Starting phenix.real_space_refine on Wed Sep 17 11:38:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9utc_64488/09_2025/9utc_64488.map" } resolution = 3.33 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= 0.000 sd= 0.014 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 59 5.16 5 Cl 3 4.86 5 C 5170 2.51 5 N 1399 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8143 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4036 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 2 Chain: "B" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4084 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'RRJ': 1, 'RRY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.11, per 1000 atoms: 0.26 Number of scatterers: 8143 At special positions: 0 Unit cell: (75.712, 91.728, 115.024, 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 3 17.00 S 59 16.00 O 1512 8.00 N 1399 7.00 C 5170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " 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 Links applied ?1-2 " RRY C 1 " - " RRJ C 2 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 344.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.032A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.810A pdb=" N ASN A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.790A pdb=" N LEU A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.672A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.962A pdb=" N PHE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 384 through 404 removed outlier: 3.767A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.778A pdb=" N ARG B 30 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.639A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 146 through 161 removed outlier: 4.229A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 4.052A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.880A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 389 through 408 Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.837A pdb=" N LEU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 4.145A pdb=" N ILE B 485 " --> pdb=" O ARG B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 98 removed outlier: 8.164A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 239 removed outlier: 7.737A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 271 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 474 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.634A pdb=" N PHE A 429 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.535A pdb=" N ASP A 439 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.509A pdb=" N LYS A 506 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.585A pdb=" N GLN A 536 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.617A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 243 removed outlier: 6.597A pdb=" N GLY B 213 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 212 " --> pdb=" O PHE B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 326 removed outlier: 3.925A pdb=" N GLY B 472 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 458 " --> pdb=" O ASP B 470 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP B 470 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 460 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU B 468 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AB5, first strand: chain 'B' and resid 507 through 511 292 hydrogen bonds defined for protein. 834 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: 1.35 Time building geometry restraints manager: 0.67 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: 2684 1.34 - 1.46: 1992 1.46 - 1.58: 3583 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8343 Sorted by residual: bond pdb=" C5 RRJ C 2 " pdb=" C6 RRJ C 2 " ideal model delta sigma weight residual 1.514 1.549 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C3 RRY C 1 " pdb=" O3 RRY C 1 " ideal model delta sigma weight residual 1.391 1.423 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CA THR B 489 " pdb=" C THR B 489 " ideal model delta sigma weight residual 1.532 1.515 0.018 1.12e-02 7.97e+03 2.44e+00 bond pdb=" N ASP A 26 " pdb=" CA ASP A 26 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 bond pdb=" C4 RRJ C 2 " pdb=" C5 RRJ C 2 " ideal model delta sigma weight residual 1.521 1.552 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 8338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 10918 1.58 - 3.16: 342 3.16 - 4.73: 74 4.73 - 6.31: 9 6.31 - 7.89: 3 Bond angle restraints: 11346 Sorted by residual: angle pdb=" C THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta sigma weight residual 116.34 110.83 5.51 1.40e+00 5.10e-01 1.55e+01 angle pdb=" N ILE A 167 " pdb=" CA ILE A 167 " pdb=" C ILE A 167 " ideal model delta sigma weight residual 113.71 109.98 3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" N ASN A 248 " pdb=" CA ASN A 248 " pdb=" C ASN A 248 " ideal model delta sigma weight residual 112.26 107.42 4.84 1.32e+00 5.74e-01 1.34e+01 angle pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " ideal model delta sigma weight residual 111.30 119.19 -7.89 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CA PRO A 277 " pdb=" N PRO A 277 " pdb=" CD PRO A 277 " ideal model delta sigma weight residual 112.00 107.45 4.55 1.40e+00 5.10e-01 1.06e+01 ... (remaining 11341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4274 17.47 - 34.94: 534 34.94 - 52.41: 176 52.41 - 69.88: 35 69.88 - 87.34: 10 Dihedral angle restraints: 5029 sinusoidal: 2038 harmonic: 2991 Sorted by residual: dihedral pdb=" CB CYS A 520 " pdb=" SG CYS A 520 " pdb=" SG CYS A 535 " pdb=" CB CYS A 535 " ideal model delta sinusoidal sigma weight residual -86.00 1.34 -87.34 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -165.28 79.28 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 551 " pdb=" CB CYS A 551 " ideal model delta sinusoidal sigma weight residual 93.00 34.77 58.23 1 1.00e+01 1.00e-02 4.55e+01 ... (remaining 5026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 813 0.033 - 0.066: 309 0.066 - 0.100: 87 0.100 - 0.133: 41 0.133 - 0.166: 6 Chirality restraints: 1256 Sorted by residual: chirality pdb=" C2 RRY C 1 " pdb=" C1 RRY C 1 " pdb=" C3 RRY C 1 " pdb=" O5 RRY C 1 " both_signs ideal model delta sigma weight residual False 2.66 2.50 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1253 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 276 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 277 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 27 " -0.015 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE A 27 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 27 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 27 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 27 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 27 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 27 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 76 " -0.198 9.50e-02 1.11e+02 8.93e-02 6.03e+00 pdb=" NE ARG A 76 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 76 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 76 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 76 " -0.001 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 28 2.35 - 2.99: 4868 2.99 - 3.62: 12529 3.62 - 4.26: 19184 4.26 - 4.90: 31917 Nonbonded interactions: 68526 Sorted by model distance: nonbonded pdb=" OD1 ASP A 439 " pdb=" CD PRO A 440 " model vdw 1.710 3.440 nonbonded pdb=" OE2 GLU A 302 " pdb=" O2 RRJ C 2 " model vdw 1.938 3.040 nonbonded pdb=" O PRO B 181 " pdb=" OH TYR B 431 " model vdw 2.039 3.040 nonbonded pdb=" O LEU A 521 " pdb=" OG1 THR A 524 " model vdw 2.055 3.040 nonbonded pdb=" O ARG A 172 " pdb=" OE1 GLN A 441 " model vdw 2.066 3.040 ... (remaining 68521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.520 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 0.063 8361 Z= 0.214 Angle : 0.688 10.438 11383 Z= 0.367 Chirality : 0.042 0.166 1256 Planarity : 0.006 0.103 1467 Dihedral : 17.197 84.590 3044 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.33 % Allowed : 30.43 % Favored : 69.23 % 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 aren not related in a simple way. whole: -1.85 (0.25), residues: 1016 helix: 0.13 (0.28), residues: 331 sheet: -1.74 (0.44), residues: 137 loop : -2.00 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 76 TYR 0.017 0.002 TYR B 454 PHE 0.042 0.002 PHE A 27 TRP 0.009 0.001 TRP B 303 HIS 0.007 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8343) covalent geometry : angle 0.68046 (11346) SS BOND : bond 0.00278 ( 17) SS BOND : angle 0.87306 ( 34) hydrogen bonds : bond 0.17891 ( 292) hydrogen bonds : angle 7.23417 ( 834) glycosidic custom : bond 0.03188 ( 1) glycosidic custom : angle 6.19920 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 PHE cc_start: 0.7622 (m-80) cc_final: 0.7291 (m-80) REVERT: B 199 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 304 LEU cc_start: 0.6987 (tp) cc_final: 0.6734 (tp) REVERT: B 535 ASP cc_start: 0.7803 (m-30) cc_final: 0.7557 (m-30) outliers start: 3 outliers final: 2 residues processed: 227 average time/residue: 0.1272 time to fit residues: 36.4168 Evaluate side-chains 215 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 221 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139971 restraints weight = 11427.075| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.34 r_work: 0.3618 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8361 Z= 0.229 Angle : 0.677 8.173 11383 Z= 0.351 Chirality : 0.046 0.233 1256 Planarity : 0.005 0.076 1467 Dihedral : 5.601 62.214 1158 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.13 % Allowed : 24.75 % Favored : 70.12 % 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 aren not related in a simple way. whole: -1.71 (0.26), residues: 1016 helix: 0.13 (0.28), residues: 338 sheet: -1.59 (0.45), residues: 135 loop : -1.87 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 76 TYR 0.017 0.002 TYR B 394 PHE 0.016 0.002 PHE A 27 TRP 0.015 0.002 TRP B 303 HIS 0.013 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8343) covalent geometry : angle 0.67448 (11346) SS BOND : bond 0.00407 ( 17) SS BOND : angle 1.26952 ( 34) hydrogen bonds : bond 0.05114 ( 292) hydrogen bonds : angle 5.68999 ( 834) glycosidic custom : bond 0.00486 ( 1) glycosidic custom : angle 1.65517 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7593 (m-80) cc_final: 0.7309 (m-10) REVERT: A 225 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7718 (tp30) REVERT: A 238 GLU cc_start: 0.7161 (tp30) cc_final: 0.6921 (mm-30) REVERT: A 248 ASN cc_start: 0.8490 (t0) cc_final: 0.7629 (t0) REVERT: A 255 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6866 (tm-30) REVERT: A 291 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6714 (mp10) REVERT: A 322 PHE cc_start: 0.7783 (m-80) cc_final: 0.7564 (m-80) REVERT: A 338 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6430 (t80) REVERT: A 511 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7830 (m90) REVERT: B 65 PHE cc_start: 0.7482 (t80) cc_final: 0.7197 (t80) REVERT: B 131 TYR cc_start: 0.7267 (p90) cc_final: 0.7054 (p90) REVERT: B 184 PHE cc_start: 0.8057 (m-80) cc_final: 0.7807 (m-80) REVERT: B 199 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 454 TYR cc_start: 0.8204 (m-80) cc_final: 0.7813 (m-80) REVERT: B 520 ASP cc_start: 0.7427 (t0) cc_final: 0.7199 (t0) REVERT: B 521 CYS cc_start: 0.6998 (m) cc_final: 0.6778 (m) outliers start: 46 outliers final: 25 residues processed: 248 average time/residue: 0.1185 time to fit residues: 37.7343 Evaluate side-chains 240 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 517 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 33 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 58 optimal weight: 0.0870 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143128 restraints weight = 11356.764| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.36 r_work: 0.3689 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8361 Z= 0.131 Angle : 0.600 8.309 11383 Z= 0.307 Chirality : 0.043 0.160 1256 Planarity : 0.005 0.064 1467 Dihedral : 5.219 61.258 1156 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.02 % Allowed : 23.97 % Favored : 70.01 % 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 aren not related in a simple way. whole: -1.42 (0.26), residues: 1016 helix: 0.37 (0.28), residues: 349 sheet: -1.67 (0.42), residues: 145 loop : -1.65 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 233 TYR 0.016 0.001 TYR B 394 PHE 0.012 0.001 PHE A 77 TRP 0.013 0.001 TRP B 303 HIS 0.012 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8343) covalent geometry : angle 0.59830 (11346) SS BOND : bond 0.00276 ( 17) SS BOND : angle 1.02667 ( 34) hydrogen bonds : bond 0.04075 ( 292) hydrogen bonds : angle 5.13185 ( 834) glycosidic custom : bond 0.00040 ( 1) glycosidic custom : angle 0.92342 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7616 (m-80) cc_final: 0.7276 (m-10) REVERT: A 145 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6573 (pp20) REVERT: A 222 LEU cc_start: 0.8394 (mt) cc_final: 0.8192 (mp) REVERT: A 248 ASN cc_start: 0.8443 (t0) cc_final: 0.7587 (t0) REVERT: A 255 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 290 ARG cc_start: 0.7282 (mtm110) cc_final: 0.6891 (ptp-110) REVERT: A 291 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6549 (mp10) REVERT: A 314 THR cc_start: 0.5366 (OUTLIER) cc_final: 0.5072 (m) REVERT: A 321 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7195 (m) REVERT: A 322 PHE cc_start: 0.7632 (m-80) cc_final: 0.7267 (m-80) REVERT: A 338 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6237 (t80) REVERT: A 400 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6315 (t-90) REVERT: A 511 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7654 (m90) REVERT: B 64 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7709 (mtp85) REVERT: B 131 TYR cc_start: 0.7251 (p90) cc_final: 0.7009 (p90) REVERT: B 172 GLU cc_start: 0.7115 (tp30) cc_final: 0.6912 (tp30) REVERT: B 427 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 454 TYR cc_start: 0.8100 (m-80) cc_final: 0.7702 (m-80) REVERT: B 520 ASP cc_start: 0.7244 (t0) cc_final: 0.6996 (t0) outliers start: 54 outliers final: 31 residues processed: 250 average time/residue: 0.1159 time to fit residues: 37.2718 Evaluate side-chains 247 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 45 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 246 ASN B 145 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140512 restraints weight = 11652.839| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.42 r_work: 0.3651 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8361 Z= 0.207 Angle : 0.641 10.849 11383 Z= 0.330 Chirality : 0.045 0.148 1256 Planarity : 0.005 0.062 1467 Dihedral : 5.399 60.290 1156 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.58 % Allowed : 24.86 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.26), residues: 1016 helix: 0.25 (0.28), residues: 340 sheet: -1.57 (0.42), residues: 147 loop : -1.62 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 76 TYR 0.016 0.001 TYR B 394 PHE 0.015 0.002 PHE B 100 TRP 0.016 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8343) covalent geometry : angle 0.63830 (11346) SS BOND : bond 0.00437 ( 17) SS BOND : angle 1.28577 ( 34) hydrogen bonds : bond 0.04428 ( 292) hydrogen bonds : angle 5.16596 ( 834) glycosidic custom : bond 0.00091 ( 1) glycosidic custom : angle 0.84585 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7660 (m-80) cc_final: 0.7396 (m-10) REVERT: A 222 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8184 (mp) REVERT: A 248 ASN cc_start: 0.8442 (t0) cc_final: 0.7920 (t0) REVERT: A 255 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6822 (tm-30) REVERT: A 287 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: A 314 THR cc_start: 0.5478 (OUTLIER) cc_final: 0.5002 (m) REVERT: A 322 PHE cc_start: 0.7750 (m-80) cc_final: 0.7316 (m-80) REVERT: A 338 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6325 (t80) REVERT: A 400 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6514 (t-90) REVERT: A 449 GLU cc_start: 0.7135 (tp30) cc_final: 0.6644 (tp30) REVERT: A 468 TYR cc_start: 0.7200 (t80) cc_final: 0.6997 (t80) REVERT: A 511 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7720 (m90) REVERT: A 534 GLU cc_start: 0.7126 (tp30) cc_final: 0.6674 (tp30) REVERT: B 64 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7768 (mtm180) REVERT: B 131 TYR cc_start: 0.7315 (p90) cc_final: 0.7035 (p90) REVERT: B 199 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 258 ASP cc_start: 0.6833 (m-30) cc_final: 0.6470 (m-30) REVERT: B 520 ASP cc_start: 0.7396 (t0) cc_final: 0.7106 (t0) outliers start: 59 outliers final: 32 residues processed: 258 average time/residue: 0.1147 time to fit residues: 38.2022 Evaluate side-chains 251 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 523 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 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 = 0.4107 r_free = 0.4107 target = 0.166626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142069 restraints weight = 11527.737| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.37 r_work: 0.3668 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8361 Z= 0.160 Angle : 0.627 9.975 11383 Z= 0.319 Chirality : 0.044 0.142 1256 Planarity : 0.005 0.060 1467 Dihedral : 5.320 60.144 1156 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.13 % Allowed : 26.64 % Favored : 68.23 % 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 aren not related in a simple way. whole: -1.30 (0.26), residues: 1016 helix: 0.39 (0.28), residues: 342 sheet: -1.45 (0.42), residues: 147 loop : -1.54 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 233 TYR 0.013 0.001 TYR B 394 PHE 0.014 0.001 PHE B 100 TRP 0.016 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8343) covalent geometry : angle 0.62420 (11346) SS BOND : bond 0.00490 ( 17) SS BOND : angle 1.19057 ( 34) hydrogen bonds : bond 0.04088 ( 292) hydrogen bonds : angle 5.01059 ( 834) glycosidic custom : bond 0.00003 ( 1) glycosidic custom : angle 0.66478 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7712 (m-80) cc_final: 0.7456 (m-10) REVERT: A 248 ASN cc_start: 0.8443 (t0) cc_final: 0.7932 (t0) REVERT: A 255 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 322 PHE cc_start: 0.7798 (m-80) cc_final: 0.7456 (m-80) REVERT: A 338 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6255 (t80) REVERT: A 400 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6498 (t-90) REVERT: A 449 GLU cc_start: 0.7103 (tp30) cc_final: 0.6589 (tp30) REVERT: A 511 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7702 (m90) REVERT: A 516 GLU cc_start: 0.6682 (tm-30) cc_final: 0.5955 (tm-30) REVERT: B 72 TRP cc_start: 0.7690 (m-10) cc_final: 0.7336 (m-10) REVERT: B 131 TYR cc_start: 0.7235 (p90) cc_final: 0.6953 (p90) REVERT: B 199 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 258 ASP cc_start: 0.6788 (m-30) cc_final: 0.6442 (m-30) REVERT: B 291 ARG cc_start: 0.6882 (mtm-85) cc_final: 0.6337 (mtm-85) REVERT: B 419 ASP cc_start: 0.7860 (p0) cc_final: 0.7634 (p0) REVERT: B 520 ASP cc_start: 0.7316 (t0) cc_final: 0.7037 (t0) outliers start: 46 outliers final: 35 residues processed: 242 average time/residue: 0.1153 time to fit residues: 36.1388 Evaluate side-chains 246 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 74 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 291 GLN B 262 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142511 restraints weight = 11408.060| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.40 r_work: 0.3673 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8361 Z= 0.152 Angle : 0.626 9.655 11383 Z= 0.318 Chirality : 0.044 0.224 1256 Planarity : 0.005 0.060 1467 Dihedral : 5.293 59.332 1156 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.69 % Allowed : 26.64 % Favored : 67.67 % 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 aren not related in a simple way. whole: -1.25 (0.26), residues: 1016 helix: 0.36 (0.28), residues: 348 sheet: -1.44 (0.42), residues: 147 loop : -1.47 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 76 TYR 0.014 0.001 TYR B 394 PHE 0.014 0.001 PHE B 100 TRP 0.016 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8343) covalent geometry : angle 0.62363 (11346) SS BOND : bond 0.00343 ( 17) SS BOND : angle 1.16604 ( 34) hydrogen bonds : bond 0.03925 ( 292) hydrogen bonds : angle 4.88522 ( 834) glycosidic custom : bond 0.00006 ( 1) glycosidic custom : angle 0.59505 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8088 (t0) cc_final: 0.7624 (t0) REVERT: A 248 ASN cc_start: 0.8442 (t0) cc_final: 0.7933 (t0) REVERT: A 255 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 266 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7491 (tp-100) REVERT: A 322 PHE cc_start: 0.7860 (m-80) cc_final: 0.7473 (m-80) REVERT: A 338 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 400 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6512 (t-90) REVERT: A 449 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: A 511 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (m90) REVERT: B 131 TYR cc_start: 0.7205 (p90) cc_final: 0.6891 (p90) REVERT: B 199 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 258 ASP cc_start: 0.6811 (m-30) cc_final: 0.6442 (m-30) REVERT: B 291 ARG cc_start: 0.6901 (mtm-85) cc_final: 0.6385 (mtm-85) REVERT: B 318 MET cc_start: 0.7248 (tpt) cc_final: 0.7016 (mmm) REVERT: B 520 ASP cc_start: 0.7310 (t0) cc_final: 0.7019 (t0) outliers start: 51 outliers final: 37 residues processed: 243 average time/residue: 0.1161 time to fit residues: 36.4661 Evaluate side-chains 245 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 0.0970 chunk 94 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.0020 chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 239 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** 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 = 0.4133 r_free = 0.4133 target = 0.168428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144814 restraints weight = 11517.649| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.24 r_work: 0.3725 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8361 Z= 0.137 Angle : 0.617 9.499 11383 Z= 0.313 Chirality : 0.043 0.172 1256 Planarity : 0.005 0.057 1467 Dihedral : 5.225 58.664 1156 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.57 % Allowed : 27.20 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.27), residues: 1016 helix: 0.44 (0.28), residues: 348 sheet: -1.56 (0.41), residues: 152 loop : -1.36 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 233 TYR 0.015 0.001 TYR B 394 PHE 0.033 0.001 PHE A 27 TRP 0.018 0.001 TRP B 303 HIS 0.010 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8343) covalent geometry : angle 0.61487 (11346) SS BOND : bond 0.00319 ( 17) SS BOND : angle 1.14737 ( 34) hydrogen bonds : bond 0.03680 ( 292) hydrogen bonds : angle 4.74534 ( 834) glycosidic custom : bond 0.00023 ( 1) glycosidic custom : angle 0.55287 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7391 (tp) REVERT: A 218 ASP cc_start: 0.8339 (t0) cc_final: 0.7828 (t0) REVERT: A 248 ASN cc_start: 0.8466 (t0) cc_final: 0.8156 (m-40) REVERT: A 255 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6933 (tm-30) REVERT: A 287 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6411 (pm20) REVERT: A 322 PHE cc_start: 0.7977 (m-80) cc_final: 0.7637 (m-80) REVERT: A 338 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 400 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6507 (t-90) REVERT: A 449 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: A 511 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7744 (m90) REVERT: B 131 TYR cc_start: 0.7322 (p90) cc_final: 0.6981 (p90) REVERT: B 185 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6719 (ptt180) REVERT: B 199 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 258 ASP cc_start: 0.6985 (m-30) cc_final: 0.6616 (m-30) REVERT: B 291 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6555 (mtm-85) REVERT: B 454 TYR cc_start: 0.8195 (m-80) cc_final: 0.7860 (m-80) REVERT: B 457 LYS cc_start: 0.8347 (mmpt) cc_final: 0.8133 (mmmt) REVERT: B 482 ARG cc_start: 0.7299 (mtp85) cc_final: 0.7092 (mtp85) REVERT: B 520 ASP cc_start: 0.7251 (t0) cc_final: 0.6957 (t0) outliers start: 50 outliers final: 34 residues processed: 229 average time/residue: 0.1194 time to fit residues: 34.8921 Evaluate side-chains 234 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 75 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 145 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 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 = 0.4111 r_free = 0.4111 target = 0.166782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143264 restraints weight = 11429.434| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.21 r_work: 0.3652 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8361 Z= 0.182 Angle : 0.638 9.347 11383 Z= 0.325 Chirality : 0.044 0.164 1256 Planarity : 0.005 0.058 1467 Dihedral : 5.321 58.493 1156 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.35 % Allowed : 27.65 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.26), residues: 1016 helix: 0.42 (0.29), residues: 341 sheet: -1.60 (0.41), residues: 152 loop : -1.42 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 233 TYR 0.016 0.001 TYR B 394 PHE 0.030 0.002 PHE A 27 TRP 0.018 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8343) covalent geometry : angle 0.63640 (11346) SS BOND : bond 0.00332 ( 17) SS BOND : angle 1.07053 ( 34) hydrogen bonds : bond 0.03997 ( 292) hydrogen bonds : angle 4.81044 ( 834) glycosidic custom : bond 0.00003 ( 1) glycosidic custom : angle 0.54252 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8363 (t0) cc_final: 0.7845 (t0) REVERT: A 248 ASN cc_start: 0.8483 (t0) cc_final: 0.8179 (m110) REVERT: A 255 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 266 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7789 (tp-100) REVERT: A 322 PHE cc_start: 0.8008 (m-80) cc_final: 0.7666 (m-80) REVERT: A 338 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6385 (t80) REVERT: A 400 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6712 (t-90) REVERT: A 449 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: A 468 TYR cc_start: 0.7298 (t80) cc_final: 0.7074 (t80) REVERT: A 511 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7811 (m90) REVERT: B 131 TYR cc_start: 0.7312 (p90) cc_final: 0.7005 (p90) REVERT: B 159 PHE cc_start: 0.8015 (t80) cc_final: 0.7671 (t80) REVERT: B 185 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6781 (ptt90) REVERT: B 199 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 258 ASP cc_start: 0.7000 (m-30) cc_final: 0.6639 (m-30) REVERT: B 291 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6566 (mtm-85) REVERT: B 454 TYR cc_start: 0.8263 (m-80) cc_final: 0.7917 (m-80) REVERT: B 504 GLN cc_start: 0.7979 (mt0) cc_final: 0.7222 (mp10) REVERT: B 520 ASP cc_start: 0.7449 (t0) cc_final: 0.7144 (t0) outliers start: 48 outliers final: 34 residues processed: 235 average time/residue: 0.1183 time to fit residues: 35.7285 Evaluate side-chains 240 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 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 = 0.4101 r_free = 0.4101 target = 0.165862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142374 restraints weight = 11444.276| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.19 r_work: 0.3638 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8361 Z= 0.209 Angle : 0.669 9.219 11383 Z= 0.341 Chirality : 0.045 0.168 1256 Planarity : 0.005 0.074 1467 Dihedral : 5.435 58.287 1156 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.02 % Allowed : 27.65 % Favored : 67.34 % 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 aren not related in a simple way. whole: -1.32 (0.26), residues: 1016 helix: 0.34 (0.28), residues: 343 sheet: -1.65 (0.41), residues: 152 loop : -1.46 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 76 TYR 0.017 0.002 TYR B 394 PHE 0.017 0.002 PHE B 100 TRP 0.018 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8343) covalent geometry : angle 0.66740 (11346) SS BOND : bond 0.00375 ( 17) SS BOND : angle 1.15205 ( 34) hydrogen bonds : bond 0.04210 ( 292) hydrogen bonds : angle 4.89646 ( 834) glycosidic custom : bond 0.00006 ( 1) glycosidic custom : angle 0.51302 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6613 (pp20) REVERT: A 197 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7322 (tp) REVERT: A 218 ASP cc_start: 0.8311 (t0) cc_final: 0.7770 (t0) REVERT: A 248 ASN cc_start: 0.8508 (t0) cc_final: 0.8222 (m110) REVERT: A 255 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 322 PHE cc_start: 0.8024 (m-80) cc_final: 0.7671 (m-80) REVERT: A 338 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 400 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6709 (t-90) REVERT: A 449 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6599 (mm-30) REVERT: A 468 TYR cc_start: 0.7297 (t80) cc_final: 0.7084 (t80) REVERT: A 511 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7839 (m90) REVERT: A 516 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6843 (tm-30) REVERT: B 72 TRP cc_start: 0.7814 (m-10) cc_final: 0.7522 (m-10) REVERT: B 131 TYR cc_start: 0.7346 (p90) cc_final: 0.7020 (p90) REVERT: B 159 PHE cc_start: 0.7971 (t80) cc_final: 0.7633 (t80) REVERT: B 185 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6773 (ptt180) REVERT: B 199 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 258 ASP cc_start: 0.7079 (m-30) cc_final: 0.6667 (m-30) REVERT: B 291 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.6607 (mtm-85) REVERT: B 454 TYR cc_start: 0.8270 (m-80) cc_final: 0.7904 (m-80) REVERT: B 482 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6983 (mtp85) REVERT: B 504 GLN cc_start: 0.8085 (mt0) cc_final: 0.7190 (mp10) REVERT: B 520 ASP cc_start: 0.7494 (t0) cc_final: 0.7197 (t0) outliers start: 45 outliers final: 36 residues processed: 237 average time/residue: 0.1173 time to fit residues: 35.6011 Evaluate side-chains 250 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 540 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 52 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.169019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145695 restraints weight = 11415.024| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.23 r_work: 0.3715 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8361 Z= 0.132 Angle : 0.634 9.186 11383 Z= 0.321 Chirality : 0.043 0.151 1256 Planarity : 0.005 0.071 1467 Dihedral : 5.182 56.603 1156 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.57 % Allowed : 28.09 % Favored : 67.34 % 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 aren not related in a simple way. whole: -1.03 (0.27), residues: 1016 helix: 0.59 (0.28), residues: 343 sheet: -1.58 (0.41), residues: 152 loop : -1.25 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 76 TYR 0.014 0.001 TYR B 394 PHE 0.016 0.001 PHE B 100 TRP 0.021 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8343) covalent geometry : angle 0.63265 (11346) SS BOND : bond 0.00334 ( 17) SS BOND : angle 0.92362 ( 34) hydrogen bonds : bond 0.03537 ( 292) hydrogen bonds : angle 4.65580 ( 834) glycosidic custom : bond 0.00043 ( 1) glycosidic custom : angle 0.50689 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7433 (tp) REVERT: A 218 ASP cc_start: 0.8277 (t0) cc_final: 0.7812 (t0) REVERT: A 248 ASN cc_start: 0.8494 (t0) cc_final: 0.8195 (m110) REVERT: A 249 MET cc_start: 0.6311 (mmm) cc_final: 0.6070 (mmm) REVERT: A 255 GLN cc_start: 0.7354 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 287 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: A 322 PHE cc_start: 0.7985 (m-80) cc_final: 0.7657 (m-80) REVERT: A 338 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6300 (t80) REVERT: A 400 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6617 (t-90) REVERT: A 449 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: A 468 TYR cc_start: 0.7291 (t80) cc_final: 0.6627 (t80) REVERT: B 100 PHE cc_start: 0.7658 (m-80) cc_final: 0.7293 (m-80) REVERT: B 131 TYR cc_start: 0.7335 (p90) cc_final: 0.7005 (p90) REVERT: B 165 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7477 (t) REVERT: B 199 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 258 ASP cc_start: 0.6931 (m-30) cc_final: 0.6597 (m-30) REVERT: B 291 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6444 (mtm-85) REVERT: B 318 MET cc_start: 0.7069 (mmm) cc_final: 0.6647 (mmt) REVERT: B 454 TYR cc_start: 0.8186 (m-80) cc_final: 0.7882 (m-80) REVERT: B 520 ASP cc_start: 0.7240 (t0) cc_final: 0.6951 (t0) outliers start: 41 outliers final: 30 residues processed: 231 average time/residue: 0.1272 time to fit residues: 37.3463 Evaluate side-chains 234 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** 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 = 0.4120 r_free = 0.4120 target = 0.167566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144391 restraints weight = 11372.976| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.20 r_work: 0.3701 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8361 Z= 0.168 Angle : 0.653 9.145 11383 Z= 0.332 Chirality : 0.044 0.158 1256 Planarity : 0.005 0.069 1467 Dihedral : 5.254 56.279 1156 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.24 % Allowed : 28.21 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.27), residues: 1016 helix: 0.43 (0.28), residues: 345 sheet: -1.55 (0.41), residues: 152 loop : -1.35 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 76 TYR 0.020 0.001 TYR A 416 PHE 0.019 0.002 PHE A 293 TRP 0.036 0.001 TRP B 303 HIS 0.010 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8343) covalent geometry : angle 0.65166 (11346) SS BOND : bond 0.00336 ( 17) SS BOND : angle 1.07504 ( 34) hydrogen bonds : bond 0.03826 ( 292) hydrogen bonds : angle 4.74200 ( 834) glycosidic custom : bond 0.00028 ( 1) glycosidic custom : angle 0.51834 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.56 seconds wall clock time: 39 minutes 38.06 seconds (2378.06 seconds total)