7765 (p0) cc_final: 0.7435 (p0) REVERT: E 122 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7085 (mmtp) REVERT: E 282 LYS cc_start: 0.7517 (tmtt) cc_final: 0.7138 (tmmt) outliers start: 43 outliers final: 24 residues processed: 237 average time/residue: 0.8948 time to fit residues: 237.1775 Evaluate side-chains 239 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 LEU 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 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 52 MET 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 110 LEU Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS 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 104 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 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 = 0.4177 r_free = 0.4177 target = 0.185481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169939 restraints weight = 13233.072| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.65 r_work: 0.3936 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11275 Z= 0.141 Angle : 0.540 11.814 15278 Z= 0.298 Chirality : 0.041 0.225 1743 Planarity : 0.003 0.041 1862 Dihedral : 4.361 20.470 1525 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.31 % Allowed : 22.98 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1389 helix: 1.27 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -2.25 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.032 0.001 PHE A 288 TYR 0.017 0.001 TYR E 251 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 774) hydrogen bonds : angle 4.28349 ( 2316) covalent geometry : bond 0.00310 (11275) covalent geometry : angle 0.54041 (15278) ********************** 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 245 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7513 (tttm) cc_final: 0.7242 (mptt) REVERT: A 207 LYS cc_start: 0.7165 (mtpt) cc_final: 0.6922 (mtmm) REVERT: A 223 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.5386 (p90) REVERT: B 52 MET cc_start: 0.5526 (tpp) cc_final: 0.5058 (tmt) REVERT: B 56 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 134 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 149 SER cc_start: 0.9053 (t) cc_final: 0.8618 (m) REVERT: B 252 GLN cc_start: 0.8296 (mt0) cc_final: 0.8086 (mt0) REVERT: C 35 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7472 (mtpp) REVERT: C 56 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7567 (tp) REVERT: C 67 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7658 (tt) REVERT: C 69 TYR cc_start: 0.8320 (t80) cc_final: 0.7116 (t80) REVERT: C 119 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8029 (mttp) REVERT: C 179 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6943 (t70) REVERT: C 267 ILE cc_start: 0.7038 (mt) cc_final: 0.6741 (mt) REVERT: D 33 LYS cc_start: 0.7387 (tttm) cc_final: 0.6967 (tppt) REVERT: D 195 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: D 200 VAL cc_start: 0.8436 (t) cc_final: 0.8191 (t) REVERT: D 223 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7097 (t80) REVERT: D 247 LYS cc_start: 0.6107 (ttpm) cc_final: 0.5885 (ttpm) REVERT: E 122 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7065 (mmtp) REVERT: E 282 LYS cc_start: 0.7520 (tmtt) cc_final: 0.7146 (tmmt) outliers start: 38 outliers final: 26 residues processed: 227 average time/residue: 0.7987 time to fit residues: 203.6465 Evaluate side-chains 242 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 223 PHE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 LEU 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 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 52 MET 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 204 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 273 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS 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 22 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 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 = 0.4187 r_free = 0.4187 target = 0.186598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171088 restraints weight = 13164.068| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.66 r_work: 0.3953 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11275 Z= 0.133 Angle : 0.531 12.042 15278 Z= 0.293 Chirality : 0.041 0.225 1743 Planarity : 0.003 0.040 1862 Dihedral : 4.309 20.445 1525 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.48 % Allowed : 23.15 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1389 helix: 1.35 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -2.23 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.032 0.001 PHE A 288 TYR 0.019 0.001 TYR A 286 ARG 0.004 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 774) hydrogen bonds : angle 4.24332 ( 2316) covalent geometry : bond 0.00289 (11275) covalent geometry : angle 0.53082 (15278) =============================================================================== Job complete usr+sys time: 7908.85 seconds wall clock time: 137 minutes 49.62 seconds (8269.62 seconds total)