Starting phenix.real_space_refine on Wed Sep 17 14:41:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr4_45832/09_2025/9cr4_45832.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 52 5.16 5 C 5833 2.51 5 N 1533 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9099 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2291 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2257 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 18, 'TRANS': 274} Chain breaks: 3 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2272 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 18, 'TRANS': 275} Chain breaks: 2 Chain: "D" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2279 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 18, 'TRANS': 276} Chain breaks: 2 Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 9099 At special positions: 0 Unit cell: (96.9525, 103.208, 88.6125, 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 52 16.00 O 1681 8.00 N 1533 7.00 C 5833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 279.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 27.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.851A pdb=" N ASP A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.512A pdb=" N LYS A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.629A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.997A pdb=" N THR A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 412 through 425 removed outlier: 3.659A pdb=" N TRP A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.515A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 144 removed outlier: 3.829A pdb=" N GLU B 144 " --> pdb=" O LYS B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 145 through 151 removed outlier: 3.540A pdb=" N ASP B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 4.289A pdb=" N LYS B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 removed outlier: 3.541A pdb=" N PHE B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.963A pdb=" N THR B 325 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.869A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 331' Processing helix chain 'B' and resid 412 through 425 removed outlier: 3.539A pdb=" N GLN B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.518A pdb=" N GLU C 132 " --> pdb=" O HIS C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 144 removed outlier: 3.825A pdb=" N GLU C 144 " --> pdb=" O LYS C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.624A pdb=" N ASP C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 4.062A pdb=" N LYS C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.749A pdb=" N TYR C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.123A pdb=" N THR C 325 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.564A pdb=" N GLU D 132 " --> pdb=" O HIS D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 144 removed outlier: 3.834A pdb=" N GLU D 144 " --> pdb=" O LYS D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 145 through 151 removed outlier: 3.656A pdb=" N ASP D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.929A pdb=" N LYS D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 320 through 325 removed outlier: 3.915A pdb=" N THR D 325 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.780A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 414 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 5.787A pdb=" N VAL A 107 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER A 106 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 179 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 108 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 181 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 110 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 282 removed outlier: 3.646A pdb=" N GLY A 313 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 299 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 309 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 313 " --> pdb=" O PRO A 350 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 315 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 282 removed outlier: 3.646A pdb=" N GLY A 313 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 299 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 309 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.709A pdb=" N MET A 335 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.074A pdb=" N VAL B 107 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.792A pdb=" N MET B 278 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 244 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER B 297 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 312 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 299 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR B 310 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 301 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY B 313 " --> pdb=" O PRO B 350 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 315 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.792A pdb=" N MET B 278 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 244 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER B 297 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 312 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 299 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR B 310 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 301 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 135 through 138 removed outlier: 5.859A pdb=" N VAL C 107 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 178 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE C 204 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS C 180 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 237 removed outlier: 4.509A pdb=" N ALA C 233 " --> pdb=" O CYS C 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 278 through 282 removed outlier: 3.634A pdb=" N GLY C 313 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 299 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C 309 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 348 removed outlier: 3.619A pdb=" N GLY C 315 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.762A pdb=" N MET C 335 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB8, first strand: chain 'D' and resid 135 through 138 removed outlier: 5.771A pdb=" N VAL D 107 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER D 106 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE D 179 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 108 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU D 181 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 110 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AC1, first strand: chain 'D' and resid 278 through 282 removed outlier: 3.742A pdb=" N MET D 278 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 399 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 297 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN D 312 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL D 299 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR D 310 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL D 301 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 347 through 348 removed outlier: 3.597A pdb=" N GLY D 315 " --> pdb=" O ILE D 348 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2923 1.34 - 1.46: 1630 1.46 - 1.57: 4660 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9297 Sorted by residual: bond pdb=" C SER A 293 " pdb=" N SER A 294 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.41e-01 bond pdb=" CB ILE C 317 " pdb=" CG1 ILE C 317 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.60e-01 bond pdb=" C GLY A 363 " pdb=" N VAL A 364 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.73e-02 3.34e+03 6.39e-01 bond pdb=" CB ILE D 317 " pdb=" CG1 ILE D 317 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.35e-01 bond pdb=" C PHE D 355 " pdb=" N ARG D 356 " ideal model delta sigma weight residual 1.340 1.295 0.045 5.87e-02 2.90e+02 5.93e-01 ... (remaining 9292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12392 1.65 - 3.30: 210 3.30 - 4.94: 23 4.94 - 6.59: 9 6.59 - 8.24: 4 Bond angle restraints: 12638 Sorted by residual: angle pdb=" N LYS B 105 " pdb=" CA LYS B 105 " pdb=" C LYS B 105 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.69e+00 angle pdb=" OG1 THR D 162 " pdb=" CB THR D 162 " pdb=" CG2 THR D 162 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" OG1 THR A 162 " pdb=" CB THR A 162 " pdb=" CG2 THR A 162 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.97e+00 angle pdb=" OG1 THR C 162 " pdb=" CB THR C 162 " pdb=" CG2 THR C 162 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" OG1 THR B 162 " pdb=" CB THR B 162 " pdb=" CG2 THR B 162 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.91e+00 ... (remaining 12633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5392 17.86 - 35.72: 186 35.72 - 53.59: 22 53.59 - 71.45: 2 71.45 - 89.31: 6 Dihedral angle restraints: 5608 sinusoidal: 2193 harmonic: 3415 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N SER C 319 " pdb=" CA SER C 319 " ideal model delta harmonic sigma weight residual 180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N SER A 319 " pdb=" CA SER A 319 " ideal model delta harmonic sigma weight residual -180.00 -163.81 -16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N SER D 319 " pdb=" CA SER D 319 " ideal model delta harmonic sigma weight residual 180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1001 0.038 - 0.077: 284 0.077 - 0.115: 154 0.115 - 0.153: 40 0.153 - 0.192: 7 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB ILE D 317 " pdb=" CA ILE D 317 " pdb=" CG1 ILE D 317 " pdb=" CG2 ILE D 317 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CB ILE C 317 " pdb=" CA ILE C 317 " pdb=" CG1 ILE C 317 " pdb=" CG2 ILE C 317 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1483 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 317 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C ILE A 317 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 317 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 318 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 317 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C ILE C 317 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE C 317 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 318 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 317 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE D 317 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE D 317 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL D 318 " 0.010 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 492 2.73 - 3.27: 9158 3.27 - 3.82: 14028 3.82 - 4.36: 17488 4.36 - 4.90: 29914 Nonbonded interactions: 71080 Sorted by model distance: nonbonded pdb=" OD1 ASP D 412 " pdb=" OG SER D 415 " model vdw 2.190 3.040 nonbonded pdb=" O LEU A 283 " pdb=" OG1 THR A 320 " model vdw 2.230 3.040 nonbonded pdb=" O GLU B 419 " pdb=" NE2 GLN B 423 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP B 412 " pdb=" OG SER B 415 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP A 412 " pdb=" OG SER A 415 " model vdw 2.251 3.040 ... (remaining 71075 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 96 through 162 or resid 174 through 246 or resid 277 throu \ gh 294 or resid 296 through 428)) selection = (chain 'B' and resid 96 through 428) selection = (chain 'C' and (resid 96 through 246 or resid 277 through 294 or resid 296 throu \ gh 428)) selection = (chain 'D' and (resid 96 through 162 or resid 174 through 246 or resid 277 throu \ gh 294 or resid 296 through 428)) } 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: 1.080 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.003 0.045 9297 Z= 0.127 Angle : 0.560 8.240 12638 Z= 0.291 Chirality : 0.048 0.192 1486 Planarity : 0.005 0.036 1598 Dihedral : 9.516 89.310 3386 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.25), residues: 1153 helix: 1.18 (0.37), residues: 218 sheet: 0.53 (0.30), residues: 325 loop : -1.28 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.015 0.001 TYR B 327 PHE 0.008 0.001 PHE B 418 TRP 0.007 0.001 TRP C 417 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9297) covalent geometry : angle 0.56040 (12638) hydrogen bonds : bond 0.24651 ( 334) hydrogen bonds : angle 8.46370 ( 954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 216 SER cc_start: 0.7938 (t) cc_final: 0.7616 (p) REVERT: A 220 PHE cc_start: 0.8060 (p90) cc_final: 0.7637 (p90) REVERT: A 312 GLN cc_start: 0.8290 (mt0) cc_final: 0.8008 (mt0) REVERT: A 369 MET cc_start: 0.8075 (ptm) cc_final: 0.7806 (ptp) REVERT: B 130 MET cc_start: 0.6839 (tpp) cc_final: 0.6610 (mmm) REVERT: B 179 ILE cc_start: 0.8316 (mt) cc_final: 0.7970 (tt) REVERT: B 216 SER cc_start: 0.8199 (t) cc_final: 0.7825 (p) REVERT: B 219 ASN cc_start: 0.8558 (t0) cc_final: 0.8250 (t0) REVERT: B 235 VAL cc_start: 0.7974 (t) cc_final: 0.7746 (m) REVERT: B 377 THR cc_start: 0.7720 (p) cc_final: 0.7418 (m) REVERT: C 110 ILE cc_start: 0.8163 (mp) cc_final: 0.7925 (mt) REVERT: C 113 MET cc_start: 0.5623 (mmm) cc_final: 0.5377 (mmm) REVERT: C 130 MET cc_start: 0.6256 (tpp) cc_final: 0.6054 (tpp) REVERT: C 179 ILE cc_start: 0.8296 (mt) cc_final: 0.8026 (mm) REVERT: C 186 THR cc_start: 0.7807 (m) cc_final: 0.7551 (p) REVERT: C 215 PHE cc_start: 0.7695 (m-80) cc_final: 0.7168 (m-80) REVERT: C 309 THR cc_start: 0.8086 (t) cc_final: 0.7653 (m) REVERT: D 179 ILE cc_start: 0.8356 (mt) cc_final: 0.8131 (mm) REVERT: D 216 SER cc_start: 0.7980 (t) cc_final: 0.7711 (p) REVERT: D 369 MET cc_start: 0.7756 (ptm) cc_final: 0.7546 (ptp) REVERT: D 377 THR cc_start: 0.8710 (p) cc_final: 0.8452 (p) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4075 time to fit residues: 98.4450 Evaluate side-chains 191 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 423 GLN C 281 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.179799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.151318 restraints weight = 11791.131| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.62 r_work: 0.3896 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9297 Z= 0.151 Angle : 0.590 7.436 12638 Z= 0.310 Chirality : 0.048 0.182 1486 Planarity : 0.005 0.035 1598 Dihedral : 4.368 15.661 1241 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.33 % Allowed : 8.16 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1153 helix: 1.10 (0.36), residues: 235 sheet: 0.64 (0.30), residues: 314 loop : -1.18 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 385 TYR 0.015 0.002 TYR B 327 PHE 0.013 0.001 PHE D 217 TRP 0.020 0.001 TRP D 379 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9297) covalent geometry : angle 0.59010 (12638) hydrogen bonds : bond 0.04775 ( 334) hydrogen bonds : angle 5.89506 ( 954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8129 (p90) cc_final: 0.7726 (p90) REVERT: A 312 GLN cc_start: 0.8498 (mt0) cc_final: 0.8269 (mm-40) REVERT: B 130 MET cc_start: 0.6725 (tpp) cc_final: 0.6506 (mmm) REVERT: B 132 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: B 179 ILE cc_start: 0.7830 (mt) cc_final: 0.7474 (tt) REVERT: B 377 THR cc_start: 0.7633 (p) cc_final: 0.6936 (t) REVERT: B 419 GLU cc_start: 0.7640 (tt0) cc_final: 0.7384 (tt0) REVERT: C 113 MET cc_start: 0.5490 (mmm) cc_final: 0.5234 (mmm) REVERT: C 130 MET cc_start: 0.6440 (tpp) cc_final: 0.6171 (tpp) REVERT: C 137 TYR cc_start: 0.7317 (m-80) cc_final: 0.6882 (m-80) REVERT: C 144 GLU cc_start: 0.6747 (pt0) cc_final: 0.6492 (pt0) REVERT: C 179 ILE cc_start: 0.7952 (mt) cc_final: 0.7622 (mm) REVERT: C 223 GLN cc_start: 0.6876 (mt0) cc_final: 0.6419 (mt0) REVERT: C 309 THR cc_start: 0.8061 (t) cc_final: 0.7764 (m) REVERT: C 312 GLN cc_start: 0.8354 (mt0) cc_final: 0.8062 (mm-40) REVERT: C 410 VAL cc_start: 0.8661 (m) cc_final: 0.8412 (p) REVERT: D 415 SER cc_start: 0.7293 (p) cc_final: 0.7033 (p) REVERT: D 419 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7171 (tm-30) outliers start: 24 outliers final: 10 residues processed: 196 average time/residue: 0.4631 time to fit residues: 97.8894 Evaluate side-chains 192 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.0070 chunk 2 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.182030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153603 restraints weight = 11844.546| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.59 r_work: 0.3932 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9297 Z= 0.109 Angle : 0.541 6.605 12638 Z= 0.282 Chirality : 0.046 0.241 1486 Planarity : 0.005 0.038 1598 Dihedral : 4.216 16.497 1241 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.04 % Allowed : 13.11 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1153 helix: 1.25 (0.36), residues: 235 sheet: 0.71 (0.30), residues: 314 loop : -1.10 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.010 0.001 TYR B 189 PHE 0.011 0.001 PHE A 177 TRP 0.009 0.001 TRP D 379 HIS 0.002 0.000 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9297) covalent geometry : angle 0.54110 (12638) hydrogen bonds : bond 0.03827 ( 334) hydrogen bonds : angle 5.34326 ( 954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 179 ILE cc_start: 0.7711 (mp) cc_final: 0.7309 (tt) REVERT: A 220 PHE cc_start: 0.8093 (p90) cc_final: 0.7708 (p90) REVERT: B 130 MET cc_start: 0.6733 (tpp) cc_final: 0.6499 (mmm) REVERT: B 179 ILE cc_start: 0.7772 (mt) cc_final: 0.7405 (tt) REVERT: B 377 THR cc_start: 0.7663 (p) cc_final: 0.7361 (t) REVERT: B 419 GLU cc_start: 0.7601 (tt0) cc_final: 0.7335 (tt0) REVERT: C 113 MET cc_start: 0.5452 (mmm) cc_final: 0.5217 (mmm) REVERT: C 130 MET cc_start: 0.6424 (tpp) cc_final: 0.6171 (tpp) REVERT: C 179 ILE cc_start: 0.7917 (mt) cc_final: 0.7486 (tt) REVERT: C 186 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7457 (p) REVERT: C 309 THR cc_start: 0.8000 (t) cc_final: 0.7725 (m) REVERT: D 179 ILE cc_start: 0.8439 (mt) cc_final: 0.8232 (mp) REVERT: D 219 ASN cc_start: 0.8149 (t0) cc_final: 0.7855 (t0) REVERT: D 220 PHE cc_start: 0.8054 (p90) cc_final: 0.7831 (p90) REVERT: D 415 SER cc_start: 0.7266 (p) cc_final: 0.6969 (p) REVERT: D 419 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7166 (tm-30) outliers start: 21 outliers final: 9 residues processed: 195 average time/residue: 0.4316 time to fit residues: 91.2282 Evaluate side-chains 188 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 104 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 284 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.182423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.153906 restraints weight = 12041.426| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.66 r_work: 0.3919 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9297 Z= 0.113 Angle : 0.544 6.799 12638 Z= 0.280 Chirality : 0.046 0.224 1486 Planarity : 0.005 0.038 1598 Dihedral : 4.234 15.768 1241 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.01 % Allowed : 13.69 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1153 helix: 1.39 (0.36), residues: 235 sheet: 0.76 (0.30), residues: 308 loop : -0.95 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 387 TYR 0.010 0.001 TYR B 137 PHE 0.014 0.001 PHE A 177 TRP 0.016 0.001 TRP B 379 HIS 0.002 0.000 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9297) covalent geometry : angle 0.54376 (12638) hydrogen bonds : bond 0.03475 ( 334) hydrogen bonds : angle 5.10731 ( 954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 179 ILE cc_start: 0.7711 (mp) cc_final: 0.7377 (tt) REVERT: A 312 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8132 (mm-40) REVERT: B 130 MET cc_start: 0.6762 (tpp) cc_final: 0.6511 (mmm) REVERT: B 137 TYR cc_start: 0.7538 (m-80) cc_final: 0.7242 (m-80) REVERT: B 179 ILE cc_start: 0.7797 (mt) cc_final: 0.7425 (tt) REVERT: B 377 THR cc_start: 0.7741 (p) cc_final: 0.7401 (t) REVERT: B 419 GLU cc_start: 0.7583 (tt0) cc_final: 0.7359 (tt0) REVERT: C 130 MET cc_start: 0.6458 (tpp) cc_final: 0.6205 (tpp) REVERT: C 179 ILE cc_start: 0.7931 (mt) cc_final: 0.7507 (tt) REVERT: C 309 THR cc_start: 0.8000 (t) cc_final: 0.7732 (m) REVERT: C 335 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7668 (mtp) REVERT: C 379 TRP cc_start: 0.8110 (m100) cc_final: 0.7773 (m100) REVERT: D 179 ILE cc_start: 0.8390 (mt) cc_final: 0.8178 (mp) REVERT: D 219 ASN cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: D 415 SER cc_start: 0.7269 (p) cc_final: 0.6952 (p) REVERT: D 419 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7217 (tm-30) outliers start: 31 outliers final: 15 residues processed: 192 average time/residue: 0.4391 time to fit residues: 91.5057 Evaluate side-chains 188 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 34 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN C 312 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149273 restraints weight = 12082.053| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.66 r_work: 0.3861 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9297 Z= 0.187 Angle : 0.598 6.846 12638 Z= 0.312 Chirality : 0.049 0.228 1486 Planarity : 0.005 0.038 1598 Dihedral : 4.555 15.452 1241 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.08 % Allowed : 13.88 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1153 helix: 1.44 (0.37), residues: 235 sheet: 0.90 (0.30), residues: 291 loop : -1.04 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 243 TYR 0.018 0.002 TYR B 137 PHE 0.013 0.002 PHE D 217 TRP 0.026 0.001 TRP B 379 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9297) covalent geometry : angle 0.59789 (12638) hydrogen bonds : bond 0.03659 ( 334) hydrogen bonds : angle 5.05885 ( 954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7741 (m-80) cc_final: 0.7521 (m-80) REVERT: A 220 PHE cc_start: 0.8230 (p90) cc_final: 0.8005 (p90) REVERT: A 312 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8037 (mm-40) REVERT: B 130 MET cc_start: 0.6947 (tpp) cc_final: 0.6713 (mmm) REVERT: B 137 TYR cc_start: 0.7707 (m-80) cc_final: 0.7227 (m-80) REVERT: B 158 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7479 (mtpt) REVERT: B 179 ILE cc_start: 0.7886 (mt) cc_final: 0.7528 (tt) REVERT: B 309 THR cc_start: 0.8203 (t) cc_final: 0.7848 (m) REVERT: B 377 THR cc_start: 0.7864 (p) cc_final: 0.7503 (t) REVERT: C 124 GLU cc_start: 0.7739 (tp30) cc_final: 0.7488 (tp30) REVERT: C 137 TYR cc_start: 0.7384 (m-80) cc_final: 0.6931 (m-80) REVERT: C 179 ILE cc_start: 0.7990 (mt) cc_final: 0.7654 (mm) REVERT: C 309 THR cc_start: 0.8076 (t) cc_final: 0.7814 (m) REVERT: C 335 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7786 (mmt) REVERT: D 179 ILE cc_start: 0.8459 (mt) cc_final: 0.8221 (mp) REVERT: D 219 ASN cc_start: 0.8112 (t0) cc_final: 0.7905 (t0) REVERT: D 415 SER cc_start: 0.7354 (p) cc_final: 0.6982 (p) REVERT: D 419 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 42 outliers final: 27 residues processed: 181 average time/residue: 0.4750 time to fit residues: 92.7181 Evaluate side-chains 191 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN C 312 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.175054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146465 restraints weight = 12011.597| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.64 r_work: 0.3830 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 9297 Z= 0.268 Angle : 0.663 7.379 12638 Z= 0.348 Chirality : 0.051 0.235 1486 Planarity : 0.006 0.049 1598 Dihedral : 4.930 20.079 1241 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.47 % Allowed : 15.24 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1153 helix: 1.28 (0.37), residues: 235 sheet: 0.89 (0.30), residues: 288 loop : -1.12 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 243 TYR 0.022 0.002 TYR B 137 PHE 0.019 0.002 PHE A 177 TRP 0.019 0.002 TRP B 379 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 9297) covalent geometry : angle 0.66286 (12638) hydrogen bonds : bond 0.04006 ( 334) hydrogen bonds : angle 5.12690 ( 954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.339 Fit side-chains REVERT: A 137 TYR cc_start: 0.7794 (m-80) cc_final: 0.7531 (m-80) REVERT: A 312 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8074 (mm-40) REVERT: B 132 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: B 137 TYR cc_start: 0.7828 (m-80) cc_final: 0.7348 (m-80) REVERT: B 179 ILE cc_start: 0.7897 (mt) cc_final: 0.7559 (tt) REVERT: B 309 THR cc_start: 0.8173 (t) cc_final: 0.7854 (m) REVERT: B 354 SER cc_start: 0.8443 (p) cc_final: 0.8214 (p) REVERT: B 364 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (t) REVERT: B 377 THR cc_start: 0.7891 (p) cc_final: 0.7496 (t) REVERT: B 400 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8107 (t) REVERT: C 137 TYR cc_start: 0.7404 (m-80) cc_final: 0.7059 (m-80) REVERT: C 179 ILE cc_start: 0.8017 (mt) cc_final: 0.7708 (mm) REVERT: C 309 THR cc_start: 0.8045 (t) cc_final: 0.7827 (m) REVERT: C 335 MET cc_start: 0.8070 (mpp) cc_final: 0.7806 (mmt) REVERT: D 137 TYR cc_start: 0.7370 (m-80) cc_final: 0.7126 (m-80) REVERT: D 179 ILE cc_start: 0.8490 (mt) cc_final: 0.8279 (mp) REVERT: D 419 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7323 (tm-30) outliers start: 46 outliers final: 30 residues processed: 194 average time/residue: 0.4996 time to fit residues: 104.2762 Evaluate side-chains 209 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.149414 restraints weight = 12025.064| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.66 r_work: 0.3857 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9297 Z= 0.146 Angle : 0.611 9.137 12638 Z= 0.318 Chirality : 0.047 0.199 1486 Planarity : 0.006 0.042 1598 Dihedral : 4.679 17.104 1241 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.59 % Allowed : 17.67 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 1153 helix: 1.38 (0.37), residues: 234 sheet: 0.89 (0.30), residues: 290 loop : -1.06 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 243 TYR 0.013 0.001 TYR B 327 PHE 0.023 0.001 PHE D 220 TRP 0.012 0.001 TRP B 379 HIS 0.002 0.000 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9297) covalent geometry : angle 0.61072 (12638) hydrogen bonds : bond 0.03649 ( 334) hydrogen bonds : angle 4.96869 ( 954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.345 Fit side-chains REVERT: A 134 MET cc_start: 0.6168 (mmt) cc_final: 0.5690 (tpt) REVERT: A 220 PHE cc_start: 0.8210 (p90) cc_final: 0.7966 (p90) REVERT: A 312 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8143 (mm-40) REVERT: B 132 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: B 137 TYR cc_start: 0.7656 (m-80) cc_final: 0.7250 (m-80) REVERT: B 158 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7520 (mtpt) REVERT: B 179 ILE cc_start: 0.7792 (mt) cc_final: 0.7432 (tt) REVERT: B 354 SER cc_start: 0.8429 (p) cc_final: 0.8201 (p) REVERT: B 377 THR cc_start: 0.7860 (p) cc_final: 0.7397 (t) REVERT: C 137 TYR cc_start: 0.7273 (m-80) cc_final: 0.6926 (m-80) REVERT: C 178 ILE cc_start: 0.7834 (mt) cc_final: 0.7554 (mt) REVERT: C 179 ILE cc_start: 0.7887 (mt) cc_final: 0.7465 (tt) REVERT: C 186 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7491 (p) REVERT: C 237 ARG cc_start: 0.8368 (mpt90) cc_final: 0.7957 (mtt90) REVERT: C 309 THR cc_start: 0.8066 (t) cc_final: 0.7820 (m) REVERT: D 179 ILE cc_start: 0.8431 (mt) cc_final: 0.8192 (mp) REVERT: D 415 SER cc_start: 0.7349 (p) cc_final: 0.6975 (p) REVERT: D 419 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7244 (tm-30) outliers start: 37 outliers final: 23 residues processed: 191 average time/residue: 0.4987 time to fit residues: 102.3259 Evaluate side-chains 198 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.178115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.149764 restraints weight = 11971.729| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.65 r_work: 0.3858 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9297 Z= 0.148 Angle : 0.602 8.498 12638 Z= 0.312 Chirality : 0.047 0.225 1486 Planarity : 0.005 0.050 1598 Dihedral : 4.608 18.305 1241 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.30 % Allowed : 19.03 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1153 helix: 1.41 (0.37), residues: 234 sheet: 0.91 (0.30), residues: 290 loop : -1.05 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 243 TYR 0.013 0.001 TYR A 137 PHE 0.017 0.002 PHE A 177 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.000 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9297) covalent geometry : angle 0.60214 (12638) hydrogen bonds : bond 0.03561 ( 334) hydrogen bonds : angle 4.89055 ( 954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.355 Fit side-chains REVERT: A 134 MET cc_start: 0.6098 (mmt) cc_final: 0.5716 (tpt) REVERT: A 312 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8136 (mm-40) REVERT: B 132 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: B 137 TYR cc_start: 0.7635 (m-80) cc_final: 0.7175 (m-80) REVERT: B 158 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7564 (mtpt) REVERT: B 179 ILE cc_start: 0.7740 (mt) cc_final: 0.7394 (tt) REVERT: B 354 SER cc_start: 0.8423 (p) cc_final: 0.8196 (p) REVERT: B 377 THR cc_start: 0.7783 (p) cc_final: 0.7067 (t) REVERT: C 137 TYR cc_start: 0.7253 (m-80) cc_final: 0.6916 (m-80) REVERT: C 178 ILE cc_start: 0.7826 (mt) cc_final: 0.7554 (mt) REVERT: C 179 ILE cc_start: 0.7901 (mt) cc_final: 0.7464 (tt) REVERT: C 237 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8000 (mtt90) REVERT: C 309 THR cc_start: 0.8044 (t) cc_final: 0.7804 (m) REVERT: C 364 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (t) REVERT: D 179 ILE cc_start: 0.8423 (mt) cc_final: 0.8187 (mp) REVERT: D 415 SER cc_start: 0.7333 (p) cc_final: 0.7003 (p) REVERT: D 419 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 34 outliers final: 26 residues processed: 191 average time/residue: 0.4962 time to fit residues: 101.9978 Evaluate side-chains 203 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.147972 restraints weight = 11970.912| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.67 r_work: 0.3836 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9297 Z= 0.205 Angle : 0.650 9.911 12638 Z= 0.337 Chirality : 0.049 0.248 1486 Planarity : 0.006 0.056 1598 Dihedral : 4.814 19.960 1241 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.79 % Allowed : 18.54 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.25), residues: 1153 helix: 1.33 (0.37), residues: 235 sheet: 0.88 (0.31), residues: 285 loop : -1.16 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 243 TYR 0.017 0.002 TYR B 137 PHE 0.019 0.002 PHE A 177 TRP 0.014 0.001 TRP B 379 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9297) covalent geometry : angle 0.64980 (12638) hydrogen bonds : bond 0.03825 ( 334) hydrogen bonds : angle 4.95994 ( 954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.348 Fit side-chains REVERT: A 134 MET cc_start: 0.6101 (mmt) cc_final: 0.5823 (tpt) REVERT: A 312 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8148 (mm-40) REVERT: B 132 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: B 137 TYR cc_start: 0.7713 (m-80) cc_final: 0.7214 (m-80) REVERT: B 179 ILE cc_start: 0.7750 (mt) cc_final: 0.7396 (tt) REVERT: B 211 PHE cc_start: 0.8081 (m-80) cc_final: 0.7673 (m-80) REVERT: B 215 PHE cc_start: 0.7928 (m-80) cc_final: 0.7349 (m-80) REVERT: B 311 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7889 (m) REVERT: B 354 SER cc_start: 0.8418 (p) cc_final: 0.8171 (p) REVERT: B 364 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8289 (t) REVERT: B 400 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (t) REVERT: C 137 TYR cc_start: 0.7301 (m-80) cc_final: 0.6962 (m-80) REVERT: C 179 ILE cc_start: 0.7949 (mt) cc_final: 0.7502 (tt) REVERT: C 186 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7524 (p) REVERT: C 237 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8031 (mtt90) REVERT: C 309 THR cc_start: 0.8054 (t) cc_final: 0.7806 (m) REVERT: D 179 ILE cc_start: 0.8457 (mt) cc_final: 0.8214 (mp) REVERT: D 415 SER cc_start: 0.7352 (p) cc_final: 0.7025 (p) REVERT: D 419 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7277 (tm-30) outliers start: 39 outliers final: 27 residues processed: 200 average time/residue: 0.4738 time to fit residues: 102.2790 Evaluate side-chains 213 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 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 = 0.4328 r_free = 0.4328 target = 0.178299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150274 restraints weight = 11987.223| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.65 r_work: 0.3865 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9297 Z= 0.134 Angle : 0.609 10.645 12638 Z= 0.316 Chirality : 0.047 0.191 1486 Planarity : 0.006 0.061 1598 Dihedral : 4.611 19.177 1241 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.62 % Allowed : 20.00 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1153 helix: 1.35 (0.36), residues: 236 sheet: 0.88 (0.31), residues: 290 loop : -1.08 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 243 TYR 0.011 0.001 TYR B 327 PHE 0.016 0.002 PHE A 217 TRP 0.010 0.001 TRP B 379 HIS 0.002 0.000 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9297) covalent geometry : angle 0.60886 (12638) hydrogen bonds : bond 0.03544 ( 334) hydrogen bonds : angle 4.85688 ( 954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.397 Fit side-chains REVERT: A 179 ILE cc_start: 0.8220 (mp) cc_final: 0.7766 (tt) REVERT: A 312 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8157 (mm-40) REVERT: B 132 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: B 137 TYR cc_start: 0.7564 (m-80) cc_final: 0.7228 (m-80) REVERT: B 158 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7629 (mtpt) REVERT: B 179 ILE cc_start: 0.7635 (mt) cc_final: 0.7293 (tt) REVERT: C 137 TYR cc_start: 0.7159 (m-80) cc_final: 0.6809 (m-80) REVERT: C 178 ILE cc_start: 0.7815 (mt) cc_final: 0.7527 (mt) REVERT: C 179 ILE cc_start: 0.7871 (mt) cc_final: 0.7460 (tt) REVERT: C 309 THR cc_start: 0.8047 (t) cc_final: 0.7813 (m) REVERT: C 411 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: D 179 ILE cc_start: 0.8393 (mt) cc_final: 0.8165 (mp) REVERT: D 415 SER cc_start: 0.7324 (p) cc_final: 0.7046 (p) REVERT: D 419 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7206 (tm-30) outliers start: 27 outliers final: 23 residues processed: 196 average time/residue: 0.5032 time to fit residues: 106.0484 Evaluate side-chains 203 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 0.0170 chunk 84 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.176615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.148545 restraints weight = 11877.753| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.64 r_work: 0.3844 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9297 Z= 0.195 Angle : 0.653 11.530 12638 Z= 0.338 Chirality : 0.049 0.261 1486 Planarity : 0.006 0.064 1598 Dihedral : 4.753 20.465 1241 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.01 % Allowed : 19.81 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1153 helix: 1.32 (0.36), residues: 236 sheet: 0.92 (0.31), residues: 285 loop : -1.11 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 243 TYR 0.018 0.002 TYR B 327 PHE 0.017 0.002 PHE A 177 TRP 0.011 0.001 TRP B 379 HIS 0.002 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9297) covalent geometry : angle 0.65254 (12638) hydrogen bonds : bond 0.03796 ( 334) hydrogen bonds : angle 4.88264 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.54 seconds wall clock time: 49 minutes 53.13 seconds (2993.13 seconds total)