Starting phenix.real_space_refine on Tue Feb 11 18:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga3_29885/02_2025/8ga3_29885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga3_29885/02_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_29885/02_2025/8ga3_29885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga3_29885/02_2025/8ga3_29885.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga3_29885/02_2025/8ga3_29885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga3_29885/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.66, 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: 1.60 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: 0.68 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: 1.70 Time building geometry restraints manager: 1.88 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: 0.880 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.230 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- 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 6730 Z= 0.307 Angle : 0.888 9.996 9147 Z= 0.471 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 *********************** 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 : 0.712 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: 0.2213 time to fit residues: 27.9061 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 : 0.647 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138183 restraints weight = 7276.243| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.87 r_work: 0.3414 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 6730 Z= 0.191 Angle : 0.615 6.360 9147 Z= 0.312 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 *********************** 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 : 0.697 Fit side-chains REVERT: A 126 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.6977 (mtt90) REVERT: A 147 ARG cc_start: 0.7833 (ptt-90) cc_final: 0.7452 (ptt-90) REVERT: A 174 ARG cc_start: 0.6766 (mtt180) cc_final: 0.5930 (mtp180) REVERT: A 186 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8226 (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: 0.1915 time to fit residues: 20.5698 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 : 0.721 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.170446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144247 restraints weight = 7243.757| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.82 r_work: 0.3404 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6730 Z= 0.172 Angle : 0.573 7.507 9147 Z= 0.284 Chirality : 0.041 0.128 1084 Planarity : 0.004 0.042 1147 Dihedral : 5.137 24.192 934 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.67 % Allowed : 12.59 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.25), residues: 882 helix: -1.70 (0.19), residues: 638 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 *********************** 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 79 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.646 Fit side-chains REVERT: A 126 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7015 (mtt90) REVERT: A 174 ARG cc_start: 0.6764 (mtt180) cc_final: 0.5925 (mtp180) REVERT: A 294 MET cc_start: 0.7259 (ttp) cc_final: 0.6786 (ttt) REVERT: B 198 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7439 (mp) outliers start: 11 outliers final: 4 residues processed: 76 average time/residue: 0.2078 time to fit residues: 21.1627 Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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: 0.4980 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.0030 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.171313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146055 restraints weight = 7173.686| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.77 r_work: 0.3402 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6730 Z= 0.183 Angle : 0.564 8.146 9147 Z= 0.278 Chirality : 0.042 0.150 1084 Planarity : 0.004 0.044 1147 Dihedral : 5.003 23.767 934 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.97 % Allowed : 13.96 % Favored : 84.07 % 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: -2.44 (0.27), residues: 882 helix: -1.09 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.70 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.006 0.001 PHE A 379 TYR 0.007 0.001 TYR A 382 ARG 0.005 0.000 ARG A 147 *********************** 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 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.624 Fit side-chains REVERT: A 126 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7145 (mtm-85) REVERT: A 174 ARG cc_start: 0.6764 (mtt180) cc_final: 0.5907 (mtp180) REVERT: A 294 MET cc_start: 0.7253 (ttp) cc_final: 0.6714 (ttp) REVERT: B 65 MET cc_start: 0.7508 (mmt) cc_final: 0.7041 (mmm) REVERT: B 198 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7379 (mp) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 0.1869 time to fit residues: 20.0158 Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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: 0.0770 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.164527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137101 restraints weight = 7295.457| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.85 r_work: 0.3477 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6730 Z= 0.190 Angle : 0.588 13.740 9147 Z= 0.289 Chirality : 0.042 0.156 1084 Planarity : 0.004 0.045 1147 Dihedral : 5.041 27.756 934 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.52 % Allowed : 15.17 % 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: -2.09 (0.27), residues: 882 helix: -0.81 (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 0.011 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 *********************** 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 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.658 Fit side-chains REVERT: A 126 ARG cc_start: 0.7763 (mtt-85) cc_final: 0.7115 (mtm-85) REVERT: A 174 ARG cc_start: 0.6774 (mtt180) cc_final: 0.5885 (mtp180) REVERT: A 294 MET cc_start: 0.7268 (ttp) cc_final: 0.6746 (ttp) REVERT: B 65 MET cc_start: 0.7457 (mmt) cc_final: 0.7011 (mmm) REVERT: B 198 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7340 (mp) REVERT: B 233 ASN cc_start: 0.7854 (m110) cc_final: 0.7407 (m110) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.1911 time to fit residues: 19.1399 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 : 0.723 ------------------------------------------------------------------------------- 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 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135356 restraints weight = 7266.315| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.88 r_work: 0.3350 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6730 Z= 0.221 Angle : 0.590 11.945 9147 Z= 0.291 Chirality : 0.043 0.167 1084 Planarity : 0.004 0.047 1147 Dihedral : 5.042 25.588 934 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.82 % Allowed : 15.17 % 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: -1.87 (0.28), residues: 882 helix: -0.66 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.021 0.001 PHE B 95 TYR 0.007 0.001 TYR B 255 ARG 0.004 0.000 ARG A 147 *********************** 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 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.683 Fit side-chains REVERT: A 174 ARG cc_start: 0.6791 (mtt180) cc_final: 0.5988 (mtp180) REVERT: B 65 MET cc_start: 0.7504 (mmt) cc_final: 0.7138 (mmm) REVERT: B 198 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7397 (mp) REVERT: B 233 ASN cc_start: 0.7851 (m110) cc_final: 0.7407 (m110) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.1816 time to fit residues: 18.4115 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 : 0.678 ------------------------------------------------------------------------------- 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 41 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 26 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.166748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139477 restraints weight = 7174.552| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.86 r_work: 0.3376 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6730 Z= 0.180 Angle : 0.558 8.482 9147 Z= 0.275 Chirality : 0.042 0.152 1084 Planarity : 0.004 0.047 1147 Dihedral : 4.941 26.425 934 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.12 % Allowed : 15.33 % 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: -1.60 (0.28), residues: 882 helix: -0.42 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.58 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.003 0.000 ARG A 147 *********************** 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 75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.663 Fit side-chains REVERT: A 126 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7100 (mtm-85) REVERT: A 174 ARG cc_start: 0.6803 (mtt180) cc_final: 0.5920 (mtp180) REVERT: A 282 ARG cc_start: 0.7339 (mpt90) cc_final: 0.6878 (mtm110) REVERT: A 294 MET cc_start: 0.7291 (ttp) cc_final: 0.6749 (ttp) REVERT: B 65 MET cc_start: 0.7505 (mmt) cc_final: 0.7066 (mmm) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.2018 time to fit residues: 20.1121 Evaluate side-chains 67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 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 A residue 435 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.162798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135082 restraints weight = 7283.768| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.87 r_work: 0.3423 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6730 Z= 0.237 Angle : 0.604 11.483 9147 Z= 0.294 Chirality : 0.044 0.225 1084 Planarity : 0.004 0.048 1147 Dihedral : 5.059 27.648 934 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.67 % Allowed : 15.48 % 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 (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: -1.54 (0.28), residues: 882 helix: -0.40 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.50 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 210 ARG 0.003 0.000 ARG A 147 *********************** 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: 11 poor density : 62 time to evaluate : 0.662 Fit side-chains REVERT: A 174 ARG cc_start: 0.6821 (mtt180) cc_final: 0.5930 (mtp180) REVERT: A 282 ARG cc_start: 0.7319 (mpt90) cc_final: 0.6853 (mtm110) REVERT: A 294 MET cc_start: 0.7240 (ttp) cc_final: 0.6678 (ttp) REVERT: B 65 MET cc_start: 0.7481 (mmt) cc_final: 0.7044 (mmm) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.1916 time to fit residues: 18.5575 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 : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 139 LEU 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 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: 0.7980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.164388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136242 restraints weight = 7287.081| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.94 r_work: 0.3457 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6730 Z= 0.168 Angle : 0.564 10.096 9147 Z= 0.275 Chirality : 0.042 0.169 1084 Planarity : 0.004 0.047 1147 Dihedral : 4.890 25.567 934 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.52 % Allowed : 15.78 % 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: -1.21 (0.28), residues: 882 helix: -0.11 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.50 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 291 HIS 0.002 0.001 HIS A 383 PHE 0.019 0.001 PHE B 95 TYR 0.005 0.001 TYR A 229 ARG 0.003 0.000 ARG A 147 *********************** 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 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.662 Fit side-chains REVERT: A 126 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7052 (mtm-85) REVERT: A 174 ARG cc_start: 0.6744 (mtt180) cc_final: 0.5853 (mtp180) REVERT: A 282 ARG cc_start: 0.7363 (mpt90) cc_final: 0.6821 (mtm110) REVERT: A 294 MET cc_start: 0.7188 (ttp) cc_final: 0.6680 (ttt) REVERT: B 65 MET cc_start: 0.7449 (mmt) cc_final: 0.7023 (mmm) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.2106 time to fit residues: 19.1481 Evaluate side-chains 66 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137918 restraints weight = 7281.222| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.90 r_work: 0.3453 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6730 Z= 0.188 Angle : 0.567 10.018 9147 Z= 0.277 Chirality : 0.042 0.174 1084 Planarity : 0.004 0.048 1147 Dihedral : 4.873 25.657 934 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.37 % Allowed : 15.78 % 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 (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: -1.08 (0.28), residues: 882 helix: -0.02 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.46 (0.34), 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 0.022 0.001 PHE B 95 TYR 0.005 0.001 TYR A 210 ARG 0.003 0.000 ARG A 147 ********************** 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: 9 poor density : 59 time to evaluate : 0.621 Fit side-chains REVERT: A 126 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7086 (mtm-85) REVERT: A 174 ARG cc_start: 0.6801 (mtt180) cc_final: 0.5913 (mtp180) REVERT: A 282 ARG cc_start: 0.7380 (mpt90) cc_final: 0.6872 (mtm110) REVERT: A 294 MET cc_start: 0.7221 (ttp) cc_final: 0.6706 (ttt) REVERT: B 65 MET cc_start: 0.7463 (mmt) cc_final: 0.7047 (mmm) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.2039 time to fit residues: 18.3121 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.162419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134428 restraints weight = 7287.421| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.90 r_work: 0.3320 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6730 Z= 0.232 Angle : 0.588 9.887 9147 Z= 0.288 Chirality : 0.043 0.185 1084 Planarity : 0.004 0.048 1147 Dihedral : 5.022 27.774 934 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.37 % Allowed : 16.08 % 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: -1.08 (0.28), residues: 882 helix: -0.03 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.40 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.003 0.001 HIS A 383 PHE 0.023 0.001 PHE B 95 TYR 0.007 0.001 TYR A 210 ARG 0.003 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3684.62 seconds wall clock time: 65 minutes 53.06 seconds (3953.06 seconds total)