Starting phenix.real_space_refine on Thu Feb 13 16:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr4_45832/02_2025/9cr4_45832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr4_45832/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cr4_45832/02_2025/9cr4_45832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr4_45832/02_2025/9cr4_45832.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr4_45832/02_2025/9cr4_45832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr4_45832/02_2025/9cr4_45832.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.65, per 1000 atoms: 0.62 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.37 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: 2.86 Time building geometry restraints manager: 2.64 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: 0.790 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.720 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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= 0.183 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.007 0.001 TRP C 417 HIS 0.002 0.000 HIS B 306 PHE 0.008 0.001 PHE B 418 TYR 0.015 0.001 TYR B 327 ARG 0.002 0.000 ARG C 356 *********************** 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 : 1.026 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: 0.9211 time to fit residues: 222.1851 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 : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 281 GLN C 339 ASN D 312 GLN D 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.173263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145586 restraints weight = 11937.430| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.56 r_work: 0.3815 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.161 9297 Z= 0.592 Angle : 0.752 9.837 12638 Z= 0.402 Chirality : 0.055 0.275 1486 Planarity : 0.007 0.058 1598 Dihedral : 5.170 19.616 1241 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.59 % Allowed : 8.45 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1153 helix: 0.65 (0.36), residues: 236 sheet: 0.59 (0.31), residues: 295 loop : -1.37 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 379 HIS 0.004 0.001 HIS D 306 PHE 0.013 0.002 PHE B 418 TYR 0.029 0.004 TYR D 137 ARG 0.006 0.001 ARG B 385 *********************** 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 237 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7823 (m-80) cc_final: 0.7463 (m-80) REVERT: A 220 PHE cc_start: 0.8170 (p90) cc_final: 0.7760 (p90) REVERT: A 311 VAL cc_start: 0.8469 (p) cc_final: 0.8224 (m) REVERT: A 312 GLN cc_start: 0.8467 (mt0) cc_final: 0.8256 (mt0) REVERT: B 130 MET cc_start: 0.6940 (tpp) cc_final: 0.6690 (mmm) REVERT: B 132 GLU cc_start: 0.6943 (mp0) cc_final: 0.6613 (mp0) REVERT: B 179 ILE cc_start: 0.7929 (mt) cc_final: 0.7555 (tt) REVERT: B 220 PHE cc_start: 0.8168 (p90) cc_final: 0.7960 (p90) REVERT: B 367 LYS cc_start: 0.8349 (tppp) cc_final: 0.8061 (mtpm) REVERT: B 377 THR cc_start: 0.7780 (p) cc_final: 0.7348 (p) REVERT: B 419 GLU cc_start: 0.7691 (tt0) cc_final: 0.7469 (tt0) REVERT: C 113 MET cc_start: 0.5407 (mmm) cc_final: 0.5201 (mmm) REVERT: C 130 MET cc_start: 0.6779 (tpp) cc_final: 0.6484 (tpp) REVERT: C 144 GLU cc_start: 0.6767 (pt0) cc_final: 0.6509 (pt0) REVERT: C 179 ILE cc_start: 0.8042 (mt) cc_final: 0.7590 (tt) REVERT: C 309 THR cc_start: 0.8098 (t) cc_final: 0.7838 (m) REVERT: C 312 GLN cc_start: 0.8412 (mt0) cc_final: 0.8047 (mt0) REVERT: D 137 TYR cc_start: 0.7526 (m-80) cc_final: 0.7181 (m-80) REVERT: D 179 ILE cc_start: 0.8479 (mt) cc_final: 0.8279 (mp) REVERT: D 211 PHE cc_start: 0.8070 (m-80) cc_final: 0.7803 (m-80) REVERT: D 278 MET cc_start: 0.7084 (mmm) cc_final: 0.6816 (mmm) REVERT: D 369 MET cc_start: 0.7833 (ptm) cc_final: 0.7620 (ptp) REVERT: D 419 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7203 (tm-30) outliers start: 37 outliers final: 24 residues processed: 212 average time/residue: 1.0864 time to fit residues: 247.9257 Evaluate side-chains 213 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 THR 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 402 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 281 GLN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 419 GLU Chi-restraints excluded: chain D residue 420 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN 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 = 0.177023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148877 restraints weight = 12194.958| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.64 r_work: 0.3858 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9297 Z= 0.215 Angle : 0.571 7.079 12638 Z= 0.304 Chirality : 0.047 0.166 1486 Planarity : 0.006 0.048 1598 Dihedral : 4.669 15.917 1241 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.20 % Allowed : 13.11 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1153 helix: 1.16 (0.37), residues: 235 sheet: 0.58 (0.30), residues: 297 loop : -1.21 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 379 HIS 0.002 0.001 HIS C 128 PHE 0.018 0.001 PHE A 177 TYR 0.013 0.001 TYR B 327 ARG 0.006 0.000 ARG C 243 *********************** 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 213 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7579 (tpp) cc_final: 0.7162 (mmt) REVERT: A 137 TYR cc_start: 0.7638 (m-80) cc_final: 0.7396 (m-80) REVERT: A 179 ILE cc_start: 0.7999 (mp) cc_final: 0.7537 (tt) REVERT: A 202 MET cc_start: 0.7947 (ttp) cc_final: 0.7708 (ttp) REVERT: A 311 VAL cc_start: 0.8505 (p) cc_final: 0.8222 (m) REVERT: A 312 GLN cc_start: 0.8483 (mt0) cc_final: 0.8228 (mm-40) REVERT: A 369 MET cc_start: 0.7914 (ptm) cc_final: 0.7692 (ptp) REVERT: B 130 MET cc_start: 0.6934 (tpp) cc_final: 0.6683 (mmm) REVERT: B 134 MET cc_start: 0.7422 (tpp) cc_final: 0.7135 (mmt) REVERT: B 179 ILE cc_start: 0.7805 (mt) cc_final: 0.7448 (tt) REVERT: B 419 GLU cc_start: 0.7653 (tt0) cc_final: 0.7391 (tt0) REVERT: C 130 MET cc_start: 0.6740 (tpp) cc_final: 0.6467 (tpp) REVERT: C 134 MET cc_start: 0.6744 (tpt) cc_final: 0.6511 (mmt) REVERT: C 137 TYR cc_start: 0.7328 (m-80) cc_final: 0.6928 (m-80) REVERT: C 179 ILE cc_start: 0.7980 (mt) cc_final: 0.7514 (tt) REVERT: C 309 THR cc_start: 0.8064 (t) cc_final: 0.7803 (m) REVERT: C 312 GLN cc_start: 0.8320 (mt0) cc_final: 0.8084 (mm-40) REVERT: C 377 THR cc_start: 0.8253 (p) cc_final: 0.8026 (p) REVERT: D 369 MET cc_start: 0.7867 (ptm) cc_final: 0.7654 (ptp) REVERT: D 415 SER cc_start: 0.7360 (p) cc_final: 0.7033 (p) REVERT: D 419 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7189 (tm-30) outliers start: 33 outliers final: 10 residues processed: 192 average time/residue: 1.0711 time to fit residues: 221.9867 Evaluate side-chains 185 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 282 VAL 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 53 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 284 ASN C 281 GLN ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.176253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.148484 restraints weight = 11964.180| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.60 r_work: 0.3852 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9297 Z= 0.256 Angle : 0.578 10.819 12638 Z= 0.302 Chirality : 0.048 0.203 1486 Planarity : 0.006 0.045 1598 Dihedral : 4.593 15.831 1241 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.20 % Allowed : 14.47 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1153 helix: 1.26 (0.37), residues: 235 sheet: 0.48 (0.29), residues: 309 loop : -1.08 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.002 0.000 HIS C 128 PHE 0.016 0.002 PHE A 177 TYR 0.015 0.002 TYR B 137 ARG 0.005 0.000 ARG C 237 *********************** 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 208 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7698 (m-80) cc_final: 0.7478 (m-80) REVERT: A 311 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 312 GLN cc_start: 0.8489 (mt0) cc_final: 0.8232 (mm-40) REVERT: A 369 MET cc_start: 0.7883 (ptm) cc_final: 0.7670 (ptp) REVERT: B 108 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6941 (tt) REVERT: B 134 MET cc_start: 0.7395 (tpp) cc_final: 0.7038 (mmt) REVERT: B 137 TYR cc_start: 0.7818 (m-80) cc_final: 0.7338 (m-80) REVERT: B 158 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7528 (mtpt) REVERT: B 179 ILE cc_start: 0.7830 (mt) cc_final: 0.7454 (tt) REVERT: B 419 GLU cc_start: 0.7668 (tt0) cc_final: 0.7399 (tt0) REVERT: C 124 GLU cc_start: 0.7761 (tp30) cc_final: 0.7536 (tp30) REVERT: C 137 TYR cc_start: 0.7390 (m-80) cc_final: 0.6955 (m-80) REVERT: C 179 ILE cc_start: 0.7970 (mt) cc_final: 0.7510 (tt) REVERT: C 309 THR cc_start: 0.8044 (t) cc_final: 0.7801 (m) REVERT: C 312 GLN cc_start: 0.8279 (mt0) cc_final: 0.8037 (mm-40) REVERT: D 137 TYR cc_start: 0.7300 (m-80) cc_final: 0.7042 (m-80) REVERT: D 369 MET cc_start: 0.7786 (ptm) cc_final: 0.7575 (ptp) REVERT: D 415 SER cc_start: 0.7331 (p) cc_final: 0.6989 (p) REVERT: D 419 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7229 (tm-30) outliers start: 33 outliers final: 21 residues processed: 187 average time/residue: 1.0206 time to fit residues: 206.3827 Evaluate side-chains 190 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 402 THR Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 108 LEU 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 335 MET Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 336 ILE 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 359 VAL Chi-restraints excluded: chain D residue 364 VAL 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 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 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 = 0.4317 r_free = 0.4317 target = 0.176564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148582 restraints weight = 11943.529| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.61 r_work: 0.3854 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9297 Z= 0.245 Angle : 0.574 8.422 12638 Z= 0.299 Chirality : 0.047 0.236 1486 Planarity : 0.005 0.045 1598 Dihedral : 4.580 15.233 1241 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.98 % Allowed : 15.53 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1153 helix: 1.35 (0.37), residues: 235 sheet: 0.58 (0.29), residues: 304 loop : -1.03 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.000 HIS D 128 PHE 0.017 0.002 PHE A 220 TYR 0.013 0.001 TYR B 137 ARG 0.004 0.000 ARG C 237 *********************** 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 217 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8050 (tp30) cc_final: 0.7816 (tp30) REVERT: A 161 PHE cc_start: 0.7817 (m-10) cc_final: 0.7615 (m-10) REVERT: A 179 ILE cc_start: 0.8047 (mp) cc_final: 0.7576 (tt) REVERT: A 311 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8260 (m) REVERT: A 312 GLN cc_start: 0.8475 (mt0) cc_final: 0.8211 (mm-40) REVERT: A 369 MET cc_start: 0.7894 (ptm) cc_final: 0.7677 (ptp) REVERT: A 376 ASN cc_start: 0.7321 (m-40) cc_final: 0.7093 (m-40) REVERT: B 108 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6957 (tt) REVERT: B 137 TYR cc_start: 0.7762 (m-80) cc_final: 0.7344 (m-80) REVERT: B 158 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7535 (mtpt) REVERT: B 179 ILE cc_start: 0.7809 (mt) cc_final: 0.7438 (tt) REVERT: B 385 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: B 419 GLU cc_start: 0.7654 (tt0) cc_final: 0.7392 (tt0) REVERT: C 134 MET cc_start: 0.5595 (mmt) cc_final: 0.5270 (tpt) REVERT: C 137 TYR cc_start: 0.7377 (m-80) cc_final: 0.6954 (m-80) REVERT: C 179 ILE cc_start: 0.7961 (mt) cc_final: 0.7515 (tt) REVERT: C 235 VAL cc_start: 0.7955 (m) cc_final: 0.7723 (p) REVERT: C 309 THR cc_start: 0.8045 (t) cc_final: 0.7803 (m) REVERT: C 312 GLN cc_start: 0.8286 (mt0) cc_final: 0.8033 (mm-40) REVERT: C 377 THR cc_start: 0.8219 (p) cc_final: 0.8014 (p) REVERT: D 137 TYR cc_start: 0.7265 (m-80) cc_final: 0.7054 (m-80) REVERT: D 369 MET cc_start: 0.7781 (ptm) cc_final: 0.7567 (ptp) REVERT: D 415 SER cc_start: 0.7330 (p) cc_final: 0.6977 (p) REVERT: D 419 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7227 (tm-30) outliers start: 41 outliers final: 27 residues processed: 196 average time/residue: 0.9983 time to fit residues: 212.0519 Evaluate side-chains 206 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 108 LEU 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 385 ARG Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 197 SER 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 336 ILE 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 316 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 397 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 106 optimal weight: 0.0370 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.178876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150872 restraints weight = 11970.530| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.62 r_work: 0.3883 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2863 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= 0.164 Angle : 0.554 11.898 12638 Z= 0.284 Chirality : 0.046 0.224 1486 Planarity : 0.005 0.040 1598 Dihedral : 4.351 15.828 1241 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.40 % Allowed : 16.21 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1153 helix: 1.49 (0.36), residues: 235 sheet: 0.65 (0.29), residues: 307 loop : -0.92 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.002 0.000 HIS C 128 PHE 0.017 0.001 PHE D 220 TYR 0.008 0.001 TYR C 302 ARG 0.005 0.000 ARG C 237 *********************** 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 214 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8023 (mp) cc_final: 0.7593 (tt) REVERT: A 311 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 312 GLN cc_start: 0.8460 (mt0) cc_final: 0.8233 (mm-40) REVERT: B 108 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6960 (tt) REVERT: B 132 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: B 137 TYR cc_start: 0.7533 (m-80) cc_final: 0.7234 (m-80) REVERT: B 158 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7543 (mtpt) REVERT: B 179 ILE cc_start: 0.7680 (mt) cc_final: 0.7337 (tt) REVERT: B 354 SER cc_start: 0.8458 (p) cc_final: 0.8232 (p) REVERT: B 385 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7827 (mtp180) REVERT: B 419 GLU cc_start: 0.7625 (tt0) cc_final: 0.7359 (tt0) REVERT: C 137 TYR cc_start: 0.7277 (m-80) cc_final: 0.6857 (m-80) REVERT: C 178 ILE cc_start: 0.7838 (mt) cc_final: 0.7554 (mt) REVERT: C 179 ILE cc_start: 0.7908 (mt) cc_final: 0.7482 (tt) REVERT: C 235 VAL cc_start: 0.7882 (m) cc_final: 0.7664 (p) REVERT: C 309 THR cc_start: 0.8072 (t) cc_final: 0.7813 (m) REVERT: C 312 GLN cc_start: 0.8259 (mt0) cc_final: 0.8054 (mm-40) REVERT: C 322 THR cc_start: 0.8448 (m) cc_final: 0.7760 (p) REVERT: D 137 TYR cc_start: 0.7162 (m-80) cc_final: 0.6950 (m-80) REVERT: D 312 GLN cc_start: 0.8395 (mt0) cc_final: 0.8089 (mm-40) REVERT: D 399 THR cc_start: 0.8331 (m) cc_final: 0.8106 (p) REVERT: D 415 SER cc_start: 0.7293 (p) cc_final: 0.6948 (p) REVERT: D 419 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7226 (tm-30) outliers start: 35 outliers final: 22 residues processed: 199 average time/residue: 0.9521 time to fit residues: 205.7306 Evaluate side-chains 199 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 409 CYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 108 LEU 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 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 130 MET 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 364 VAL Chi-restraints excluded: chain D residue 397 SER 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 84 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 44 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 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 376 ASN ** 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 = 0.4355 r_free = 0.4355 target = 0.180355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151387 restraints weight = 11870.444| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.65 r_work: 0.3892 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9297 Z= 0.173 Angle : 0.565 12.385 12638 Z= 0.286 Chirality : 0.046 0.256 1486 Planarity : 0.005 0.040 1598 Dihedral : 4.329 16.010 1241 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.79 % Allowed : 16.41 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1153 helix: 1.51 (0.36), residues: 235 sheet: 0.75 (0.30), residues: 306 loop : -0.92 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 100 HIS 0.001 0.000 HIS C 128 PHE 0.014 0.001 PHE A 177 TYR 0.008 0.001 TYR B 137 ARG 0.004 0.000 ARG C 237 *********************** 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 219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.5960 (mmt) cc_final: 0.5601 (tpt) REVERT: A 179 ILE cc_start: 0.8024 (mp) cc_final: 0.7691 (tt) REVERT: A 311 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8321 (m) REVERT: A 312 GLN cc_start: 0.8472 (mt0) cc_final: 0.8268 (mm-40) REVERT: B 108 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.7029 (tt) REVERT: B 132 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 137 TYR cc_start: 0.7501 (m-80) cc_final: 0.7163 (m-80) REVERT: B 158 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7555 (mtpt) REVERT: B 179 ILE cc_start: 0.7688 (mt) cc_final: 0.7352 (tt) REVERT: B 335 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7968 (mmt) REVERT: B 354 SER cc_start: 0.8458 (p) cc_final: 0.8237 (p) REVERT: B 385 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7874 (mtp180) REVERT: B 419 GLU cc_start: 0.7565 (tt0) cc_final: 0.7328 (tt0) REVERT: C 124 GLU cc_start: 0.7804 (tp30) cc_final: 0.7579 (tp30) REVERT: C 137 TYR cc_start: 0.7265 (m-80) cc_final: 0.6856 (m-80) REVERT: C 178 ILE cc_start: 0.7848 (mt) cc_final: 0.7572 (mt) REVERT: C 179 ILE cc_start: 0.7913 (mt) cc_final: 0.7495 (tt) REVERT: C 235 VAL cc_start: 0.7930 (m) cc_final: 0.7723 (p) REVERT: C 309 THR cc_start: 0.8036 (t) cc_final: 0.7788 (m) REVERT: C 322 THR cc_start: 0.8432 (m) cc_final: 0.7743 (p) REVERT: D 137 TYR cc_start: 0.7133 (m-80) cc_final: 0.6925 (m-80) REVERT: D 312 GLN cc_start: 0.8391 (mt0) cc_final: 0.8096 (mm-40) REVERT: D 415 SER cc_start: 0.7304 (p) cc_final: 0.6962 (p) REVERT: D 419 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7228 (tm-30) outliers start: 39 outliers final: 27 residues processed: 200 average time/residue: 0.9202 time to fit residues: 200.7104 Evaluate side-chains 203 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain B residue 129 LEU 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 385 ARG Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 397 SER 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 90 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** D 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.178834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.149626 restraints weight = 11973.955| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.67 r_work: 0.3877 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9297 Z= 0.242 Angle : 0.605 12.814 12638 Z= 0.304 Chirality : 0.048 0.262 1486 Planarity : 0.005 0.040 1598 Dihedral : 4.466 18.032 1241 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.66 % Allowed : 16.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1153 helix: 1.48 (0.36), residues: 235 sheet: 0.85 (0.30), residues: 300 loop : -0.94 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 379 HIS 0.002 0.000 HIS D 128 PHE 0.031 0.002 PHE D 220 TYR 0.013 0.001 TYR B 137 ARG 0.004 0.000 ARG C 237 *********************** 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 230 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 161 PHE cc_start: 0.7777 (m-10) cc_final: 0.7577 (m-10) REVERT: A 311 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8326 (m) REVERT: A 312 GLN cc_start: 0.8471 (mt0) cc_final: 0.8267 (mm-40) REVERT: B 132 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: B 137 TYR cc_start: 0.7578 (m-80) cc_final: 0.7150 (m-80) REVERT: B 158 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7595 (mtpt) REVERT: B 179 ILE cc_start: 0.7740 (mt) cc_final: 0.7398 (tt) REVERT: B 211 PHE cc_start: 0.8093 (m-80) cc_final: 0.7866 (m-80) REVERT: B 354 SER cc_start: 0.8448 (p) cc_final: 0.8218 (p) REVERT: B 385 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: B 419 GLU cc_start: 0.7576 (tt0) cc_final: 0.7324 (tt0) REVERT: C 124 GLU cc_start: 0.7745 (tp30) cc_final: 0.7517 (tp30) REVERT: C 137 TYR cc_start: 0.7307 (m-80) cc_final: 0.6882 (m-80) REVERT: C 178 ILE cc_start: 0.7870 (mt) cc_final: 0.7609 (mt) REVERT: C 179 ILE cc_start: 0.7923 (mt) cc_final: 0.7499 (tt) REVERT: C 237 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8090 (mmt90) REVERT: C 309 THR cc_start: 0.8064 (t) cc_final: 0.7832 (m) REVERT: C 377 THR cc_start: 0.8163 (p) cc_final: 0.7921 (p) REVERT: C 411 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7349 (mtm-85) REVERT: D 137 TYR cc_start: 0.7233 (m-80) cc_final: 0.6980 (m-80) REVERT: D 312 GLN cc_start: 0.8437 (mt0) cc_final: 0.8126 (mm-40) REVERT: D 415 SER cc_start: 0.7322 (p) cc_final: 0.6968 (p) REVERT: D 419 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7258 (tm-30) outliers start: 48 outliers final: 30 residues processed: 208 average time/residue: 0.9907 time to fit residues: 223.1310 Evaluate side-chains 214 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 129 LEU 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 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 SER 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 310 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 397 SER 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 104 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.174913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.145907 restraints weight = 11939.497| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.70 r_work: 0.3811 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 9297 Z= 0.454 Angle : 0.719 13.899 12638 Z= 0.367 Chirality : 0.052 0.221 1486 Planarity : 0.006 0.050 1598 Dihedral : 4.985 23.176 1241 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.88 % Allowed : 17.77 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1153 helix: 1.24 (0.36), residues: 235 sheet: 0.76 (0.30), residues: 297 loop : -1.05 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS D 128 PHE 0.016 0.002 PHE B 217 TYR 0.022 0.002 TYR B 137 ARG 0.008 0.001 ARG C 243 *********************** 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 222 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 311 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 312 GLN cc_start: 0.8469 (mt0) cc_final: 0.8210 (mt0) REVERT: B 132 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: B 137 TYR cc_start: 0.7733 (m-80) cc_final: 0.7241 (m-80) REVERT: B 179 ILE cc_start: 0.7824 (mt) cc_final: 0.7482 (tt) REVERT: B 354 SER cc_start: 0.8430 (p) cc_final: 0.8197 (p) REVERT: B 419 GLU cc_start: 0.7628 (tt0) cc_final: 0.7409 (tt0) REVERT: C 124 GLU cc_start: 0.7803 (tp30) cc_final: 0.7541 (tp30) REVERT: C 179 ILE cc_start: 0.8003 (mt) cc_final: 0.7684 (mm) REVERT: C 237 ARG cc_start: 0.8484 (mmt90) cc_final: 0.8133 (mmt180) REVERT: C 309 THR cc_start: 0.8076 (t) cc_final: 0.7820 (m) REVERT: D 419 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7262 (tm-30) outliers start: 40 outliers final: 30 residues processed: 200 average time/residue: 1.0525 time to fit residues: 226.9481 Evaluate side-chains 209 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 359 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 132 GLU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 SER 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 310 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 397 SER 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 37 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.177717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149332 restraints weight = 12122.244| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.68 r_work: 0.3850 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9297 Z= 0.249 Angle : 0.641 12.921 12638 Z= 0.326 Chirality : 0.048 0.240 1486 Planarity : 0.006 0.060 1598 Dihedral : 4.698 19.355 1241 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.79 % Allowed : 18.25 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1153 helix: 1.32 (0.36), residues: 235 sheet: 0.81 (0.30), residues: 299 loop : -0.98 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 100 HIS 0.002 0.000 HIS D 128 PHE 0.025 0.002 PHE A 220 TYR 0.011 0.001 TYR A 137 ARG 0.014 0.000 ARG C 243 ********************** 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 219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 311 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 312 GLN cc_start: 0.8481 (mt0) cc_final: 0.8236 (mm-40) REVERT: B 108 LEU cc_start: 0.6977 (tt) cc_final: 0.6406 (mp) REVERT: B 132 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 137 TYR cc_start: 0.7568 (m-80) cc_final: 0.7179 (m-80) REVERT: B 179 ILE cc_start: 0.7696 (mt) cc_final: 0.7337 (tt) REVERT: B 354 SER cc_start: 0.8439 (p) cc_final: 0.8200 (p) REVERT: C 124 GLU cc_start: 0.7763 (tp30) cc_final: 0.7543 (tp30) REVERT: C 137 TYR cc_start: 0.7246 (m-80) cc_final: 0.6852 (m-80) REVERT: C 178 ILE cc_start: 0.7876 (mt) cc_final: 0.7527 (mt) REVERT: C 179 ILE cc_start: 0.7908 (mt) cc_final: 0.7606 (mm) REVERT: C 237 ARG cc_start: 0.8437 (mmt90) cc_final: 0.8063 (mmt90) REVERT: C 309 THR cc_start: 0.8091 (t) cc_final: 0.7843 (m) REVERT: D 137 TYR cc_start: 0.7350 (m-80) cc_final: 0.7082 (m-80) REVERT: D 415 SER cc_start: 0.7299 (p) cc_final: 0.7001 (p) REVERT: D 419 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7232 (tm-30) outliers start: 39 outliers final: 29 residues processed: 200 average time/residue: 1.0664 time to fit residues: 229.9520 Evaluate side-chains 208 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 359 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 132 GLU 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 359 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 SER 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 310 THR 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 198 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 397 SER 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 22 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.178703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.150706 restraints weight = 12032.330| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.67 r_work: 0.3867 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9297 Z= 0.215 Angle : 0.626 12.720 12638 Z= 0.319 Chirality : 0.048 0.246 1486 Planarity : 0.006 0.062 1598 Dihedral : 4.580 19.154 1241 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.30 % Allowed : 19.61 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1153 helix: 1.41 (0.36), residues: 235 sheet: 0.78 (0.30), residues: 296 loop : -0.96 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 100 HIS 0.002 0.000 HIS C 128 PHE 0.024 0.001 PHE A 220 TYR 0.010 0.001 TYR A 137 ARG 0.015 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5770.88 seconds wall clock time: 102 minutes 35.25 seconds (6155.25 seconds total)