Starting phenix.real_space_refine on Wed Feb 4 15:16:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.map" model { file = "/net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ums_64293/02_2026/9ums_64293.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.716 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 49 5.16 5 C 7232 2.51 5 N 1935 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11411 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "C" Number of atoms: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3588 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1476 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1476 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "D" Number of atoms: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3588 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.00, per 1000 atoms: 0.26 Number of scatterers: 11411 At special positions: 0 Unit cell: (110.16, 114.24, 221.68, 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 49 16.00 O 2195 8.00 N 1935 7.00 C 7232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 517.2 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 15 sheets defined 47.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 88 through 106 removed outlier: 3.604A pdb=" N LEU B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'C' and resid 86 through 98 Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.813A pdb=" N ASP C 139 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.621A pdb=" N CYS C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.668A pdb=" N LYS C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLY C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 197 removed outlier: 3.630A pdb=" N LEU C 195 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Proline residue: C 196 - end of helix Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.911A pdb=" N LYS C 222 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 281 through 303 removed outlier: 4.098A pdb=" N LYS C 303 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 344 removed outlier: 3.918A pdb=" N GLY C 344 " --> pdb=" O ARG C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 379 removed outlier: 3.633A pdb=" N GLY C 379 " --> pdb=" O ASP C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 379' Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.638A pdb=" N LEU C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.718A pdb=" N LEU C 401 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 450 removed outlier: 3.838A pdb=" N ALA C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 500 removed outlier: 3.875A pdb=" N ASN C 500 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 506 removed outlier: 4.343A pdb=" N SER C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 516 removed outlier: 4.304A pdb=" N TYR C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.854A pdb=" N ARG A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.846A pdb=" N ILE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix removed outlier: 4.171A pdb=" N ASP A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 174 removed outlier: 3.535A pdb=" N LEU A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.767A pdb=" N ARG E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.722A pdb=" N ILE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Proline residue: E 134 - end of helix removed outlier: 4.493A pdb=" N ASP E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 174 removed outlier: 3.604A pdb=" N ARG E 174 " --> pdb=" O MET E 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 98 Proline residue: D 92 - end of helix Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.636A pdb=" N ASP D 139 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 152 through 171 removed outlier: 3.807A pdb=" N LYS D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 197 removed outlier: 3.564A pdb=" N LEU D 195 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 280 through 303 removed outlier: 4.316A pdb=" N LYS D 303 " --> pdb=" O PHE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 344 removed outlier: 3.636A pdb=" N ILE D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 344 " --> pdb=" O ARG D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.534A pdb=" N LEU D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 389 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 420 through 450 removed outlier: 3.861A pdb=" N ALA D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 500 removed outlier: 3.768A pdb=" N ASN D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.500A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 516 Processing helix chain 'D' and resid 524 through 532 Processing sheet with id=AA1, first strand: chain 'B' and resid 110 through 115 removed outlier: 5.294A pdb=" N LEU B 181 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER B 223 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B 222 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN B 215 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 224 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 213 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR B 226 " --> pdb=" O HIS B 211 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 115 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 195 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP B 111 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 162 removed outlier: 4.684A pdb=" N TYR B 161 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.522A pdb=" N LYS C 462 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 176 through 180 removed outlier: 7.304A pdb=" N ARG C 176 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE C 188 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR C 178 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 213 removed outlier: 4.421A pdb=" N GLY C 210 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 202 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 304 through 311 removed outlier: 4.320A pdb=" N GLN C 365 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.557A pdb=" N ASN C 353 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 352 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 310 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 305 " --> pdb=" O GLN D 371 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 369 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 48 removed outlier: 3.786A pdb=" N SER A 67 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 102 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 65 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.908A pdb=" N TYR A 77 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 43 through 48 removed outlier: 4.191A pdb=" N SER E 67 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU E 102 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 65 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AB4, first strand: chain 'D' and resid 126 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 176 through 180 removed outlier: 7.074A pdb=" N ARG D 176 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE D 188 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR D 178 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 207 through 213 removed outlier: 4.496A pdb=" N PHE D 202 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE D 211 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS D 200 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 203 " --> pdb=" O ILE D 267 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3807 1.35 - 1.46: 2588 1.46 - 1.58: 5153 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11638 Sorted by residual: bond pdb=" N ASP D 369 " pdb=" CA ASP D 369 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.18e-02 7.18e+03 8.98e+00 bond pdb=" N TYR B 85 " pdb=" CA TYR B 85 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.62e+00 bond pdb=" N ARG B 82 " pdb=" CA ARG B 82 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N HIS B 83 " pdb=" CA HIS B 83 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.76e+00 bond pdb=" N TYR A 126 " pdb=" CA TYR A 126 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.48e+00 ... (remaining 11633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 15245 1.67 - 3.33: 457 3.33 - 5.00: 73 5.00 - 6.67: 14 6.67 - 8.33: 8 Bond angle restraints: 15797 Sorted by residual: angle pdb=" CA TYR C 255 " pdb=" CB TYR C 255 " pdb=" CG TYR C 255 " ideal model delta sigma weight residual 113.90 121.80 -7.90 1.80e+00 3.09e-01 1.92e+01 angle pdb=" C GLY D 122 " pdb=" N GLN D 123 " pdb=" CA GLN D 123 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N LEU E 187 " pdb=" CA LEU E 187 " pdb=" C LEU E 187 " ideal model delta sigma weight residual 113.28 108.94 4.34 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N TRP D 239 " pdb=" CA TRP D 239 " pdb=" C TRP D 239 " ideal model delta sigma weight residual 110.55 105.93 4.62 1.35e+00 5.49e-01 1.17e+01 angle pdb=" C VAL A 94 " pdb=" N TYR A 95 " pdb=" CA TYR A 95 " ideal model delta sigma weight residual 120.09 124.16 -4.07 1.25e+00 6.40e-01 1.06e+01 ... (remaining 15792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6024 17.92 - 35.84: 780 35.84 - 53.77: 204 53.77 - 71.69: 20 71.69 - 89.61: 11 Dihedral angle restraints: 7039 sinusoidal: 2800 harmonic: 4239 Sorted by residual: dihedral pdb=" CA TRP D 239 " pdb=" C TRP D 239 " pdb=" N ARG D 240 " pdb=" CA ARG D 240 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR E 15 " pdb=" C THR E 15 " pdb=" N PRO E 16 " pdb=" CA PRO E 16 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N LEU E 102 " pdb=" CA LEU E 102 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1307 0.040 - 0.080: 326 0.080 - 0.120: 121 0.120 - 0.160: 23 0.160 - 0.200: 4 Chirality restraints: 1781 Sorted by residual: chirality pdb=" CA TRP D 239 " pdb=" N TRP D 239 " pdb=" C TRP D 239 " pdb=" CB TRP D 239 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB THR C 491 " pdb=" CA THR C 491 " pdb=" OG1 THR C 491 " pdb=" CG2 THR C 491 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1778 not shown) Planarity restraints: 2057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 15 " 0.054 5.00e-02 4.00e+02 8.31e-02 1.11e+01 pdb=" N PRO E 16 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 16 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 16 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 239 " -0.026 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP D 239 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP D 239 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 239 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 239 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 239 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 239 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 239 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 239 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 240 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO D 241 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 241 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 241 " 0.043 5.00e-02 4.00e+02 ... (remaining 2054 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1219 2.74 - 3.28: 11162 3.28 - 3.82: 17347 3.82 - 4.36: 18693 4.36 - 4.90: 33313 Nonbonded interactions: 81734 Sorted by model distance: nonbonded pdb=" NH2 ARG E 140 " pdb=" O SER E 154 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN D 132 " pdb=" N GLY D 133 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR A 77 " pdb=" OD2 ASP D 336 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP C 336 " pdb=" OH TYR E 77 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG A 140 " pdb=" O SER A 154 " model vdw 2.235 3.120 ... (remaining 81729 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' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.004 0.045 11638 Z= 0.182 Angle : 0.694 8.334 15797 Z= 0.384 Chirality : 0.043 0.200 1781 Planarity : 0.005 0.083 2057 Dihedral : 16.851 89.609 4311 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.90 % Allowed : 25.81 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1438 helix: 2.56 (0.22), residues: 570 sheet: -0.17 (0.37), residues: 189 loop : -1.46 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 240 TYR 0.041 0.001 TYR C 255 PHE 0.019 0.002 PHE D 125 TRP 0.056 0.002 TRP D 239 HIS 0.004 0.001 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00353 (11638) covalent geometry : angle 0.69395 (15797) hydrogen bonds : bond 0.17217 ( 539) hydrogen bonds : angle 5.67099 ( 1530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 441 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 PHE cc_start: 0.8705 (p90) cc_final: 0.8492 (p90) REVERT: B 212 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8638 (mtpp) REVERT: B 216 TYR cc_start: 0.8829 (m-80) cc_final: 0.8544 (m-80) REVERT: B 220 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7465 (ttm170) REVERT: A 65 LEU cc_start: 0.8373 (mt) cc_final: 0.8144 (mt) REVERT: E 114 GLU cc_start: 0.7020 (tp30) cc_final: 0.6804 (tp30) REVERT: D 521 ASP cc_start: 0.5152 (p0) cc_final: 0.4768 (p0) outliers start: 11 outliers final: 4 residues processed: 448 average time/residue: 0.1308 time to fit residues: 79.3397 Evaluate side-chains 279 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 275 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 92 ASN C 132 ASN C 260 ASN C 270 GLN C 492 GLN A 54 ASN A 98 ASN E 71 HIS E 98 ASN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080050 restraints weight = 32944.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081939 restraints weight = 16005.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083170 restraints weight = 9839.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083971 restraints weight = 7032.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.084502 restraints weight = 5599.611| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11638 Z= 0.211 Angle : 0.721 11.604 15797 Z= 0.371 Chirality : 0.046 0.216 1781 Planarity : 0.005 0.056 2057 Dihedral : 5.003 53.934 1600 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.11 % Allowed : 22.48 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1438 helix: 2.51 (0.21), residues: 581 sheet: -0.10 (0.34), residues: 212 loop : -1.56 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 140 TYR 0.019 0.002 TYR C 284 PHE 0.023 0.002 PHE C 509 TRP 0.048 0.003 TRP D 239 HIS 0.007 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00491 (11638) covalent geometry : angle 0.72121 (15797) hydrogen bonds : bond 0.05617 ( 539) hydrogen bonds : angle 4.51763 ( 1530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8966 (mtpp) REVERT: C 82 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7136 (mm-40) REVERT: C 217 LYS cc_start: 0.7731 (mmtp) cc_final: 0.7521 (mtpp) REVERT: C 239 TRP cc_start: 0.8803 (t60) cc_final: 0.7747 (t60) REVERT: C 242 LYS cc_start: 0.8807 (mtmm) cc_final: 0.8464 (mtmm) REVERT: C 282 GLU cc_start: 0.7820 (mp0) cc_final: 0.7377 (mp0) REVERT: C 336 ASP cc_start: 0.8364 (m-30) cc_final: 0.7997 (m-30) REVERT: A 164 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9126 (mm) REVERT: E 44 LYS cc_start: 0.7300 (pptt) cc_final: 0.6911 (pttm) REVERT: E 49 THR cc_start: 0.9253 (p) cc_final: 0.8832 (t) REVERT: E 165 ASP cc_start: 0.8058 (m-30) cc_final: 0.7847 (m-30) REVERT: D 95 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 474 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8336 (mt0) outliers start: 75 outliers final: 42 residues processed: 313 average time/residue: 0.1128 time to fit residues: 49.8573 Evaluate side-chains 262 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 492 GLN Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 474 GLN Chi-restraints excluded: chain D residue 509 PHE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN D 123 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077656 restraints weight = 32924.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079611 restraints weight = 15783.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080883 restraints weight = 9633.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081725 restraints weight = 6848.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082270 restraints weight = 5415.849| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11638 Z= 0.161 Angle : 0.638 9.714 15797 Z= 0.330 Chirality : 0.044 0.207 1781 Planarity : 0.005 0.054 2057 Dihedral : 4.840 56.387 1596 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.11 % Allowed : 22.39 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1438 helix: 2.55 (0.21), residues: 585 sheet: 0.03 (0.35), residues: 213 loop : -1.55 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.016 0.001 TYR D 255 PHE 0.024 0.002 PHE C 170 TRP 0.025 0.002 TRP D 239 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00369 (11638) covalent geometry : angle 0.63850 (15797) hydrogen bonds : bond 0.05297 ( 539) hydrogen bonds : angle 4.28070 ( 1530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8949 (mtpp) REVERT: C 82 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7182 (mm-40) REVERT: C 217 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7603 (mtpp) REVERT: C 242 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8464 (mtmm) REVERT: C 282 GLU cc_start: 0.7840 (mp0) cc_final: 0.7296 (mp0) REVERT: C 336 ASP cc_start: 0.8389 (m-30) cc_final: 0.8159 (m-30) REVERT: A 160 TYR cc_start: 0.8507 (t80) cc_final: 0.8303 (t80) REVERT: E 44 LYS cc_start: 0.7578 (pptt) cc_final: 0.7164 (pttm) REVERT: E 49 THR cc_start: 0.9045 (p) cc_final: 0.8611 (t) REVERT: D 95 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7577 (mt-10) REVERT: D 249 HIS cc_start: 0.5388 (t70) cc_final: 0.4653 (t-90) REVERT: D 474 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8340 (mt0) outliers start: 75 outliers final: 56 residues processed: 284 average time/residue: 0.1139 time to fit residues: 45.6601 Evaluate side-chains 272 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 448 PHE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 474 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 492 GLN A 71 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074827 restraints weight = 32951.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076733 restraints weight = 15994.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077983 restraints weight = 9838.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078803 restraints weight = 7037.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079301 restraints weight = 5599.043| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11638 Z= 0.190 Angle : 0.654 9.519 15797 Z= 0.341 Chirality : 0.045 0.222 1781 Planarity : 0.005 0.059 2057 Dihedral : 5.023 58.824 1596 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 7.08 % Allowed : 22.15 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1438 helix: 2.53 (0.21), residues: 585 sheet: 0.04 (0.36), residues: 213 loop : -1.60 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.017 0.002 TYR E 95 PHE 0.020 0.002 PHE C 509 TRP 0.030 0.002 TRP D 239 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00442 (11638) covalent geometry : angle 0.65450 (15797) hydrogen bonds : bond 0.05765 ( 539) hydrogen bonds : angle 4.29175 ( 1530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 220 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 212 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8919 (mtpp) REVERT: C 193 TYR cc_start: 0.8568 (m-80) cc_final: 0.8313 (m-80) REVERT: C 217 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7649 (mtpp) REVERT: C 242 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8386 (mtmm) REVERT: C 282 GLU cc_start: 0.7977 (mp0) cc_final: 0.7438 (mp0) REVERT: C 336 ASP cc_start: 0.8467 (m-30) cc_final: 0.8216 (m-30) REVERT: E 44 LYS cc_start: 0.7617 (pptt) cc_final: 0.7328 (pttm) REVERT: E 49 THR cc_start: 0.8984 (p) cc_final: 0.8636 (t) REVERT: D 95 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7495 (mt-10) REVERT: D 149 MET cc_start: 0.9056 (tpp) cc_final: 0.8726 (mmm) REVERT: D 208 LEU cc_start: 0.8799 (tt) cc_final: 0.8561 (tp) REVERT: D 246 MET cc_start: 0.8486 (mmm) cc_final: 0.8280 (tpt) REVERT: D 249 HIS cc_start: 0.5409 (t70) cc_final: 0.4484 (t-90) REVERT: D 474 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8102 (mt0) outliers start: 87 outliers final: 61 residues processed: 285 average time/residue: 0.1139 time to fit residues: 45.5820 Evaluate side-chains 269 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 492 GLN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 474 GLN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 509 PHE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075614 restraints weight = 32592.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077529 restraints weight = 15788.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078771 restraints weight = 9726.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079590 restraints weight = 6985.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080136 restraints weight = 5563.696| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11638 Z= 0.133 Angle : 0.598 9.282 15797 Z= 0.309 Chirality : 0.043 0.197 1781 Planarity : 0.004 0.058 2057 Dihedral : 4.503 46.905 1594 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.68 % Allowed : 22.15 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1438 helix: 2.72 (0.21), residues: 583 sheet: 0.05 (0.36), residues: 213 loop : -1.58 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 240 TYR 0.015 0.001 TYR E 95 PHE 0.014 0.001 PHE D 509 TRP 0.018 0.001 TRP D 239 HIS 0.009 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00305 (11638) covalent geometry : angle 0.59755 (15797) hydrogen bonds : bond 0.05004 ( 539) hydrogen bonds : angle 4.10810 ( 1530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 228 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8909 (mtpp) REVERT: C 154 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8109 (ptp90) REVERT: C 193 TYR cc_start: 0.8601 (m-80) cc_final: 0.8211 (m-80) REVERT: C 217 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7592 (mtpp) REVERT: C 242 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8471 (mtmm) REVERT: C 312 MET cc_start: 0.8332 (ptp) cc_final: 0.8067 (ptt) REVERT: C 336 ASP cc_start: 0.8411 (m-30) cc_final: 0.8139 (m-30) REVERT: A 79 ASP cc_start: 0.7473 (t0) cc_final: 0.7264 (t0) REVERT: E 44 LYS cc_start: 0.7594 (pptt) cc_final: 0.7357 (pttm) REVERT: E 49 THR cc_start: 0.8942 (p) cc_final: 0.8617 (t) REVERT: D 194 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9002 (t) REVERT: D 203 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: D 208 LEU cc_start: 0.8746 (tt) cc_final: 0.8509 (tp) REVERT: D 249 HIS cc_start: 0.5479 (t70) cc_final: 0.4767 (t-90) outliers start: 82 outliers final: 62 residues processed: 286 average time/residue: 0.1058 time to fit residues: 43.1015 Evaluate side-chains 275 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN E 112 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN D 389 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074484 restraints weight = 32572.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076375 restraints weight = 15822.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077621 restraints weight = 9760.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078384 restraints weight = 6999.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078982 restraints weight = 5614.284| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11638 Z= 0.169 Angle : 0.617 8.155 15797 Z= 0.318 Chirality : 0.043 0.208 1781 Planarity : 0.004 0.056 2057 Dihedral : 4.556 48.923 1594 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 7.57 % Allowed : 21.82 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1438 helix: 2.69 (0.21), residues: 583 sheet: 0.05 (0.36), residues: 214 loop : -1.61 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 47 TYR 0.022 0.001 TYR A 95 PHE 0.017 0.002 PHE D 509 TRP 0.016 0.001 TRP D 239 HIS 0.002 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00400 (11638) covalent geometry : angle 0.61702 (15797) hydrogen bonds : bond 0.05279 ( 539) hydrogen bonds : angle 4.20107 ( 1530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 207 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8914 (mtpp) REVERT: C 154 ARG cc_start: 0.8685 (mtt180) cc_final: 0.8196 (ptp90) REVERT: C 193 TYR cc_start: 0.8656 (m-80) cc_final: 0.8236 (m-80) REVERT: C 217 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7644 (mtpp) REVERT: C 312 MET cc_start: 0.8383 (ptp) cc_final: 0.8102 (ptt) REVERT: C 336 ASP cc_start: 0.8442 (m-30) cc_final: 0.8159 (m-30) REVERT: A 79 ASP cc_start: 0.7536 (t0) cc_final: 0.7284 (t0) REVERT: E 49 THR cc_start: 0.8944 (p) cc_final: 0.8628 (t) REVERT: D 79 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: D 194 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.8986 (t) REVERT: D 203 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: D 208 LEU cc_start: 0.8766 (tt) cc_final: 0.8545 (tt) REVERT: D 249 HIS cc_start: 0.5416 (t70) cc_final: 0.4483 (t-90) REVERT: D 381 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7913 (mp0) outliers start: 93 outliers final: 74 residues processed: 274 average time/residue: 0.0988 time to fit residues: 38.8138 Evaluate side-chains 278 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 200 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 474 GLN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 102 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN E 112 ASN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074326 restraints weight = 32735.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076218 restraints weight = 15935.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077463 restraints weight = 9838.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078303 restraints weight = 7052.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078838 restraints weight = 5599.629| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11638 Z= 0.171 Angle : 0.626 8.510 15797 Z= 0.324 Chirality : 0.043 0.215 1781 Planarity : 0.005 0.061 2057 Dihedral : 4.617 54.146 1594 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 7.25 % Allowed : 21.74 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1438 helix: 2.70 (0.21), residues: 583 sheet: 0.07 (0.36), residues: 214 loop : -1.62 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 121 TYR 0.023 0.001 TYR A 95 PHE 0.019 0.002 PHE D 509 TRP 0.017 0.001 TRP D 239 HIS 0.008 0.001 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00399 (11638) covalent geometry : angle 0.62610 (15797) hydrogen bonds : bond 0.05313 ( 539) hydrogen bonds : angle 4.20750 ( 1530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 212 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8923 (mtpp) REVERT: C 154 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8297 (ptp90) REVERT: C 217 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7789 (mtpp) REVERT: C 234 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.6967 (tmm) REVERT: C 282 GLU cc_start: 0.7931 (mp0) cc_final: 0.7373 (mp0) REVERT: C 336 ASP cc_start: 0.8424 (m-30) cc_final: 0.8147 (m-30) REVERT: A 79 ASP cc_start: 0.7589 (t0) cc_final: 0.7305 (t0) REVERT: E 49 THR cc_start: 0.8879 (p) cc_final: 0.8596 (t) REVERT: D 79 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: D 194 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8975 (t) REVERT: D 203 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: D 208 LEU cc_start: 0.8784 (tt) cc_final: 0.8579 (tt) REVERT: D 249 HIS cc_start: 0.5324 (t70) cc_final: 0.4473 (t-90) REVERT: D 381 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: D 446 LEU cc_start: 0.8699 (mm) cc_final: 0.8411 (mm) outliers start: 89 outliers final: 72 residues processed: 273 average time/residue: 0.1087 time to fit residues: 42.2725 Evaluate side-chains 273 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 196 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.0020 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN E 5 GLN E 112 ASN D 110 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077560 restraints weight = 32578.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079489 restraints weight = 15687.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080755 restraints weight = 9631.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081587 restraints weight = 6892.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082158 restraints weight = 5470.754| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11638 Z= 0.115 Angle : 0.605 10.504 15797 Z= 0.311 Chirality : 0.042 0.173 1781 Planarity : 0.004 0.057 2057 Dihedral : 4.350 53.783 1594 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.07 % Allowed : 25.98 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1438 helix: 2.81 (0.21), residues: 584 sheet: 0.05 (0.36), residues: 214 loop : -1.55 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 121 TYR 0.016 0.001 TYR E 95 PHE 0.020 0.001 PHE D 509 TRP 0.016 0.001 TRP D 229 HIS 0.006 0.001 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00251 (11638) covalent geometry : angle 0.60526 (15797) hydrogen bonds : bond 0.04080 ( 539) hydrogen bonds : angle 3.92960 ( 1530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 212 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8939 (mtpp) REVERT: C 154 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8231 (ptp90) REVERT: C 174 TYR cc_start: 0.8084 (m-80) cc_final: 0.7789 (m-80) REVERT: C 193 TYR cc_start: 0.8629 (m-80) cc_final: 0.8272 (m-80) REVERT: C 217 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7699 (mtpp) REVERT: C 234 MET cc_start: 0.8003 (tmm) cc_final: 0.7651 (tpp) REVERT: C 242 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8542 (mtmm) REVERT: C 312 MET cc_start: 0.8243 (ptp) cc_final: 0.7867 (ptt) REVERT: C 333 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8393 (mmm-85) REVERT: C 336 ASP cc_start: 0.8375 (m-30) cc_final: 0.8045 (m-30) REVERT: E 37 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: E 49 THR cc_start: 0.8791 (p) cc_final: 0.8519 (t) REVERT: D 194 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.8933 (t) REVERT: D 203 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: D 249 HIS cc_start: 0.5669 (t70) cc_final: 0.5019 (t-90) REVERT: D 260 ASN cc_start: 0.8852 (m-40) cc_final: 0.8606 (m-40) REVERT: D 446 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8326 (mm) outliers start: 50 outliers final: 34 residues processed: 260 average time/residue: 0.1117 time to fit residues: 40.8745 Evaluate side-chains 251 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN D 110 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078007 restraints weight = 32523.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079895 restraints weight = 15461.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081133 restraints weight = 9406.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081918 restraints weight = 6675.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082460 restraints weight = 5304.712| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11638 Z= 0.122 Angle : 0.622 9.849 15797 Z= 0.319 Chirality : 0.043 0.178 1781 Planarity : 0.004 0.058 2057 Dihedral : 4.314 55.584 1594 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.15 % Allowed : 26.38 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1438 helix: 2.77 (0.21), residues: 584 sheet: 0.13 (0.36), residues: 209 loop : -1.53 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 340 TYR 0.020 0.001 TYR A 95 PHE 0.021 0.001 PHE D 509 TRP 0.013 0.001 TRP D 229 HIS 0.004 0.000 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00284 (11638) covalent geometry : angle 0.62168 (15797) hydrogen bonds : bond 0.04198 ( 539) hydrogen bonds : angle 4.00091 ( 1530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 212 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8929 (mtpp) REVERT: C 154 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8209 (ptp90) REVERT: C 234 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.6896 (tmm) REVERT: C 312 MET cc_start: 0.8090 (ptp) cc_final: 0.7684 (ptt) REVERT: C 333 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8394 (mmm-85) REVERT: C 336 ASP cc_start: 0.8405 (m-30) cc_final: 0.8056 (m-30) REVERT: C 519 GLU cc_start: 0.6333 (pt0) cc_final: 0.6102 (pp20) REVERT: A 79 ASP cc_start: 0.7472 (t0) cc_final: 0.7233 (t0) REVERT: E 37 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: E 49 THR cc_start: 0.8730 (p) cc_final: 0.8464 (t) REVERT: D 194 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9194 (t) REVERT: D 249 HIS cc_start: 0.5507 (t70) cc_final: 0.4911 (t-90) REVERT: D 366 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7954 (mtm) REVERT: D 381 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: D 446 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8307 (mm) outliers start: 51 outliers final: 39 residues processed: 243 average time/residue: 0.1098 time to fit residues: 38.0985 Evaluate side-chains 251 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 75 optimal weight: 0.3980 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN E 112 ASN D 110 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075853 restraints weight = 32904.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.077712 restraints weight = 15698.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078907 restraints weight = 9583.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079732 restraints weight = 6850.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080265 restraints weight = 5431.000| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11638 Z= 0.177 Angle : 0.665 13.567 15797 Z= 0.340 Chirality : 0.044 0.194 1781 Planarity : 0.005 0.056 2057 Dihedral : 4.490 59.161 1594 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.40 % Allowed : 26.38 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1438 helix: 2.71 (0.21), residues: 585 sheet: 0.06 (0.36), residues: 214 loop : -1.58 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 121 TYR 0.020 0.001 TYR A 95 PHE 0.023 0.002 PHE D 509 TRP 0.014 0.001 TRP D 239 HIS 0.005 0.001 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00416 (11638) covalent geometry : angle 0.66496 (15797) hydrogen bonds : bond 0.04911 ( 539) hydrogen bonds : angle 4.14996 ( 1530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 212 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8940 (mtpp) REVERT: C 154 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8220 (ptp90) REVERT: C 234 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7017 (tmm) REVERT: C 312 MET cc_start: 0.8241 (ptp) cc_final: 0.7782 (ptt) REVERT: C 333 ARG cc_start: 0.8860 (tpp-160) cc_final: 0.8485 (mmm-85) REVERT: C 336 ASP cc_start: 0.8405 (m-30) cc_final: 0.8098 (m-30) REVERT: A 79 ASP cc_start: 0.7541 (t0) cc_final: 0.7323 (t0) REVERT: E 37 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: E 49 THR cc_start: 0.8793 (p) cc_final: 0.8543 (t) REVERT: D 194 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9164 (t) REVERT: D 249 HIS cc_start: 0.5633 (t70) cc_final: 0.4931 (t-90) REVERT: D 366 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7932 (mtm) REVERT: D 381 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: D 446 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8376 (mm) outliers start: 54 outliers final: 42 residues processed: 229 average time/residue: 0.1094 time to fit residues: 35.7061 Evaluate side-chains 244 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 229 TRP Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 ASN A 51 GLN E 5 GLN D 110 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078437 restraints weight = 32641.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080348 restraints weight = 15490.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081608 restraints weight = 9339.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082430 restraints weight = 6589.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082983 restraints weight = 5192.229| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11638 Z= 0.117 Angle : 0.623 12.414 15797 Z= 0.317 Chirality : 0.043 0.175 1781 Planarity : 0.004 0.057 2057 Dihedral : 4.264 57.699 1594 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.15 % Allowed : 26.87 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1438 helix: 2.77 (0.21), residues: 584 sheet: 0.12 (0.36), residues: 209 loop : -1.54 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 106 TYR 0.021 0.001 TYR A 95 PHE 0.020 0.001 PHE D 509 TRP 0.015 0.001 TRP D 229 HIS 0.004 0.000 HIS D 131 Details of bonding type rmsd covalent geometry : bond 0.00268 (11638) covalent geometry : angle 0.62319 (15797) hydrogen bonds : bond 0.03979 ( 539) hydrogen bonds : angle 3.98528 ( 1530) =============================================================================== Job complete usr+sys time: 2191.67 seconds wall clock time: 38 minutes 28.70 seconds (2308.70 seconds total)