Starting phenix.real_space_refine on Sun Oct 25 09:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xfg_66821/10_2026/9xfg_66821.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 10045 2.51 5 N 2771 2.21 5 O 3159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16027 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6233 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2795 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2333 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2220 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 2 Time building chain proxies: 3.72, per 1000 atoms: 0.23 Number of scatterers: 16027 At special positions: 0 Unit cell: (128.592, 116.56, 141.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 3159 8.00 N 2771 7.00 C 10045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS F 297 " distance=2.15 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: 1.31 Conformation dependent library (CDL) restraints added in 775.1 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 26 sheets defined 31.3% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.288A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.741A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.771A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.856A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 111 through 114 removed outlier: 6.660A pdb=" N ASN C 114 " --> pdb=" O GLY C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 190 through 218 removed outlier: 3.631A pdb=" N MET C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 284 through 292 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.856A pdb=" N LYS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.568A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.561A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.563A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 135 " --> pdb=" O ARG D 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 135' Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.781A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.622A pdb=" N MET D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.865A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 50 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 124 through 150 Processing helix chain 'F' and resid 153 through 167 removed outlier: 3.619A pdb=" N VAL F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 320 through 326 Processing helix chain 'F' and resid 331 through 338 Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 350 through 360 Processing helix chain 'F' and resid 389 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.442A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.725A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 5.837A pdb=" N THR A 93 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 165 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA A 95 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 12.353A pdb=" N LEU A 167 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N ILE A 97 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 12.780A pdb=" N PHE A 169 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N PHE A 99 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 183 removed outlier: 6.439A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLN A 178 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 12.835A pdb=" N VAL A 258 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N ILE A 180 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ILE A 260 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ILE A 182 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.181A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.745A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.763A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.763A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.620A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.263A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.076A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.529A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.892A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 206 through 210 removed outlier: 7.119A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.518A pdb=" N ALA B 260 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 268 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.553A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.617A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AC1, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.785A pdb=" N GLN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN C 168 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 180 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 230 through 234 removed outlier: 5.720A pdb=" N PHE C 318 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.927A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC5, first strand: chain 'F' and resid 28 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 280 through 282 Processing sheet with id=AC7, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.301A pdb=" N ARG F 288 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU F 380 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 369 through 371 891 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5428 1.34 - 1.46: 3643 1.46 - 1.58: 7171 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 16344 Sorted by residual: bond pdb=" N ILE F 91 " pdb=" CA ILE F 91 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.63e+00 bond pdb=" N ILE F 150 " pdb=" CA ILE F 150 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" N VAL F 89 " pdb=" CA VAL F 89 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.02e+00 bond pdb=" N VAL F 146 " pdb=" CA VAL F 146 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.76e+00 bond pdb=" N MET F 298 " pdb=" CA MET F 298 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.24e+00 ... (remaining 16339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 21710 2.22 - 4.44: 421 4.44 - 6.66: 42 6.66 - 8.89: 13 8.89 - 11.11: 4 Bond angle restraints: 22190 Sorted by residual: angle pdb=" CA MET F 76 " pdb=" CB MET F 76 " pdb=" CG MET F 76 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 angle pdb=" C TYR A 674 " pdb=" N PHE A 675 " pdb=" CA PHE A 675 " ideal model delta sigma weight residual 122.31 133.42 -11.11 2.34e+00 1.83e-01 2.25e+01 angle pdb=" CA MET F 71 " pdb=" CB MET F 71 " pdb=" CG MET F 71 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" C ASN F 33 " pdb=" CA ASN F 33 " pdb=" CB ASN F 33 " ideal model delta sigma weight residual 115.79 111.20 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" CA CYS F 297 " pdb=" C CYS F 297 " pdb=" O CYS F 297 " ideal model delta sigma weight residual 120.81 116.66 4.15 1.15e+00 7.56e-01 1.30e+01 ... (remaining 22185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8741 18.00 - 36.00: 829 36.00 - 54.00: 156 54.00 - 71.99: 23 71.99 - 89.99: 10 Dihedral angle restraints: 9759 sinusoidal: 3840 harmonic: 5919 Sorted by residual: dihedral pdb=" CA MET C 276 " pdb=" C MET C 276 " pdb=" N ALA C 277 " pdb=" CA ALA C 277 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP F 350 " pdb=" CB ASP F 350 " pdb=" CG ASP F 350 " pdb=" OD1 ASP F 350 " ideal model delta sinusoidal sigma weight residual -30.00 -87.15 57.15 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU A 305 " pdb=" CG GLU A 305 " pdb=" CD GLU A 305 " pdb=" OE1 GLU A 305 " ideal model delta sinusoidal sigma weight residual 0.00 89.88 -89.88 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 9756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1784 0.044 - 0.089: 476 0.089 - 0.133: 157 0.133 - 0.177: 21 0.177 - 0.222: 7 Chirality restraints: 2445 Sorted by residual: chirality pdb=" CA ILE F 138 " pdb=" N ILE F 138 " pdb=" C ILE F 138 " pdb=" CB ILE F 138 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE F 137 " pdb=" N ILE F 137 " pdb=" C ILE F 137 " pdb=" CB ILE F 137 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE F 91 " pdb=" N ILE F 91 " pdb=" C ILE F 91 " pdb=" CB ILE F 91 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 2442 not shown) Planarity restraints: 2929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 129 " 0.389 9.50e-02 1.11e+02 1.74e-01 1.86e+01 pdb=" NE ARG F 129 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG F 129 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG F 129 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 129 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 148 " 0.273 9.50e-02 1.11e+02 1.22e-01 9.20e+00 pdb=" NE ARG F 148 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 148 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 148 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 148 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 112 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ARG D 112 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG D 112 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY D 113 " 0.014 2.00e-02 2.50e+03 ... (remaining 2926 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2926 2.77 - 3.30: 16146 3.30 - 3.84: 27289 3.84 - 4.37: 31380 4.37 - 4.90: 52191 Nonbonded interactions: 129932 Sorted by model distance: nonbonded pdb=" OG SER F 295 " pdb=" O CYS F 297 " model vdw 2.241 3.040 nonbonded pdb=" O ASP B 375 " pdb=" OD1 ASP B 375 " model vdw 2.412 3.040 nonbonded pdb=" C THR A 511 " pdb=" OG1 THR A 511 " model vdw 2.532 2.616 nonbonded pdb=" O ASP C 309 " pdb=" O ARG C 313 " model vdw 2.538 3.040 nonbonded pdb=" N ASP C 285 " pdb=" OD1 ASP C 285 " model vdw 2.574 3.120 ... (remaining 129927 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.590 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 0.123 16345 Z= 0.247 Angle : 0.723 11.107 22192 Z= 0.431 Chirality : 0.046 0.222 2445 Planarity : 0.006 0.174 2929 Dihedral : 14.326 89.993 5972 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 2.32 % Allowed : 17.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.19), residues: 2037 helix: 1.47 (0.21), residues: 602 sheet: -0.09 (0.23), residues: 525 loop : -0.89 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 271 TYR 0.025 0.001 TYR F 398 PHE 0.016 0.001 PHE C 99 TRP 0.021 0.001 TRP C 148 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.24 (16344) covalent geometry : angle 0.71988 / 0.43 (22190) SS BOND : bond 0.12323 / 7.70 ( 1) SS BOND : angle 6.61224 / 2.74 ( 2) hydrogen bonds : bond 0.12465 / 8.21 ( 773) hydrogen bonds : angle 6.47903 / 4.58 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.595 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: A 64 ARG cc_start: 0.8961 (mpt180) cc_final: 0.8089 (mmt180) REVERT: A 304 MET cc_start: 0.9217 (mmp) cc_final: 0.8978 (tpp) REVERT: A 325 MET cc_start: 0.8899 (tmm) cc_final: 0.7986 (tmm) REVERT: A 512 ASP cc_start: 0.8770 (t0) cc_final: 0.8307 (p0) REVERT: A 539 MET cc_start: 0.9556 (mtm) cc_final: 0.9114 (mpp) REVERT: B 220 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 57 ILE cc_start: 0.9141 (mm) cc_final: 0.8812 (tt) REVERT: C 129 TYR cc_start: 0.6765 (m-80) cc_final: 0.6520 (m-80) REVERT: C 148 TRP cc_start: 0.7072 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: C 153 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7504 (mt-10) REVERT: C 157 TYR cc_start: 0.9365 (m-80) cc_final: 0.8724 (m-80) REVERT: C 236 ASP cc_start: 0.9246 (p0) cc_final: 0.8883 (p0) REVERT: C 241 MET cc_start: 0.9276 (ptp) cc_final: 0.8749 (pmm) REVERT: C 262 VAL cc_start: 0.9268 (m) cc_final: 0.8901 (p) REVERT: C 305 LEU cc_start: 0.9317 (tp) cc_final: 0.9089 (tp) REVERT: D 178 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: D 187 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8971 (tp30) REVERT: F 109 MET cc_start: -0.2193 (mtp) cc_final: -0.4677 (ptm) REVERT: F 400 MET cc_start: 0.8921 (mmm) cc_final: 0.8586 (mmm) outliers start: 40 outliers final: 26 residues processed: 204 average time/residue: 0.1131 time to fit residues: 35.7293 Evaluate side-chains 154 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 373 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 70 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.069969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046054 restraints weight = 81648.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047768 restraints weight = 41501.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048832 restraints weight = 28088.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049472 restraints weight = 22372.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049856 restraints weight = 19616.632| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16345 Z= 0.115 Angle : 0.566 8.356 22192 Z= 0.289 Chirality : 0.043 0.252 2445 Planarity : 0.004 0.045 2929 Dihedral : 5.275 68.362 2286 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.37 % Allowed : 16.31 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.19), residues: 2037 helix: 1.65 (0.21), residues: 609 sheet: 0.02 (0.22), residues: 536 loop : -0.89 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.018 0.001 TYR F 398 PHE 0.015 0.001 PHE C 318 TRP 0.016 0.001 TRP A 635 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (16344) covalent geometry : angle 0.56462 / 0.29 (22190) SS BOND : bond 0.02635 / 1.65 ( 1) SS BOND : angle 3.65924 / 1.73 ( 2) hydrogen bonds : bond 0.03932 / 2.66 ( 773) hydrogen bonds : angle 4.93211 / 3.49 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.653 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: A 64 ARG cc_start: 0.9000 (mpt180) cc_final: 0.8041 (mmt180) REVERT: A 325 MET cc_start: 0.8741 (tmm) cc_final: 0.8127 (tmm) REVERT: A 512 ASP cc_start: 0.8637 (t0) cc_final: 0.8380 (p0) REVERT: A 539 MET cc_start: 0.9445 (mtm) cc_final: 0.9089 (mpp) REVERT: A 558 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8337 (t) REVERT: A 741 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7629 (mpp) REVERT: A 768 MET cc_start: 0.7804 (mtp) cc_final: 0.7354 (ttm) REVERT: B 103 TRP cc_start: 0.6980 (t60) cc_final: 0.6772 (t60) REVERT: B 278 MET cc_start: 0.9057 (mpp) cc_final: 0.8832 (mpp) REVERT: B 384 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8355 (p0) REVERT: C 56 MET cc_start: 0.8910 (pmm) cc_final: 0.7918 (pmm) REVERT: C 57 ILE cc_start: 0.9143 (mm) cc_final: 0.8908 (tt) REVERT: C 129 TYR cc_start: 0.6778 (m-80) cc_final: 0.6320 (m-80) REVERT: C 153 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7750 (mt-10) REVERT: C 157 TYR cc_start: 0.9265 (m-80) cc_final: 0.8859 (m-80) REVERT: C 200 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8769 (mt-10) REVERT: C 242 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9133 (mt) REVERT: F 83 MET cc_start: 0.9430 (mpp) cc_final: 0.8865 (mpp) REVERT: F 87 MET cc_start: 0.8271 (mmt) cc_final: 0.7848 (mpp) REVERT: F 109 MET cc_start: -0.1554 (mtp) cc_final: -0.2468 (ptm) REVERT: F 156 GLU cc_start: 0.8825 (tp30) cc_final: 0.8571 (tp30) REVERT: F 298 MET cc_start: 0.9063 (tpt) cc_final: 0.8851 (tpp) REVERT: F 400 MET cc_start: 0.8945 (mmm) cc_final: 0.8689 (mmm) outliers start: 58 outliers final: 28 residues processed: 195 average time/residue: 0.1119 time to fit residues: 34.4748 Evaluate side-chains 153 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 399 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [6, 200, 2, 8, 47, 57, 50, 15, 163, 65, 128] chunk 6 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.068168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044140 restraints weight = 83231.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045787 restraints weight = 42115.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046827 restraints weight = 28560.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047445 restraints weight = 22795.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047697 restraints weight = 20069.676| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16345 Z= 0.161 Angle : 0.564 8.206 22192 Z= 0.290 Chirality : 0.043 0.200 2445 Planarity : 0.004 0.043 2929 Dihedral : 4.744 69.537 2262 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.89 % Allowed : 15.79 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.19), residues: 2037 helix: 1.74 (0.21), residues: 608 sheet: 0.08 (0.22), residues: 538 loop : -0.85 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 129 TYR 0.016 0.001 TYR C 197 PHE 0.019 0.001 PHE C 99 TRP 0.015 0.001 TRP A 635 HIS 0.013 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (16344) covalent geometry : angle 0.56327 / 0.29 (22190) SS BOND : bond 0.01251 / 0.78 ( 1) SS BOND : angle 2.80110 / 1.14 ( 2) hydrogen bonds : bond 0.03958 / 2.67 ( 773) hydrogen bonds : angle 4.67832 / 3.31 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 0.628 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: A 64 ARG cc_start: 0.8997 (mpt180) cc_final: 0.8013 (mmt180) REVERT: A 108 ASP cc_start: 0.9280 (OUTLIER) cc_final: 0.8750 (p0) REVERT: A 109 MET cc_start: 0.9129 (mmm) cc_final: 0.8673 (mmm) REVERT: A 304 MET cc_start: 0.9174 (tpp) cc_final: 0.8816 (tpp) REVERT: A 539 MET cc_start: 0.9491 (mtm) cc_final: 0.9185 (mpp) REVERT: A 558 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 677 HIS cc_start: 0.2071 (p-80) cc_final: 0.1338 (p-80) REVERT: B 127 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 57 ILE cc_start: 0.9252 (mm) cc_final: 0.9018 (tt) REVERT: C 200 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8787 (mt-10) REVERT: C 241 MET cc_start: 0.9527 (ptp) cc_final: 0.9045 (pmm) REVERT: C 264 MET cc_start: 0.9312 (mmp) cc_final: 0.8981 (mmp) REVERT: C 280 TYR cc_start: 0.6355 (t80) cc_final: 0.5825 (t80) REVERT: C 303 TYR cc_start: 0.7744 (m-80) cc_final: 0.7226 (m-80) REVERT: C 328 GLN cc_start: 0.9781 (pm20) cc_final: 0.9306 (tm-30) REVERT: D 225 MET cc_start: 0.9272 (mmm) cc_final: 0.8925 (mtt) REVERT: F 109 MET cc_start: -0.1394 (mtp) cc_final: -0.2237 (ptm) REVERT: F 156 GLU cc_start: 0.8866 (tp30) cc_final: 0.8626 (tp30) REVERT: F 298 MET cc_start: 0.9198 (tpt) cc_final: 0.8900 (tpp) REVERT: F 400 MET cc_start: 0.8938 (mmm) cc_final: 0.8690 (mmm) outliers start: 67 outliers final: 38 residues processed: 181 average time/residue: 0.1030 time to fit residues: 29.8214 Evaluate side-chains 154 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [198, 118, 31, 199, 21, 48, 172, 103, 83, 178, 26] chunk 198 optimal weight: 2.9990 chunk 118 optimal weight: 0.0070 chunk 31 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.068941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045148 restraints weight = 82398.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046839 restraints weight = 41524.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047913 restraints weight = 27966.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048555 restraints weight = 22250.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048943 restraints weight = 19524.396| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16345 Z= 0.104 Angle : 0.543 9.158 22192 Z= 0.275 Chirality : 0.043 0.205 2445 Planarity : 0.003 0.045 2929 Dihedral : 4.509 68.355 2261 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 16.37 % Favored : 80.56 % 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: 0.35 (0.19), residues: 2037 helix: 1.76 (0.21), residues: 610 sheet: 0.21 (0.22), residues: 543 loop : -0.81 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 129 TYR 0.023 0.001 TYR F 398 PHE 0.016 0.001 PHE C 99 TRP 0.033 0.001 TRP B 103 HIS 0.005 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (16344) covalent geometry : angle 0.54226 / 0.27 (22190) SS BOND : bond 0.01272 / 0.80 ( 1) SS BOND : angle 3.02683 / 1.21 ( 2) hydrogen bonds : bond 0.03569 / 2.41 ( 773) hydrogen bonds : angle 4.44449 / 3.15 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.632 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: A 64 ARG cc_start: 0.9008 (mpt180) cc_final: 0.8006 (mmt180) REVERT: A 304 MET cc_start: 0.9140 (tpp) cc_final: 0.8796 (tpp) REVERT: A 325 MET cc_start: 0.8437 (tmm) cc_final: 0.7404 (tmm) REVERT: A 539 MET cc_start: 0.9445 (mtm) cc_final: 0.9214 (mpp) REVERT: A 558 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 677 HIS cc_start: 0.1920 (p-80) cc_final: 0.1440 (p-80) REVERT: B 103 TRP cc_start: 0.7377 (t60) cc_final: 0.7025 (t60) REVERT: B 104 PHE cc_start: 0.6462 (m-80) cc_final: 0.6087 (m-10) REVERT: B 127 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7993 (mm-30) REVERT: C 49 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8098 (tm-30) REVERT: C 57 ILE cc_start: 0.9198 (mm) cc_final: 0.8970 (tt) REVERT: C 200 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8782 (mt-10) REVERT: C 228 MET cc_start: 0.7199 (ppp) cc_final: 0.6815 (ppp) REVERT: C 241 MET cc_start: 0.9541 (ptp) cc_final: 0.9050 (pmm) REVERT: C 280 TYR cc_start: 0.6314 (t80) cc_final: 0.5724 (t80) REVERT: C 303 TYR cc_start: 0.7837 (m-80) cc_final: 0.7508 (m-80) REVERT: C 318 PHE cc_start: 0.8470 (m-80) cc_final: 0.8270 (m-80) REVERT: C 328 GLN cc_start: 0.9794 (pm20) cc_final: 0.9343 (tm-30) REVERT: D 55 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9219 (mm) REVERT: D 58 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9208 (mt) REVERT: D 225 MET cc_start: 0.9220 (mmm) cc_final: 0.8972 (mtt) REVERT: E 54 GLN cc_start: 0.9547 (mt0) cc_final: 0.9242 (mt0) REVERT: F 83 MET cc_start: 0.9453 (mpp) cc_final: 0.9047 (mpp) REVERT: F 87 MET cc_start: 0.8319 (mmt) cc_final: 0.7856 (mpp) REVERT: F 109 MET cc_start: -0.1541 (mtp) cc_final: -0.2286 (ptm) REVERT: F 156 GLU cc_start: 0.8819 (tp30) cc_final: 0.8576 (tp30) REVERT: F 400 MET cc_start: 0.8991 (mmm) cc_final: 0.8745 (mmm) outliers start: 53 outliers final: 37 residues processed: 173 average time/residue: 0.1010 time to fit residues: 28.2613 Evaluate side-chains 154 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [147, 125, 15, 57, 103, 142, 74, 49, 29, 137, 98] chunk 147 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 142 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.068081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044060 restraints weight = 82393.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045722 restraints weight = 41890.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046755 restraints weight = 28457.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047372 restraints weight = 22801.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047755 restraints weight = 20103.408| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16345 Z= 0.114 Angle : 0.558 15.739 22192 Z= 0.276 Chirality : 0.043 0.246 2445 Planarity : 0.003 0.044 2929 Dihedral : 4.459 68.130 2261 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 3.54 % Allowed : 16.42 % Favored : 80.03 % 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: 0.48 (0.19), residues: 2037 helix: 1.84 (0.21), residues: 610 sheet: 0.42 (0.22), residues: 543 loop : -0.82 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 129 TYR 0.016 0.001 TYR C 197 PHE 0.013 0.001 PHE C 99 TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16344) covalent geometry : angle 0.55712 / 0.28 (22190) SS BOND : bond 0.00299 / 0.19 ( 1) SS BOND : angle 2.94671 / 1.13 ( 2) hydrogen bonds : bond 0.03488 / 2.36 ( 773) hydrogen bonds : angle 4.35936 / 3.09 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.661 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: A 64 ARG cc_start: 0.9022 (mpt180) cc_final: 0.8021 (mmt180) REVERT: A 325 MET cc_start: 0.8508 (tmm) cc_final: 0.8248 (tmm) REVERT: A 539 MET cc_start: 0.9482 (mtm) cc_final: 0.9206 (mpp) REVERT: A 558 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 677 HIS cc_start: 0.2255 (p-80) cc_final: 0.1909 (p-80) REVERT: B 103 TRP cc_start: 0.7386 (t60) cc_final: 0.7017 (t60) REVERT: B 104 PHE cc_start: 0.6393 (m-80) cc_final: 0.6106 (m-10) REVERT: B 127 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8037 (mm-30) REVERT: C 57 ILE cc_start: 0.9212 (mm) cc_final: 0.8986 (tt) REVERT: C 157 TYR cc_start: 0.9222 (m-80) cc_final: 0.8677 (m-80) REVERT: C 228 MET cc_start: 0.7416 (ppp) cc_final: 0.6575 (ppp) REVERT: C 241 MET cc_start: 0.9532 (ptp) cc_final: 0.8982 (pmm) REVERT: C 280 TYR cc_start: 0.6567 (t80) cc_final: 0.6143 (t80) REVERT: C 303 TYR cc_start: 0.7974 (m-80) cc_final: 0.7653 (m-10) REVERT: C 317 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 328 GLN cc_start: 0.9786 (pm20) cc_final: 0.9311 (tm-30) REVERT: D 55 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9242 (mm) REVERT: D 58 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9251 (mt) REVERT: D 225 MET cc_start: 0.9201 (mmm) cc_final: 0.8753 (mtt) REVERT: E 54 GLN cc_start: 0.9533 (mt0) cc_final: 0.9250 (mt0) REVERT: F 109 MET cc_start: -0.1556 (mtp) cc_final: -0.2243 (ptm) REVERT: F 156 GLU cc_start: 0.8825 (tp30) cc_final: 0.8589 (tp30) REVERT: F 400 MET cc_start: 0.8971 (mmm) cc_final: 0.8724 (mmm) outliers start: 61 outliers final: 44 residues processed: 176 average time/residue: 0.1031 time to fit residues: 29.5056 Evaluate side-chains 160 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [200, 151, 28, 174, 122, 153, 63, 95, 194, 125, 130] chunk 200 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN C 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.067249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043432 restraints weight = 82773.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045038 restraints weight = 42422.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046063 restraints weight = 28827.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046674 restraints weight = 23068.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047039 restraints weight = 20291.941| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16345 Z= 0.129 Angle : 0.568 14.782 22192 Z= 0.282 Chirality : 0.042 0.231 2445 Planarity : 0.003 0.044 2929 Dihedral : 4.474 69.571 2261 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.61 % Rotamer: Outliers : 3.25 % Allowed : 17.06 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.19), residues: 2037 helix: 1.88 (0.21), residues: 610 sheet: 0.53 (0.22), residues: 535 loop : -0.83 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.023 0.001 TYR F 398 PHE 0.016 0.001 PHE C 318 TRP 0.014 0.001 TRP B 103 HIS 0.007 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16344) covalent geometry : angle 0.56748 / 0.28 (22190) SS BOND : bond 0.00764 / 0.48 ( 1) SS BOND : angle 2.92966 / 1.11 ( 2) hydrogen bonds : bond 0.03491 / 2.37 ( 773) hydrogen bonds : angle 4.31929 / 3.07 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.587 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: A 64 ARG cc_start: 0.9032 (mpt180) cc_final: 0.8009 (mmt180) REVERT: A 304 MET cc_start: 0.9117 (tpp) cc_final: 0.8901 (tpt) REVERT: A 325 MET cc_start: 0.8534 (tmm) cc_final: 0.8298 (tmm) REVERT: A 539 MET cc_start: 0.9472 (mtm) cc_final: 0.9210 (mpp) REVERT: A 558 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8801 (t) REVERT: B 103 TRP cc_start: 0.7462 (t60) cc_final: 0.7095 (t60) REVERT: B 104 PHE cc_start: 0.6390 (m-80) cc_final: 0.6052 (m-10) REVERT: C 57 ILE cc_start: 0.9261 (mm) cc_final: 0.9024 (tt) REVERT: C 157 TYR cc_start: 0.9228 (m-80) cc_final: 0.8797 (m-80) REVERT: C 228 MET cc_start: 0.7469 (ppp) cc_final: 0.6426 (ppp) REVERT: C 241 MET cc_start: 0.9518 (ptp) cc_final: 0.9006 (pmm) REVERT: C 328 GLN cc_start: 0.9791 (pm20) cc_final: 0.9274 (tp-100) REVERT: D 55 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9246 (mm) REVERT: D 225 MET cc_start: 0.9238 (mmm) cc_final: 0.8760 (mtt) REVERT: E 54 GLN cc_start: 0.9518 (mt0) cc_final: 0.9229 (mt0) REVERT: F 109 MET cc_start: -0.1403 (mtp) cc_final: -0.2187 (ptm) REVERT: F 156 GLU cc_start: 0.8839 (tp30) cc_final: 0.8518 (tp30) REVERT: F 298 MET cc_start: 0.9224 (tpp) cc_final: 0.8913 (tpp) REVERT: F 400 MET cc_start: 0.8959 (mmm) cc_final: 0.8716 (mmm) outliers start: 56 outliers final: 43 residues processed: 173 average time/residue: 0.1047 time to fit residues: 29.1177 Evaluate side-chains 157 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [177, 196, 175, 144, 115, 35, 22, 54, 114, 118, 0] chunk 177 optimal weight: 9.9990 chunk 196 optimal weight: 0.0870 chunk 175 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 115 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 overall best weight: 1.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.067355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.043503 restraints weight = 82330.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045127 restraints weight = 42093.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046161 restraints weight = 28646.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046762 restraints weight = 22890.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047068 restraints weight = 20165.421| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16345 Z= 0.117 Angle : 0.583 14.801 22192 Z= 0.287 Chirality : 0.043 0.313 2445 Planarity : 0.003 0.044 2929 Dihedral : 4.377 69.474 2260 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 3.08 % Allowed : 17.70 % Favored : 79.22 % 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: 0.56 (0.19), residues: 2037 helix: 1.94 (0.21), residues: 610 sheet: 0.51 (0.22), residues: 540 loop : -0.82 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.027 0.001 TYR C 303 PHE 0.012 0.001 PHE F 373 TRP 0.011 0.001 TRP B 103 HIS 0.011 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (16344) covalent geometry : angle 0.58234 / 0.29 (22190) SS BOND : bond 0.00442 / 0.28 ( 1) SS BOND : angle 2.88018 / 1.10 ( 2) hydrogen bonds : bond 0.03425 / 2.34 ( 773) hydrogen bonds : angle 4.25163 / 3.03 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.561 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: A 64 ARG cc_start: 0.9039 (mpt180) cc_final: 0.8009 (mmt180) REVERT: A 325 MET cc_start: 0.8543 (tmm) cc_final: 0.8324 (tmm) REVERT: A 539 MET cc_start: 0.9483 (mtm) cc_final: 0.9159 (mpp) REVERT: A 558 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 677 HIS cc_start: 0.2267 (p-80) cc_final: 0.2058 (p-80) REVERT: C 57 ILE cc_start: 0.9235 (mm) cc_final: 0.8993 (tt) REVERT: C 157 TYR cc_start: 0.9280 (m-80) cc_final: 0.8839 (m-80) REVERT: C 200 GLU cc_start: 0.9417 (mt-10) cc_final: 0.8995 (pt0) REVERT: C 228 MET cc_start: 0.7516 (ppp) cc_final: 0.6436 (ppp) REVERT: C 241 MET cc_start: 0.9521 (ptp) cc_final: 0.9057 (pmm) REVERT: C 280 TYR cc_start: 0.6540 (t80) cc_final: 0.6314 (t80) REVERT: C 317 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 328 GLN cc_start: 0.9789 (pm20) cc_final: 0.9285 (tp-100) REVERT: D 55 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9235 (mm) REVERT: D 225 MET cc_start: 0.9241 (mmm) cc_final: 0.8765 (mtt) REVERT: E 54 GLN cc_start: 0.9517 (mt0) cc_final: 0.9229 (mt0) REVERT: F 109 MET cc_start: -0.1374 (mtp) cc_final: -0.2143 (ptm) REVERT: F 156 GLU cc_start: 0.8826 (tp30) cc_final: 0.8505 (tp30) REVERT: F 298 MET cc_start: 0.9252 (tpp) cc_final: 0.8961 (tpp) REVERT: F 400 MET cc_start: 0.8965 (mmm) cc_final: 0.8716 (mmm) outliers start: 53 outliers final: 45 residues processed: 171 average time/residue: 0.1063 time to fit residues: 29.2645 Evaluate side-chains 160 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [62, 82, 92, 63, 28, 182, 153, 75, 52, 163, 101] chunk 62 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 153 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN C 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.042466 restraints weight = 83674.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.044047 restraints weight = 42879.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045046 restraints weight = 29312.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045641 restraints weight = 23499.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045996 restraints weight = 20727.949| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16345 Z= 0.164 Angle : 0.605 15.149 22192 Z= 0.300 Chirality : 0.043 0.325 2445 Planarity : 0.003 0.044 2929 Dihedral : 4.501 71.151 2260 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 2.90 % Allowed : 18.46 % Favored : 78.64 % 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: 0.54 (0.19), residues: 2037 helix: 1.95 (0.21), residues: 610 sheet: 0.45 (0.22), residues: 544 loop : -0.82 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.018 0.001 TYR C 303 PHE 0.019 0.001 PHE C 318 TRP 0.018 0.001 TRP B 103 HIS 0.011 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16344) covalent geometry : angle 0.60465 / 0.30 (22190) SS BOND : bond 0.01119 / 0.70 ( 1) SS BOND : angle 2.95556 / 1.11 ( 2) hydrogen bonds : bond 0.03695 / 2.52 ( 773) hydrogen bonds : angle 4.34343 / 3.11 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.679 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: A 64 ARG cc_start: 0.9040 (mpt180) cc_final: 0.7990 (mmt180) REVERT: A 304 MET cc_start: 0.9081 (tpp) cc_final: 0.8671 (tpt) REVERT: A 539 MET cc_start: 0.9543 (mtm) cc_final: 0.9136 (mpp) REVERT: A 558 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8895 (t) REVERT: A 677 HIS cc_start: 0.2513 (p-80) cc_final: 0.2306 (p-80) REVERT: B 104 PHE cc_start: 0.6547 (m-80) cc_final: 0.6123 (m-10) REVERT: B 278 MET cc_start: 0.9092 (mpp) cc_final: 0.8664 (mpp) REVERT: C 153 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7753 (mt-10) REVERT: C 228 MET cc_start: 0.7526 (ppp) cc_final: 0.6126 (ppp) REVERT: C 317 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 328 GLN cc_start: 0.9789 (pm20) cc_final: 0.9262 (tp-100) REVERT: D 55 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9350 (mm) REVERT: D 225 MET cc_start: 0.9274 (mmm) cc_final: 0.8785 (mtt) REVERT: F 109 MET cc_start: -0.1359 (mtp) cc_final: -0.2134 (ptm) REVERT: F 156 GLU cc_start: 0.8858 (tp30) cc_final: 0.8584 (tp30) REVERT: F 298 MET cc_start: 0.9325 (tpp) cc_final: 0.9058 (tpp) REVERT: F 400 MET cc_start: 0.8968 (mmm) cc_final: 0.8719 (mmm) outliers start: 50 outliers final: 44 residues processed: 162 average time/residue: 0.1061 time to fit residues: 27.5348 Evaluate side-chains 155 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [12, 30, 182, 184, 122, 137, 5, 115, 4, 127, 190] chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 182 optimal weight: 40.0000 chunk 184 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 115 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.040866 restraints weight = 83959.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.042363 restraints weight = 43515.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043311 restraints weight = 30033.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043881 restraints weight = 24217.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.044219 restraints weight = 21391.952| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16345 Z= 0.230 Angle : 0.662 14.305 22192 Z= 0.331 Chirality : 0.044 0.311 2445 Planarity : 0.004 0.043 2929 Dihedral : 4.820 73.731 2259 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 3.02 % Allowed : 18.40 % Favored : 78.58 % 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: 0.42 (0.19), residues: 2037 helix: 1.84 (0.21), residues: 607 sheet: 0.45 (0.22), residues: 535 loop : -0.93 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 149 TYR 0.020 0.002 TYR C 303 PHE 0.027 0.002 PHE A 648 TRP 0.025 0.001 TRP C 148 HIS 0.012 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (16344) covalent geometry : angle 0.66172 / 0.33 (22190) SS BOND : bond 0.00936 / 0.58 ( 1) SS BOND : angle 2.93331 / 1.09 ( 2) hydrogen bonds : bond 0.04036 / 2.76 ( 773) hydrogen bonds : angle 4.56014 / 3.27 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.9017 (mpt180) cc_final: 0.7955 (mmt180) REVERT: A 304 MET cc_start: 0.9142 (tpp) cc_final: 0.8933 (tpt) REVERT: A 325 MET cc_start: 0.8573 (tmm) cc_final: 0.7891 (tmm) REVERT: A 539 MET cc_start: 0.9628 (mtm) cc_final: 0.9225 (mpp) REVERT: A 558 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8782 (t) REVERT: B 221 MET cc_start: 0.9026 (tpt) cc_final: 0.8513 (tpp) REVERT: B 278 MET cc_start: 0.9192 (mpp) cc_final: 0.8648 (mpp) REVERT: C 228 MET cc_start: 0.7749 (ppp) cc_final: 0.6344 (ppp) REVERT: C 241 MET cc_start: 0.9499 (ptp) cc_final: 0.9054 (pmm) REVERT: C 317 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 225 MET cc_start: 0.9407 (mmm) cc_final: 0.8870 (mtt) REVERT: F 109 MET cc_start: -0.1145 (mtp) cc_final: -0.1934 (ptm) REVERT: F 156 GLU cc_start: 0.8918 (tp30) cc_final: 0.8638 (tp30) REVERT: F 400 MET cc_start: 0.8954 (mmm) cc_final: 0.8722 (mmm) outliers start: 52 outliers final: 44 residues processed: 158 average time/residue: 0.1020 time to fit residues: 26.1259 Evaluate side-chains 149 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [103, 38, 105, 53, 49, 97, 143, 70, 57, 11, 137] chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.065282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.041313 restraints weight = 83016.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.042845 restraints weight = 42805.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043798 restraints weight = 29397.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044391 restraints weight = 23648.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044682 restraints weight = 20835.329| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16345 Z= 0.165 Angle : 0.644 15.153 22192 Z= 0.319 Chirality : 0.044 0.295 2445 Planarity : 0.004 0.044 2929 Dihedral : 4.719 73.226 2259 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 2.61 % Allowed : 19.15 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.19), residues: 2037 helix: 1.94 (0.21), residues: 606 sheet: 0.36 (0.22), residues: 547 loop : -0.88 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.020 0.001 TYR C 197 PHE 0.022 0.001 PHE A 648 TRP 0.016 0.001 TRP C 148 HIS 0.010 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (16344) covalent geometry : angle 0.64313 / 0.32 (22190) SS BOND : bond 0.00901 / 0.56 ( 1) SS BOND : angle 2.78189 / 1.06 ( 2) hydrogen bonds : bond 0.03802 / 2.60 ( 773) hydrogen bonds : angle 4.44669 / 3.19 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.9007 (mpt180) cc_final: 0.7988 (mmt180) REVERT: A 304 MET cc_start: 0.9133 (tpp) cc_final: 0.8715 (tpt) REVERT: A 325 MET cc_start: 0.8477 (tmm) cc_final: 0.7746 (tmm) REVERT: A 539 MET cc_start: 0.9535 (mtm) cc_final: 0.8979 (mpp) REVERT: A 558 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8738 (t) REVERT: B 221 MET cc_start: 0.9012 (tpt) cc_final: 0.8492 (tpp) REVERT: B 278 MET cc_start: 0.9165 (mpp) cc_final: 0.8681 (mpp) REVERT: C 153 GLU cc_start: 0.8458 (tt0) cc_final: 0.8232 (tt0) REVERT: C 228 MET cc_start: 0.7747 (ppp) cc_final: 0.6330 (ppp) REVERT: C 241 MET cc_start: 0.9450 (ptp) cc_final: 0.8945 (pmm) REVERT: C 317 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 328 GLN cc_start: 0.9603 (OUTLIER) cc_final: 0.9350 (mm110) REVERT: D 109 MET cc_start: 0.9193 (mtp) cc_final: 0.8886 (ttm) REVERT: D 225 MET cc_start: 0.9400 (mmm) cc_final: 0.8848 (mtt) REVERT: F 87 MET cc_start: 0.8707 (mmt) cc_final: 0.8192 (mpp) REVERT: F 109 MET cc_start: -0.1205 (mtp) cc_final: -0.1980 (ptm) REVERT: F 156 GLU cc_start: 0.8907 (tp30) cc_final: 0.8628 (tp30) REVERT: F 298 MET cc_start: 0.9249 (tpp) cc_final: 0.9036 (tpp) REVERT: F 400 MET cc_start: 0.8955 (mmm) cc_final: 0.8721 (mmm) outliers start: 45 outliers final: 42 residues processed: 152 average time/residue: 0.1041 time to fit residues: 25.4929 Evaluate side-chains 148 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 62 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 373 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 399 ARG Chi-restraints excluded: chain F residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [22, 2, 169, 186, 34, 180, 63, 136, 151, 179, 184] chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.041392 restraints weight = 82233.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.042915 restraints weight = 42549.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043869 restraints weight = 29255.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.044458 restraints weight = 23519.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.044803 restraints weight = 20742.985| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 16345 Z= 0.242 Angle : 0.814 59.187 22192 Z= 0.448 Chirality : 0.044 0.296 2445 Planarity : 0.004 0.044 2929 Dihedral : 4.714 73.250 2259 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 2.55 % Allowed : 19.62 % Favored : 77.83 % 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: 0.44 (0.19), residues: 2037 helix: 1.90 (0.21), residues: 606 sheet: 0.37 (0.22), residues: 547 loop : -0.89 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.020 0.001 TYR C 197 PHE 0.022 0.001 PHE A 648 TRP 0.014 0.001 TRP B 103 HIS 0.010 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (16344) covalent geometry : angle 0.81410 / 0.45 (22190) SS BOND : bond 0.01101 / 0.69 ( 1) SS BOND : angle 2.70801 / 1.05 ( 2) hydrogen bonds : bond 0.03836 / 2.63 ( 773) hydrogen bonds : angle 4.45753 / 3.20 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.10 seconds wall clock time: 59 minutes 9.12 seconds (3549.12 seconds total)