Starting phenix.real_space_refine on Wed Mar 4 00:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2026/6xwr_10636.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6309 2.51 5 N 1551 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9564 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Chain: "B" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3227 Chain: "C" Number of atoms: 3188 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 8 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 8 " occ=0.50 residue: pdb=" N ALYS B 86 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 86 " occ=0.50 residue: pdb=" N AHIS C 334 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 334 " occ=0.50 Time building chain proxies: 3.95, per 1000 atoms: 0.41 Number of scatterers: 9564 At special positions: 0 Unit cell: (82.984, 102.212, 116.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1656 8.00 N 1551 7.00 C 6309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 695.0 milliseconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.541A pdb=" N TYR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 36 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.907A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 81 through 110 removed outlier: 3.813A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.787A pdb=" N VAL A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 226 through 255 removed outlier: 3.529A pdb=" N ALA A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.615A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.109A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.627A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.507A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 420 removed outlier: 3.813A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 13 through 35 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.740A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.761A pdb=" N ILE B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 4.056A pdb=" N ALYS B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.528A pdb=" N THR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.762A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 222 removed outlier: 3.739A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.837A pdb=" N PHE B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 removed outlier: 3.702A pdb=" N VAL B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.672A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.891A pdb=" N GLU B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.842A pdb=" N VAL B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.530A pdb=" N SER B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.712A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 removed outlier: 4.290A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 420 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 76 removed outlier: 3.938A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 81 through 108 removed outlier: 3.882A pdb=" N VAL C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 223 Proline residue: C 208 - end of helix removed outlier: 4.156A pdb=" N GLN C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 236 through 255 removed outlier: 4.593A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.742A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.649A pdb=" N GLU C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 313 removed outlier: 5.347A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.937A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 4.229A pdb=" N GLN C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.550A pdb=" N VAL C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.590A pdb=" N ALA C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.771A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 removed outlier: 3.594A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 420 removed outlier: 4.504A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.537A pdb=" N LYS C 427 " --> pdb=" O ASP C 424 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2086 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: 1.49 Time building geometry restraints manager: 1.02 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: 2975 1.34 - 1.46: 1451 1.46 - 1.57: 5223 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9745 Sorted by residual: bond pdb=" CG LEU C 68 " pdb=" CD1 LEU C 68 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" C ILE A 75 " pdb=" N SER A 76 " ideal model delta sigma weight residual 1.332 1.313 0.018 1.21e-02 6.83e+03 2.32e+00 bond pdb=" CB THR C 168 " pdb=" CG2 THR C 168 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB TRP A 20 " pdb=" CG TRP A 20 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.82e+00 bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12695 1.59 - 3.18: 466 3.18 - 4.77: 77 4.77 - 6.36: 25 6.36 - 7.95: 5 Bond angle restraints: 13268 Sorted by residual: angle pdb=" N GLY C 235 " pdb=" CA GLY C 235 " pdb=" C GLY C 235 " ideal model delta sigma weight residual 114.69 109.10 5.59 1.19e+00 7.06e-01 2.21e+01 angle pdb=" C VAL A 246 " pdb=" N ILE A 247 " pdb=" CA ILE A 247 " ideal model delta sigma weight residual 122.97 119.16 3.81 9.80e-01 1.04e+00 1.51e+01 angle pdb=" N ILE B 301 " pdb=" CA ILE B 301 " pdb=" C ILE B 301 " ideal model delta sigma weight residual 111.48 108.67 2.81 9.40e-01 1.13e+00 8.92e+00 angle pdb=" N THR B 378 " pdb=" CA THR B 378 " pdb=" C THR B 378 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.61e+00 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.27e+00 ... (remaining 13263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5287 18.00 - 36.00: 400 36.00 - 53.99: 48 53.99 - 71.99: 6 71.99 - 89.99: 6 Dihedral angle restraints: 5747 sinusoidal: 2132 harmonic: 3615 Sorted by residual: dihedral pdb=" CA LEU B 342 " pdb=" C LEU B 342 " pdb=" N VAL B 343 " pdb=" CA VAL B 343 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU C 59 " pdb=" C LEU C 59 " pdb=" N VAL C 60 " pdb=" CA VAL C 60 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 814 0.031 - 0.062: 585 0.062 - 0.094: 177 0.094 - 0.125: 61 0.125 - 0.156: 13 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA THR B 378 " pdb=" N THR B 378 " pdb=" C THR B 378 " pdb=" CB THR B 378 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB VAL B 105 " pdb=" CA VAL B 105 " pdb=" CG1 VAL B 105 " pdb=" CG2 VAL B 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" C PRO B 47 " pdb=" CB PRO B 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1647 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 64 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A 64 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 64 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 245 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ILE A 245 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 245 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 246 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 381 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 382 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 167 2.68 - 3.23: 10503 3.23 - 3.79: 15341 3.79 - 4.34: 20170 4.34 - 4.90: 33962 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG1 THR C 305 " pdb=" OG1 THR C 413 " model vdw 2.122 3.040 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 287 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 249 " pdb=" OD2 ASP A 315 " model vdw 2.197 3.040 nonbonded pdb=" O THR A 378 " pdb=" OG SER A 381 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR C 249 " pdb=" OD2 ASP C 315 " model vdw 2.224 3.040 ... (remaining 80138 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 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'B' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'C' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) } 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=0.50 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.110 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.008 0.055 9745 Z= 0.344 Angle : 0.754 7.950 13268 Z= 0.406 Chirality : 0.046 0.156 1650 Planarity : 0.005 0.049 1632 Dihedral : 12.807 89.991 3455 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.21), residues: 1281 helix: -1.38 (0.15), residues: 997 sheet: None (None), residues: 0 loop : -2.70 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.016 0.002 TYR A 320 PHE 0.020 0.002 PHE A 302 TRP 0.009 0.001 TRP A 20 HIS 0.002 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 9745) covalent geometry : angle 0.75414 (13268) hydrogen bonds : bond 0.12704 ( 700) hydrogen bonds : angle 6.53243 ( 2086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8686 (mmt) cc_final: 0.8448 (mmm) REVERT: A 393 ILE cc_start: 0.9333 (tp) cc_final: 0.8994 (tp) REVERT: B 259 ASP cc_start: 0.8312 (t0) cc_final: 0.8105 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0872 time to fit residues: 16.3230 Evaluate side-chains 95 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 138 ASN B 321 GLN B 340 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058958 restraints weight = 75273.961| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.41 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9745 Z= 0.141 Angle : 0.614 7.874 13268 Z= 0.310 Chirality : 0.041 0.160 1650 Planarity : 0.005 0.053 1632 Dihedral : 4.340 21.811 1369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.70 % Allowed : 9.75 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1281 helix: -0.09 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -1.97 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 289 TYR 0.013 0.001 TYR B 320 PHE 0.023 0.001 PHE A 302 TRP 0.008 0.001 TRP C 20 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9745) covalent geometry : angle 0.61382 (13268) hydrogen bonds : bond 0.03840 ( 700) hydrogen bonds : angle 4.74953 ( 2086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.9319 (m110) cc_final: 0.9045 (m110) REVERT: A 219 MET cc_start: 0.9024 (mmm) cc_final: 0.8809 (mmm) REVERT: A 313 ASN cc_start: 0.8942 (t0) cc_final: 0.8646 (t0) REVERT: A 321 GLN cc_start: 0.8128 (mt0) cc_final: 0.7890 (mt0) REVERT: A 365 MET cc_start: 0.9337 (ttm) cc_final: 0.9005 (ttt) REVERT: A 393 ILE cc_start: 0.9108 (tp) cc_final: 0.8693 (tp) REVERT: B 46 LYS cc_start: 0.8703 (tptt) cc_final: 0.8440 (tptp) REVERT: B 50 ASP cc_start: 0.8594 (m-30) cc_final: 0.8213 (m-30) REVERT: B 259 ASP cc_start: 0.8638 (t0) cc_final: 0.8130 (t0) REVERT: B 295 MET cc_start: 0.8445 (mmm) cc_final: 0.8146 (mmt) REVERT: B 424 ASP cc_start: 0.8801 (t0) cc_final: 0.7817 (p0) REVERT: C 340 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: C 403 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7160 (tpp) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.0757 time to fit residues: 14.6841 Evaluate side-chains 116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 0.0170 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.080364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060071 restraints weight = 65453.488| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 5.14 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9745 Z= 0.128 Angle : 0.591 7.684 13268 Z= 0.297 Chirality : 0.040 0.171 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.118 23.654 1369 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.90 % Allowed : 12.54 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1281 helix: 0.45 (0.17), residues: 1039 sheet: None (None), residues: 0 loop : -1.68 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.011 0.001 TYR B 320 PHE 0.020 0.001 PHE A 302 TRP 0.008 0.001 TRP B 16 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9745) covalent geometry : angle 0.59113 (13268) hydrogen bonds : bond 0.03537 ( 700) hydrogen bonds : angle 4.49303 ( 2086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.9266 (ttm) cc_final: 0.8719 (ttt) REVERT: A 393 ILE cc_start: 0.9052 (tp) cc_final: 0.8644 (tp) REVERT: B 46 LYS cc_start: 0.8725 (tptt) cc_final: 0.8416 (tptp) REVERT: B 50 ASP cc_start: 0.8623 (m-30) cc_final: 0.8209 (m-30) REVERT: B 150 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9122 (mtmm) REVERT: B 238 TYR cc_start: 0.8857 (m-80) cc_final: 0.8649 (m-80) REVERT: B 259 ASP cc_start: 0.8570 (t0) cc_final: 0.8202 (t0) REVERT: C 340 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: C 403 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7121 (tpp) outliers start: 8 outliers final: 3 residues processed: 128 average time/residue: 0.0787 time to fit residues: 15.1283 Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 138 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058973 restraints weight = 70039.079| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 5.15 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9745 Z= 0.161 Angle : 0.601 7.615 13268 Z= 0.301 Chirality : 0.041 0.173 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.108 26.960 1369 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.90 % Allowed : 13.53 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1281 helix: 0.73 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.48 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 401 TYR 0.014 0.001 TYR B 320 PHE 0.026 0.001 PHE B 242 TRP 0.006 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9745) covalent geometry : angle 0.60098 (13268) hydrogen bonds : bond 0.03634 ( 700) hydrogen bonds : angle 4.45634 ( 2086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.9140 (ttm) cc_final: 0.8786 (ttm) REVERT: A 393 ILE cc_start: 0.9171 (tp) cc_final: 0.8756 (tp) REVERT: B 46 LYS cc_start: 0.8761 (tptt) cc_final: 0.8434 (tptp) REVERT: B 150 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9086 (mtmm) REVERT: B 259 ASP cc_start: 0.8631 (t0) cc_final: 0.8270 (t0) REVERT: C 314 MET cc_start: 0.8542 (mtp) cc_final: 0.8117 (mtm) REVERT: C 340 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: C 403 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6980 (tpp) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.0730 time to fit residues: 12.4687 Evaluate side-chains 109 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060445 restraints weight = 87278.002| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.79 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9745 Z= 0.122 Angle : 0.579 7.683 13268 Z= 0.289 Chirality : 0.040 0.146 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.044 27.128 1369 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.80 % Allowed : 15.32 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1281 helix: 0.91 (0.17), residues: 1034 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.012 0.001 TYR B 320 PHE 0.016 0.001 PHE A 302 TRP 0.006 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9745) covalent geometry : angle 0.57863 (13268) hydrogen bonds : bond 0.03441 ( 700) hydrogen bonds : angle 4.33773 ( 2086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8976 (ttm) cc_final: 0.8572 (ttm) REVERT: A 393 ILE cc_start: 0.9062 (tp) cc_final: 0.8649 (tp) REVERT: B 46 LYS cc_start: 0.8708 (tptt) cc_final: 0.8430 (tptp) REVERT: B 50 ASP cc_start: 0.8590 (m-30) cc_final: 0.8192 (m-30) REVERT: B 134 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8881 (tp40) REVERT: B 138 ASN cc_start: 0.9325 (m-40) cc_final: 0.9077 (m110) REVERT: B 150 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8991 (mtmm) REVERT: B 238 TYR cc_start: 0.8832 (m-80) cc_final: 0.8614 (m-80) REVERT: B 259 ASP cc_start: 0.8633 (t0) cc_final: 0.8277 (t0) REVERT: C 314 MET cc_start: 0.8606 (mtp) cc_final: 0.8102 (mtm) REVERT: C 340 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: C 403 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7065 (tpp) outliers start: 7 outliers final: 2 residues processed: 116 average time/residue: 0.0804 time to fit residues: 14.0300 Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN ** B 334 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 = 0.3371 r_free = 0.3371 target = 0.080431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059678 restraints weight = 92097.761| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.95 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.133 Angle : 0.605 12.311 13268 Z= 0.297 Chirality : 0.040 0.141 1650 Planarity : 0.004 0.052 1632 Dihedral : 4.026 27.533 1369 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.90 % Allowed : 16.22 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1281 helix: 1.01 (0.17), residues: 1034 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 289 TYR 0.012 0.001 TYR B 320 PHE 0.019 0.001 PHE B 242 TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9745) covalent geometry : angle 0.60543 (13268) hydrogen bonds : bond 0.03459 ( 700) hydrogen bonds : angle 4.34693 ( 2086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.8962 (ttm) cc_final: 0.8616 (ttt) REVERT: A 393 ILE cc_start: 0.9055 (tp) cc_final: 0.8628 (tp) REVERT: B 46 LYS cc_start: 0.8745 (tptt) cc_final: 0.8450 (tptp) REVERT: B 50 ASP cc_start: 0.8628 (m-30) cc_final: 0.8210 (m-30) REVERT: B 238 TYR cc_start: 0.8846 (m-80) cc_final: 0.8614 (m-80) REVERT: B 259 ASP cc_start: 0.8646 (t0) cc_final: 0.8293 (t0) REVERT: B 396 ILE cc_start: 0.8651 (mt) cc_final: 0.8392 (mt) REVERT: C 314 MET cc_start: 0.8636 (mtp) cc_final: 0.8415 (mtt) REVERT: C 340 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: C 403 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7068 (tpp) outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.0701 time to fit residues: 12.4800 Evaluate side-chains 109 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 chunk 26 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 59 optimal weight: 0.0040 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062317 restraints weight = 88526.211| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.92 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9745 Z= 0.113 Angle : 0.585 8.686 13268 Z= 0.288 Chirality : 0.040 0.196 1650 Planarity : 0.004 0.051 1632 Dihedral : 3.964 28.293 1369 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.80 % Allowed : 17.31 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1281 helix: 1.11 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.010 0.001 TYR B 320 PHE 0.016 0.001 PHE B 302 TRP 0.004 0.001 TRP C 20 HIS 0.004 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9745) covalent geometry : angle 0.58535 (13268) hydrogen bonds : bond 0.03248 ( 700) hydrogen bonds : angle 4.27832 ( 2086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8967 (ttm) cc_final: 0.8613 (ttm) REVERT: B 46 LYS cc_start: 0.8669 (tptt) cc_final: 0.8349 (tptp) REVERT: B 150 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8929 (mtmm) REVERT: B 238 TYR cc_start: 0.8804 (m-80) cc_final: 0.8577 (m-80) REVERT: B 396 ILE cc_start: 0.8683 (mt) cc_final: 0.8411 (mt) REVERT: C 314 MET cc_start: 0.8637 (mtp) cc_final: 0.8371 (mtp) REVERT: C 340 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 7 outliers final: 3 residues processed: 137 average time/residue: 0.0782 time to fit residues: 16.0732 Evaluate side-chains 129 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 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 = 0.3419 r_free = 0.3419 target = 0.083098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062586 restraints weight = 80106.987| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 5.65 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.116 Angle : 0.607 11.141 13268 Z= 0.293 Chirality : 0.041 0.316 1650 Planarity : 0.004 0.050 1632 Dihedral : 3.959 27.615 1369 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.60 % Allowed : 17.91 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1281 helix: 1.16 (0.17), residues: 1033 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.013 0.001 TYR B 320 PHE 0.018 0.001 PHE B 242 TRP 0.004 0.000 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9745) covalent geometry : angle 0.60667 (13268) hydrogen bonds : bond 0.03259 ( 700) hydrogen bonds : angle 4.29058 ( 2086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.9002 (ttm) cc_final: 0.8560 (ttt) REVERT: B 97 MET cc_start: 0.9194 (tpp) cc_final: 0.8927 (tpp) REVERT: C 314 MET cc_start: 0.8625 (mtp) cc_final: 0.8349 (mtp) REVERT: C 340 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: C 403 MET cc_start: 0.7438 (tpp) cc_final: 0.7215 (tpp) outliers start: 5 outliers final: 3 residues processed: 129 average time/residue: 0.0703 time to fit residues: 14.2808 Evaluate side-chains 121 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 340 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.079653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059481 restraints weight = 65181.859| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 5.01 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9745 Z= 0.175 Angle : 0.644 11.651 13268 Z= 0.315 Chirality : 0.043 0.380 1650 Planarity : 0.004 0.050 1632 Dihedral : 4.032 27.498 1369 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.90 % Allowed : 17.91 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1281 helix: 1.17 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.014 0.001 TYR A 197 PHE 0.017 0.001 PHE A 302 TRP 0.005 0.001 TRP A 428 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9745) covalent geometry : angle 0.64430 (13268) hydrogen bonds : bond 0.03608 ( 700) hydrogen bonds : angle 4.41682 ( 2086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9035 (tp40) cc_final: 0.8581 (tp-100) REVERT: A 365 MET cc_start: 0.9080 (ttm) cc_final: 0.8698 (ttm) REVERT: B 243 LEU cc_start: 0.8851 (mt) cc_final: 0.8586 (tp) REVERT: B 259 ASP cc_start: 0.8661 (t0) cc_final: 0.8289 (t0) REVERT: C 340 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: C 403 MET cc_start: 0.7464 (tpp) cc_final: 0.7207 (tpp) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.0694 time to fit residues: 12.7395 Evaluate side-chains 113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 340 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** B 334 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 = 0.3383 r_free = 0.3383 target = 0.081127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060539 restraints weight = 80212.488| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 5.60 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9745 Z= 0.131 Angle : 0.624 12.339 13268 Z= 0.304 Chirality : 0.042 0.387 1650 Planarity : 0.004 0.050 1632 Dihedral : 4.040 27.410 1369 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.70 % Allowed : 18.11 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1281 helix: 1.23 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 289 TYR 0.014 0.001 TYR A 197 PHE 0.019 0.001 PHE B 242 TRP 0.004 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9745) covalent geometry : angle 0.62373 (13268) hydrogen bonds : bond 0.03441 ( 700) hydrogen bonds : angle 4.35947 ( 2086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.9007 (tp40) cc_final: 0.8553 (tp-100) REVERT: A 365 MET cc_start: 0.9041 (ttm) cc_final: 0.8823 (ttm) REVERT: B 259 ASP cc_start: 0.8671 (t0) cc_final: 0.8298 (t0) REVERT: C 314 MET cc_start: 0.8717 (mtp) cc_final: 0.8237 (mtm) REVERT: C 340 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: C 403 MET cc_start: 0.7456 (tpp) cc_final: 0.7235 (tpp) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.0695 time to fit residues: 12.8532 Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 340 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 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 = 0.3392 r_free = 0.3392 target = 0.081613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061140 restraints weight = 78421.780| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 5.53 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9745 Z= 0.126 Angle : 0.619 13.155 13268 Z= 0.301 Chirality : 0.042 0.403 1650 Planarity : 0.004 0.050 1632 Dihedral : 3.984 27.248 1369 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.60 % Allowed : 18.01 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1281 helix: 1.26 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.013 0.001 TYR A 197 PHE 0.016 0.001 PHE B 302 TRP 0.004 0.000 TRP C 20 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9745) covalent geometry : angle 0.61864 (13268) hydrogen bonds : bond 0.03400 ( 700) hydrogen bonds : angle 4.33584 ( 2086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.26 seconds wall clock time: 32 minutes 20.42 seconds (1940.42 seconds total)