Starting phenix.real_space_refine on Sun Apr 27 20:05:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_29885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_29885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_29885.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_29885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga3_29885/04_2025/8ga3_29885.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.71 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: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.54 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: 1.42 Time building geometry restraints manager: 1.92 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 461 or resid 501 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: 1.420 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.110 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.001 TRP B 291 HIS 0.007 0.002 HIS B 284 PHE 0.009 0.001 PHE A 219 TYR 0.019 0.002 TYR A 210 ARG 0.003 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.31015 ( 336) hydrogen bonds : angle 12.35050 ( 999) SS BOND : bond 0.00150 ( 2) SS BOND : angle 3.19013 ( 4) covalent geometry : bond 0.00450 ( 6730) covalent geometry : angle 0.88834 ( 9147) *********************** 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 : 0.735 Fit side-chains REVERT: A 54 ASP cc_start: 0.8663 (m-30) cc_final: 0.8459 (m-30) REVERT: A 174 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6544 (mtp180) REVERT: B 290 LYS cc_start: 0.7985 (mttp) cc_final: 0.7784 (mtmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2323 time to fit residues: 29.3201 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 : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.0000 chunk 44 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3860 r_free = 0.3860 target = 0.165362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138181 restraints weight = 7276.255| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.88 r_work: 0.3413 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6732 Z= 0.130 Angle : 0.616 6.360 9151 Z= 0.313 Chirality : 0.042 0.149 1084 Planarity : 0.006 0.046 1147 Dihedral : 5.457 24.884 934 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.37 % Allowed : 11.08 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.22), residues: 882 helix: -2.81 (0.16), residues: 630 sheet: None (None), residues: 0 loop : -2.91 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.007 0.001 PHE A 219 TYR 0.009 0.001 TYR A 210 ARG 0.003 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 336) hydrogen bonds : angle 5.60938 ( 999) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.95309 ( 4) covalent geometry : bond 0.00285 ( 6730) covalent geometry : angle 0.61478 ( 9147) *********************** 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 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.676 Fit side-chains REVERT: A 126 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.6976 (mtt90) REVERT: A 147 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.7451 (ptt-90) REVERT: A 174 ARG cc_start: 0.6773 (mtt180) cc_final: 0.5937 (mtp180) REVERT: A 186 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 294 MET cc_start: 0.7127 (ttp) cc_final: 0.6598 (ttt) outliers start: 9 outliers final: 2 residues processed: 79 average time/residue: 0.1833 time to fit residues: 19.8120 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 : 0.644 ------------------------------------------------------------------------------- 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 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 47 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3927 r_free = 0.3927 target = 0.170414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.145026 restraints weight = 7231.736| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.77 r_work: 0.3393 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6732 Z= 0.123 Angle : 0.585 7.325 9151 Z= 0.290 Chirality : 0.042 0.129 1084 Planarity : 0.004 0.044 1147 Dihedral : 5.169 24.423 934 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.82 % Allowed : 12.59 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.26), residues: 882 helix: -1.69 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.71 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.007 0.001 PHE A 379 TYR 0.008 0.001 TYR B 94 ARG 0.002 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 336) hydrogen bonds : angle 4.69288 ( 999) SS BOND : bond 0.00688 ( 2) SS BOND : angle 2.57093 ( 4) covalent geometry : bond 0.00282 ( 6730) covalent geometry : angle 0.58216 ( 9147) *********************** 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: 12 poor density : 68 time to evaluate : 0.622 Fit side-chains REVERT: A 126 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.6926 (mtt90) REVERT: A 174 ARG cc_start: 0.6759 (mtt180) cc_final: 0.5910 (mtp180) REVERT: A 294 MET cc_start: 0.7236 (ttp) cc_final: 0.6752 (ttt) REVERT: B 91 MET cc_start: 0.7629 (mtp) cc_final: 0.7421 (mtt) REVERT: B 198 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (mp) outliers start: 12 outliers final: 4 residues processed: 77 average time/residue: 0.1824 time to fit residues: 19.0583 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3917 r_free = 0.3917 target = 0.169591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144166 restraints weight = 7205.380| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.78 r_work: 0.3380 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2020 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= 0.130 Angle : 0.577 7.808 9151 Z= 0.285 Chirality : 0.042 0.153 1084 Planarity : 0.004 0.046 1147 Dihedral : 5.086 24.047 934 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.82 % Allowed : 14.42 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.27), residues: 882 helix: -1.14 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 291 HIS 0.003 0.001 HIS B 284 PHE 0.006 0.001 PHE B 307 TYR 0.007 0.001 TYR B 94 ARG 0.005 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 336) hydrogen bonds : angle 4.43782 ( 999) SS BOND : bond 0.00159 ( 2) SS BOND : angle 2.49902 ( 4) covalent geometry : bond 0.00307 ( 6730) covalent geometry : angle 0.57466 ( 9147) *********************** 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 77 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.678 Fit side-chains REVERT: A 126 ARG cc_start: 0.7763 (mtt-85) cc_final: 0.6966 (mtt90) REVERT: A 174 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5905 (mtp180) REVERT: A 294 MET cc_start: 0.7263 (ttp) cc_final: 0.6724 (ttp) REVERT: B 65 MET cc_start: 0.7507 (mmt) cc_final: 0.7054 (mmm) REVERT: B 91 MET cc_start: 0.7631 (mtp) cc_final: 0.7420 (mtt) REVERT: B 198 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7392 (mp) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.1777 time to fit residues: 18.6768 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 : 0.693 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3867 r_free = 0.3867 target = 0.166356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139134 restraints weight = 7251.737| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.87 r_work: 0.3498 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6732 Z= 0.112 Angle : 0.596 14.181 9151 Z= 0.292 Chirality : 0.042 0.149 1084 Planarity : 0.004 0.045 1147 Dihedral : 5.043 27.306 934 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.97 % Allowed : 14.72 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.28), residues: 882 helix: -0.80 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.63 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.019 0.001 PHE B 95 TYR 0.009 0.001 TYR A 229 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 336) hydrogen bonds : angle 4.26403 ( 999) SS BOND : bond 0.00690 ( 2) SS BOND : angle 5.44286 ( 4) covalent geometry : bond 0.00263 ( 6730) covalent geometry : angle 0.58500 ( 9147) *********************** 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 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.743 Fit side-chains REVERT: A 126 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.6925 (mtt90) REVERT: A 174 ARG cc_start: 0.6753 (mtt180) cc_final: 0.5876 (mtp180) REVERT: A 294 MET cc_start: 0.7250 (ttp) cc_final: 0.6756 (ttt) REVERT: B 65 MET cc_start: 0.7464 (mmt) cc_final: 0.7005 (mmm) REVERT: B 198 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7341 (mp) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.2028 time to fit residues: 20.9380 Evaluate side-chains 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain B residue 283 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 0.0000 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138608 restraints weight = 7212.273| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.87 r_work: 0.3489 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6732 Z= 0.114 Angle : 0.576 11.656 9151 Z= 0.285 Chirality : 0.041 0.142 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.916 24.955 934 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.52 % Allowed : 15.48 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 882 helix: -0.55 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.61 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.020 0.001 PHE B 95 TYR 0.008 0.001 TYR A 229 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 336) hydrogen bonds : angle 4.11389 ( 999) SS BOND : bond 0.00192 ( 2) SS BOND : angle 5.13699 ( 4) covalent geometry : bond 0.00270 ( 6730) covalent geometry : angle 0.56610 ( 9147) *********************** 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 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.676 Fit side-chains REVERT: A 126 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7093 (mtm-85) REVERT: A 174 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5902 (mtp180) REVERT: A 294 MET cc_start: 0.7223 (ttp) cc_final: 0.6717 (ttt) REVERT: B 65 MET cc_start: 0.7454 (mmt) cc_final: 0.7019 (mmm) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1913 time to fit residues: 18.1307 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 : 0.663 ------------------------------------------------------------------------------- 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 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 73 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 26 optimal weight: 0.0570 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143445 restraints weight = 7147.770| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.88 r_work: 0.3525 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6732 Z= 0.096 Angle : 0.540 9.126 9151 Z= 0.267 Chirality : 0.041 0.166 1084 Planarity : 0.004 0.044 1147 Dihedral : 4.752 24.003 934 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.82 % Allowed : 15.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.28), residues: 882 helix: -0.14 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.63 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.002 0.001 HIS A 383 PHE 0.020 0.001 PHE B 95 TYR 0.004 0.001 TYR A 94 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 336) hydrogen bonds : angle 3.94150 ( 999) SS BOND : bond 0.00104 ( 2) SS BOND : angle 3.44334 ( 4) covalent geometry : bond 0.00213 ( 6730) covalent geometry : angle 0.53542 ( 9147) *********************** 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 79 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.711 Fit side-chains REVERT: A 126 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7084 (mtm-85) REVERT: A 174 ARG cc_start: 0.6746 (mtt180) cc_final: 0.5882 (mtp180) REVERT: A 294 MET cc_start: 0.7233 (ttp) cc_final: 0.6723 (ttt) REVERT: B 65 MET cc_start: 0.7444 (mmt) cc_final: 0.7012 (mmm) outliers start: 12 outliers final: 5 residues processed: 77 average time/residue: 0.2068 time to fit residues: 21.3479 Evaluate side-chains 69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138032 restraints weight = 7240.417| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.86 r_work: 0.3464 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6732 Z= 0.145 Angle : 0.619 11.522 9151 Z= 0.299 Chirality : 0.043 0.183 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.922 24.667 934 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.52 % Allowed : 16.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 882 helix: -0.17 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.52 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.022 0.001 PHE B 95 TYR 0.007 0.001 TYR A 255 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 336) hydrogen bonds : angle 4.11255 ( 999) SS BOND : bond 0.00483 ( 2) SS BOND : angle 5.29238 ( 4) covalent geometry : bond 0.00356 ( 6730) covalent geometry : angle 0.60966 ( 9147) *********************** 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 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.702 Fit side-chains REVERT: A 174 ARG cc_start: 0.6937 (mtt180) cc_final: 0.6024 (mtp180) REVERT: A 282 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6697 (mtm110) REVERT: A 294 MET cc_start: 0.7255 (ttp) cc_final: 0.6729 (ttt) REVERT: B 65 MET cc_start: 0.7466 (mmt) cc_final: 0.7033 (mmm) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.1989 time to fit residues: 19.3327 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 : 0.669 ------------------------------------------------------------------------------- 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 418 ASN 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 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.147005 restraints weight = 7098.014| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.82 r_work: 0.3471 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6732 Z= 0.116 Angle : 0.584 10.216 9151 Z= 0.284 Chirality : 0.042 0.158 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.856 25.447 934 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.06 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 882 helix: 0.06 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.021 0.001 PHE B 95 TYR 0.005 0.001 TYR A 229 ARG 0.009 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 336) hydrogen bonds : angle 4.00585 ( 999) SS BOND : bond 0.00154 ( 2) SS BOND : angle 4.47736 ( 4) covalent geometry : bond 0.00276 ( 6730) covalent geometry : angle 0.57624 ( 9147) *********************** 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 72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7084 (mtm-85) REVERT: A 174 ARG cc_start: 0.6866 (mtt180) cc_final: 0.5948 (mtp180) REVERT: A 282 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6538 (mtm110) REVERT: A 294 MET cc_start: 0.7226 (ttp) cc_final: 0.6693 (ttt) REVERT: B 65 MET cc_start: 0.7447 (mmt) cc_final: 0.7021 (mmm) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.2227 time to fit residues: 21.1983 Evaluate side-chains 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137445 restraints weight = 7316.063| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.90 r_work: 0.3460 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6732 Z= 0.125 Angle : 0.589 10.147 9151 Z= 0.285 Chirality : 0.042 0.162 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.876 26.130 934 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.91 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.28), residues: 882 helix: 0.11 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -2.55 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.003 0.000 HIS A 383 PHE 0.022 0.001 PHE B 95 TYR 0.006 0.001 TYR A 255 ARG 0.010 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 336) hydrogen bonds : angle 4.01033 ( 999) SS BOND : bond 0.00030 ( 2) SS BOND : angle 3.96847 ( 4) covalent geometry : bond 0.00301 ( 6730) covalent geometry : angle 0.58301 ( 9147) ********************** 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 68 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 174 ARG cc_start: 0.6869 (mtt180) cc_final: 0.5939 (mtp180) REVERT: A 282 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6723 (mtm110) REVERT: A 294 MET cc_start: 0.7229 (ttp) cc_final: 0.6697 (ttt) REVERT: B 65 MET cc_start: 0.7465 (mmt) cc_final: 0.7045 (mmm) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.2003 time to fit residues: 18.3627 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 : 0.728 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147636 restraints weight = 7053.163| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.81 r_work: 0.3475 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6732 Z= 0.110 Angle : 0.570 10.067 9151 Z= 0.277 Chirality : 0.042 0.152 1084 Planarity : 0.004 0.046 1147 Dihedral : 4.786 24.793 934 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.91 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.29), residues: 882 helix: 0.27 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -2.52 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.002 0.000 HIS A 383 PHE 0.021 0.001 PHE B 95 TYR 0.004 0.001 TYR A 229 ARG 0.009 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 336) hydrogen bonds : angle 3.93732 ( 999) SS BOND : bond 0.00098 ( 2) SS BOND : angle 3.37664 ( 4) covalent geometry : bond 0.00256 ( 6730) covalent geometry : angle 0.56621 ( 9147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.57 seconds wall clock time: 73 minutes 32.12 seconds (4412.12 seconds total)