Starting phenix.real_space_refine on Thu Jul 2 03:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga3_29885/07_2026/8ga3_29885.map" } resolution = 3.1 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= 0.005 sd= 0.090 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 4 4.86 5 C 4336 2.51 5 N 1085 2.21 5 O 1123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3291 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6590 At special positions: 0 Unit cell: (73.425, 89.925, 110.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 42 16.00 O 1123 8.00 N 1085 7.00 C 4336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS B 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS B 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 415.0 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 72.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.655A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 49 removed outlier: 3.814A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.733A pdb=" N ARG A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.019A pdb=" N THR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 102 through 105 removed outlier: 3.615A pdb=" N GLY A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.596A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.564A pdb=" N PHE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.888A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 190 removed outlier: 3.677A pdb=" N ALA A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.899A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.570A pdb=" N SER A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 280 Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.065A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.752A pdb=" N VAL A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.654A pdb=" N LEU A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.532A pdb=" N ALA A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 4.708A pdb=" N ARG A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.647A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.590A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 417 Processing helix chain 'A' and resid 422 through 439 removed outlier: 3.516A pdb=" N THR A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.706A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 67 removed outlier: 3.559A pdb=" N PHE B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.236A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 removed outlier: 4.223A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Proline residue: B 129 - end of helix removed outlier: 3.667A pdb=" N PHE B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 148 through 166 removed outlier: 3.591A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 188 removed outlier: 3.629A pdb=" N LEU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.775A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 231 removed outlier: 3.575A pdb=" N PHE B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 280 Proline residue: B 267 - end of helix removed outlier: 3.866A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 309 removed outlier: 3.873A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.587A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 346 removed outlier: 3.516A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.528A pdb=" N SER B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 351 " --> pdb=" O PHE B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 363 through 373 removed outlier: 3.661A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.707A pdb=" N TYR B 382 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 383' Processing helix chain 'B' and resid 387 through 395 removed outlier: 4.002A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 423 through 440 removed outlier: 3.679A pdb=" N ALA B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 461 removed outlier: 3.776A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 999 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: 0.78 Time building geometry restraints manager: 0.75 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: 2062 1.34 - 1.46: 1227 1.46 - 1.57: 3365 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 6730 Sorted by residual: bond pdb=" C THR B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" CA ILE B 109 " pdb=" C ILE B 109 " ideal model delta sigma weight residual 1.520 1.533 -0.013 8.80e-03 1.29e+04 2.26e+00 bond pdb=" C ILE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.01e+00 bond pdb=" C LEU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.81e+00 bond pdb=" C ARG B 205 " pdb=" N PRO B 206 " ideal model delta sigma weight residual 1.335 1.347 -0.012 9.40e-03 1.13e+04 1.74e+00 ... (remaining 6725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8799 2.00 - 4.00: 278 4.00 - 6.00: 41 6.00 - 8.00: 24 8.00 - 10.00: 5 Bond angle restraints: 9147 Sorted by residual: angle pdb=" N LEU B 411 " pdb=" CA LEU B 411 " pdb=" C LEU B 411 " ideal model delta sigma weight residual 114.62 108.19 6.43 1.14e+00 7.69e-01 3.18e+01 angle pdb=" C LEU B 319 " pdb=" N ILE B 320 " pdb=" CA ILE B 320 " ideal model delta sigma weight residual 120.33 123.85 -3.52 8.00e-01 1.56e+00 1.94e+01 angle pdb=" CA ILE B 320 " pdb=" C ILE B 320 " pdb=" N PRO B 321 " ideal model delta sigma weight residual 120.83 123.41 -2.58 6.10e-01 2.69e+00 1.79e+01 angle pdb=" C GLY B 108 " pdb=" N ILE B 109 " pdb=" CA ILE B 109 " ideal model delta sigma weight residual 120.24 122.73 -2.49 6.30e-01 2.52e+00 1.57e+01 angle pdb=" C THR B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 ... (remaining 9142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3426 17.85 - 35.70: 395 35.70 - 53.55: 59 53.55 - 71.40: 10 71.40 - 89.24: 3 Dihedral angle restraints: 3893 sinusoidal: 1447 harmonic: 2446 Sorted by residual: dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS B 249 " pdb=" CB CYS B 249 " ideal model delta sinusoidal sigma weight residual 93.00 153.98 -60.98 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CA CYS A 249 " pdb=" C CYS A 249 " pdb=" N ASN A 250 " pdb=" CA ASN A 250 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASP A 118 " pdb=" C ASP A 118 " pdb=" N GLN A 119 " pdb=" CA GLN A 119 " ideal model delta harmonic sigma weight residual 180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 891 0.063 - 0.125: 169 0.125 - 0.188: 18 0.188 - 0.250: 4 0.250 - 0.313: 2 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB THR B 31 " pdb=" CA THR B 31 " pdb=" OG1 THR B 31 " pdb=" CG2 THR B 31 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR B 31 " pdb=" N THR B 31 " pdb=" C THR B 31 " pdb=" CB THR B 31 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1081 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 358 " 0.045 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO B 359 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 266 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO A 267 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 423 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.56e+00 pdb=" N PRO A 424 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.036 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2042 2.81 - 3.34: 5683 3.34 - 3.86: 11120 3.86 - 4.38: 13691 4.38 - 4.90: 22872 Nonbonded interactions: 55408 Sorted by model distance: nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.294 3.040 nonbonded pdb=" O ARG A 147 " pdb=" OG1 THR A 151 " model vdw 2.295 3.040 nonbonded pdb=" O LEU B 435 " pdb=" OG1 THR B 439 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 86 " pdb=" O GLY B 141 " model vdw 2.320 3.040 nonbonded pdb=" O LEU A 345 " pdb=" OG SER A 349 " model vdw 2.327 3.040 ... (remaining 55403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 502)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.005 0.052 6732 Z= 0.202 Angle : 0.891 9.996 9151 Z= 0.472 Chirality : 0.051 0.313 1084 Planarity : 0.007 0.067 1147 Dihedral : 14.759 89.245 2343 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % 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: -6.60 (0.16), residues: 882 helix: -4.64 (0.08), residues: 604 sheet: None (None), residues: 0 loop : -3.13 (0.29), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.019 0.002 TYR A 210 PHE 0.009 0.001 PHE A 219 TRP 0.038 0.001 TRP B 291 HIS 0.007 0.002 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 6730) covalent geometry : angle 0.88834 / 0.47 ( 9147) SS BOND : bond 0.00150 / 0.08 ( 2) SS BOND : angle 3.19013 / 1.83 ( 4) hydrogen bonds : bond 0.31015 / 19.97 ( 336) hydrogen bonds : angle 12.35050 / 8.62 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.225 Fit side-chains REVERT: A 54 ASP cc_start: 0.8663 (m-30) cc_final: 0.8458 (m-30) REVERT: A 174 ARG cc_start: 0.6751 (mtt180) cc_final: 0.6544 (mtp180) REVERT: B 290 LYS cc_start: 0.7985 (mttp) cc_final: 0.7785 (mtmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0885 time to fit residues: 11.2978 Evaluate side-chains 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 HIS B 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137606 restraints weight = 7377.127| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.89 r_work: 0.3482 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6732 Z= 0.133 Angle : 0.620 6.480 9151 Z= 0.316 Chirality : 0.042 0.154 1084 Planarity : 0.006 0.046 1147 Dihedral : 5.491 24.913 934 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.21 % Allowed : 10.93 % Favored : 87.86 % 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: -4.55 (0.22), residues: 882 helix: -2.84 (0.16), residues: 630 sheet: None (None), residues: 0 loop : -2.91 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.009 0.001 TYR A 210 PHE 0.007 0.001 PHE A 379 TRP 0.018 0.001 TRP B 291 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6730) covalent geometry : angle 0.61899 / 0.32 ( 9147) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 1.96140 / 1.13 ( 4) hydrogen bonds : bond 0.04314 / 2.82 ( 336) hydrogen bonds : angle 5.65039 / 3.75 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.222 Fit side-chains REVERT: A 126 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7116 (mtm-85) REVERT: A 147 ARG cc_start: 0.7810 (ptt-90) cc_final: 0.7434 (ptt-90) REVERT: A 174 ARG cc_start: 0.6747 (mtt180) cc_final: 0.5911 (mtp180) REVERT: A 186 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 294 MET cc_start: 0.7193 (ttp) cc_final: 0.6654 (ttt) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 0.0728 time to fit residues: 7.8241 Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.0010 chunk 14 optimal weight: 0.2980 chunk 73 optimal weight: 0.0020 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 284 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 = 0.3889 r_free = 0.3889 target = 0.168393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141492 restraints weight = 7232.642| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.86 r_work: 0.3527 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6732 Z= 0.100 Angle : 0.562 8.125 9151 Z= 0.279 Chirality : 0.040 0.122 1084 Planarity : 0.004 0.039 1147 Dihedral : 5.056 23.597 934 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.37 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.26), residues: 882 helix: -1.65 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 167 TYR 0.007 0.001 TYR B 94 PHE 0.007 0.001 PHE A 379 TRP 0.012 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6730) covalent geometry : angle 0.56028 / 0.28 ( 9147) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 2.25320 / 1.30 ( 4) hydrogen bonds : bond 0.03161 / 2.06 ( 336) hydrogen bonds : angle 4.59273 / 2.99 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.137 Fit side-chains REVERT: A 126 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7164 (mtm-85) REVERT: A 174 ARG cc_start: 0.6715 (mtt180) cc_final: 0.5892 (mtp180) REVERT: A 276 MET cc_start: 0.7953 (tpt) cc_final: 0.7195 (tpt) REVERT: A 294 MET cc_start: 0.7188 (ttp) cc_final: 0.6732 (ttt) REVERT: B 160 ARG cc_start: 0.8246 (tpt90) cc_final: 0.7833 (mmm-85) REVERT: B 198 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7362 (mp) outliers start: 9 outliers final: 2 residues processed: 77 average time/residue: 0.0764 time to fit residues: 7.8493 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135870 restraints weight = 7387.041| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.88 r_work: 0.3360 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6732 Z= 0.146 Angle : 0.590 7.657 9151 Z= 0.292 Chirality : 0.043 0.157 1084 Planarity : 0.004 0.045 1147 Dihedral : 5.098 24.212 934 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.67 % Allowed : 13.96 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.51 (0.27), residues: 882 helix: -1.15 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.009 0.001 TYR A 210 PHE 0.020 0.001 PHE B 95 TRP 0.014 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6730) covalent geometry : angle 0.58797 / 0.29 ( 9147) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 2.56127 / 1.48 ( 4) hydrogen bonds : bond 0.03287 / 2.15 ( 336) hydrogen bonds : angle 4.49289 / 2.93 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.215 Fit side-chains REVERT: A 174 ARG cc_start: 0.6806 (mtt180) cc_final: 0.5935 (mtp180) REVERT: A 294 MET cc_start: 0.7257 (ttp) cc_final: 0.6713 (ttp) REVERT: B 65 MET cc_start: 0.7525 (mmt) cc_final: 0.7076 (mmm) REVERT: B 198 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7400 (mp) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.0677 time to fit residues: 7.2197 Evaluate side-chains 68 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144725 restraints weight = 7188.042| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.76 r_work: 0.3385 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6732 Z= 0.127 Angle : 0.612 15.553 9151 Z= 0.300 Chirality : 0.042 0.165 1084 Planarity : 0.004 0.045 1147 Dihedral : 5.092 26.914 934 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.82 % Allowed : 14.57 % Favored : 83.61 % 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: -2.13 (0.27), residues: 882 helix: -0.86 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.61 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.010 0.001 TYR A 229 PHE 0.019 0.001 PHE B 95 TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6730) covalent geometry : angle 0.59815 / 0.29 ( 9147) SS BOND : bond 0.00701 / 0.37 ( 2) SS BOND : angle 6.28362 / 3.41 ( 4) hydrogen bonds : bond 0.03121 / 2.07 ( 336) hydrogen bonds : angle 4.31854 / 2.80 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.235 Fit side-chains REVERT: A 174 ARG cc_start: 0.6780 (mtt180) cc_final: 0.5899 (mtp180) REVERT: A 294 MET cc_start: 0.7283 (ttp) cc_final: 0.6742 (ttp) REVERT: B 65 MET cc_start: 0.7506 (mmt) cc_final: 0.7097 (mmm) REVERT: B 198 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7435 (mp) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.0686 time to fit residues: 7.2028 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 0.0000 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139917 restraints weight = 7294.167| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.88 r_work: 0.3462 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 6732 Z= 0.106 Angle : 0.579 12.995 9151 Z= 0.284 Chirality : 0.041 0.140 1084 Planarity : 0.004 0.045 1147 Dihedral : 4.883 23.936 934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.82 % Allowed : 15.33 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.28), residues: 882 helix: -0.54 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.008 0.001 TYR A 229 PHE 0.019 0.001 PHE B 95 TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6730) covalent geometry : angle 0.56813 / 0.28 ( 9147) SS BOND : bond 0.00180 / 0.09 ( 2) SS BOND : angle 5.25885 / 2.82 ( 4) hydrogen bonds : bond 0.02874 / 1.91 ( 336) hydrogen bonds : angle 4.07905 / 2.63 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.238 Fit side-chains REVERT: A 126 ARG cc_start: 0.7723 (mtt-85) cc_final: 0.7157 (mtm-85) REVERT: A 174 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6035 (mtp180) REVERT: A 282 ARG cc_start: 0.7278 (mpt90) cc_final: 0.6852 (mtm110) REVERT: A 294 MET cc_start: 0.7310 (ttp) cc_final: 0.6814 (ttt) REVERT: B 65 MET cc_start: 0.7482 (mmt) cc_final: 0.7042 (mmm) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.0755 time to fit residues: 7.2860 Evaluate side-chains 67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 0.0070 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142715 restraints weight = 7102.562| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.83 r_work: 0.3497 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6732 Z= 0.108 Angle : 0.559 8.713 9151 Z= 0.276 Chirality : 0.041 0.197 1084 Planarity : 0.004 0.045 1147 Dihedral : 4.831 25.601 934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.67 % Allowed : 15.63 % Favored : 82.70 % 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: -1.45 (0.28), residues: 882 helix: -0.31 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.52 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.006 0.001 TYR A 229 PHE 0.020 0.001 PHE B 95 TRP 0.009 0.001 TRP B 291 HIS 0.002 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6730) covalent geometry : angle 0.55144 / 0.27 ( 9147) SS BOND : bond 0.00110 / 0.05 ( 2) SS BOND : angle 4.40797 / 2.40 ( 4) hydrogen bonds : bond 0.02839 / 1.90 ( 336) hydrogen bonds : angle 4.02303 / 2.61 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.149 Fit side-chains REVERT: A 126 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7149 (mtm-85) REVERT: A 174 ARG cc_start: 0.6744 (mtt180) cc_final: 0.5879 (mtp180) REVERT: A 282 ARG cc_start: 0.7234 (mpt90) cc_final: 0.6810 (mtm110) REVERT: A 294 MET cc_start: 0.7238 (ttp) cc_final: 0.6716 (ttt) REVERT: B 65 MET cc_start: 0.7470 (mmt) cc_final: 0.7040 (mmm) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.0813 time to fit residues: 7.5866 Evaluate side-chains 65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 74 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.172316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147137 restraints weight = 7105.792| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.74 r_work: 0.3464 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6732 Z= 0.121 Angle : 0.580 10.799 9151 Z= 0.285 Chirality : 0.042 0.168 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.864 24.119 934 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.37 % Allowed : 15.93 % Favored : 82.70 % 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: -1.24 (0.28), residues: 882 helix: -0.14 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.007 0.001 TYR A 229 PHE 0.021 0.001 PHE B 95 TRP 0.010 0.001 TRP B 291 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 6730) covalent geometry : angle 0.56734 / 0.28 ( 9147) SS BOND : bond 0.00059 / 0.03 ( 2) SS BOND : angle 5.88347 / 3.19 ( 4) hydrogen bonds : bond 0.02895 / 1.95 ( 336) hydrogen bonds : angle 4.01827 / 2.60 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.154 Fit side-chains REVERT: A 126 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7124 (mtm-85) REVERT: A 174 ARG cc_start: 0.6759 (mtt180) cc_final: 0.5965 (mtp180) REVERT: A 282 ARG cc_start: 0.7303 (mpt90) cc_final: 0.6845 (mtm110) REVERT: A 294 MET cc_start: 0.7243 (ttp) cc_final: 0.6724 (ttt) REVERT: B 65 MET cc_start: 0.7497 (mmt) cc_final: 0.7079 (mmm) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.0812 time to fit residues: 7.6546 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139626 restraints weight = 7275.534| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.87 r_work: 0.3472 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6732 Z= 0.124 Angle : 0.576 8.787 9151 Z= 0.284 Chirality : 0.042 0.165 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.868 25.086 934 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.21 % Allowed : 16.39 % Favored : 82.40 % 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: -1.13 (0.28), residues: 882 helix: -0.05 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.006 0.001 TYR A 229 PHE 0.022 0.001 PHE B 95 TRP 0.010 0.001 TRP B 291 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 6730) covalent geometry : angle 0.56572 / 0.28 ( 9147) SS BOND : bond 0.00085 / 0.04 ( 2) SS BOND : angle 5.10381 / 2.77 ( 4) hydrogen bonds : bond 0.02891 / 1.95 ( 336) hydrogen bonds : angle 4.01621 / 2.60 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7165 (mtm-85) REVERT: A 147 ARG cc_start: 0.7951 (ptt-90) cc_final: 0.7525 (ptt-90) REVERT: A 174 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6010 (mtp180) REVERT: A 282 ARG cc_start: 0.7373 (mpt90) cc_final: 0.6875 (mtm110) REVERT: A 294 MET cc_start: 0.7246 (ttp) cc_final: 0.6728 (ttt) REVERT: B 65 MET cc_start: 0.7479 (mmt) cc_final: 0.7062 (mmm) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.0837 time to fit residues: 7.8823 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136834 restraints weight = 7227.037| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.91 r_work: 0.3500 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6732 Z= 0.116 Angle : 0.560 8.463 9151 Z= 0.277 Chirality : 0.042 0.158 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.819 25.375 934 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.91 % Allowed : 16.54 % Favored : 82.55 % 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: -0.97 (0.28), residues: 882 helix: 0.09 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.47 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.007 0.001 TYR A 229 PHE 0.022 0.001 PHE B 95 TRP 0.010 0.001 TRP B 291 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6730) covalent geometry : angle 0.55322 / 0.27 ( 9147) SS BOND : bond 0.00094 / 0.05 ( 2) SS BOND : angle 4.10375 / 2.24 ( 4) hydrogen bonds : bond 0.02818 / 1.89 ( 336) hydrogen bonds : angle 3.97519 / 2.56 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7148 (mtm-85) REVERT: A 147 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7452 (ptt-90) REVERT: A 174 ARG cc_start: 0.6768 (mtt180) cc_final: 0.5870 (mtp180) REVERT: A 282 ARG cc_start: 0.7344 (mpt90) cc_final: 0.6848 (mtm110) REVERT: A 294 MET cc_start: 0.7241 (ttp) cc_final: 0.6716 (ttt) REVERT: B 65 MET cc_start: 0.7437 (mmt) cc_final: 0.7030 (mmm) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.0758 time to fit residues: 7.0260 Evaluate side-chains 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 13 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139532 restraints weight = 7149.367| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.89 r_work: 0.3494 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6732 Z= 0.107 Angle : 0.552 8.569 9151 Z= 0.273 Chirality : 0.042 0.148 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.739 24.697 934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.06 % Allowed : 16.69 % Favored : 82.25 % 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: -0.79 (0.29), residues: 882 helix: 0.27 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.005 0.001 TYR A 229 PHE 0.021 0.001 PHE B 95 TRP 0.009 0.001 TRP B 291 HIS 0.002 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6730) covalent geometry : angle 0.54696 / 0.27 ( 9147) SS BOND : bond 0.00090 / 0.05 ( 2) SS BOND : angle 3.47927 / 1.90 ( 4) hydrogen bonds : bond 0.02710 / 1.82 ( 336) hydrogen bonds : angle 3.90872 / 2.51 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.99 seconds wall clock time: 29 minutes 21.12 seconds (1761.12 seconds total)