Starting phenix.real_space_refine on Sat Jul 26 07:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9utc_64488/07_2025/9utc_64488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9utc_64488/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9utc_64488/07_2025/9utc_64488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9utc_64488/07_2025/9utc_64488.map" model { file = "/net/cci-nas-00/data/ceres_data/9utc_64488/07_2025/9utc_64488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9utc_64488/07_2025/9utc_64488.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.09, per 1000 atoms: 0.63 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: 2.20 Conformation dependent library (CDL) restraints added in 976.8 milliseconds 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: 0.80 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: 2.41 Time building geometry restraints manager: 2.50 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- 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 : 14.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (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 TRP 0.009 0.001 TRP B 303 HIS 0.007 0.001 HIS B 488 PHE 0.042 0.002 PHE A 27 TYR 0.017 0.002 TYR B 454 ARG 0.019 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.17891 ( 292) hydrogen bonds : angle 7.23417 ( 834) SS BOND : bond 0.00278 ( 17) SS BOND : angle 0.87306 ( 34) glycosidic custom : bond 0.03188 ( 1) glycosidic custom : angle 6.19920 ( 3) covalent geometry : bond 0.00465 ( 8343) covalent geometry : angle 0.68046 (11346) *********************** 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 : 0.820 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: 0.2728 time to fit residues: 78.3717 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 : 0.915 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 79 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN 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 = 0.4088 r_free = 0.4088 target = 0.165523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140925 restraints weight = 11304.629| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.33 r_work: 0.3643 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1067 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= 0.196 Angle : 0.656 8.151 11383 Z= 0.339 Chirality : 0.045 0.211 1256 Planarity : 0.005 0.075 1467 Dihedral : 5.505 61.741 1158 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.02 % Allowed : 25.20 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.26), residues: 1016 helix: 0.20 (0.28), residues: 339 sheet: -1.58 (0.45), residues: 135 loop : -1.82 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 303 HIS 0.013 0.001 HIS B 488 PHE 0.017 0.002 PHE A 27 TYR 0.017 0.002 TYR B 394 ARG 0.007 0.001 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 292) hydrogen bonds : angle 5.60875 ( 834) SS BOND : bond 0.00349 ( 17) SS BOND : angle 1.23599 ( 34) glycosidic custom : bond 0.00166 ( 1) glycosidic custom : angle 1.55953 ( 3) covalent geometry : bond 0.00449 ( 8343) covalent geometry : angle 0.65338 (11346) *********************** 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 267 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7568 (m-80) cc_final: 0.7303 (m-10) REVERT: A 225 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7700 (tp30) REVERT: A 238 GLU cc_start: 0.7139 (tp30) cc_final: 0.6853 (mm-30) REVERT: A 248 ASN cc_start: 0.8463 (t0) cc_final: 0.7578 (t0) REVERT: A 255 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 291 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: A 322 PHE cc_start: 0.7767 (m-80) cc_final: 0.7551 (m-80) REVERT: A 338 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6395 (t80) REVERT: A 511 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7768 (m90) REVERT: B 64 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7661 (mtp180) REVERT: B 65 PHE cc_start: 0.7619 (t80) cc_final: 0.7325 (t80) REVERT: B 131 TYR cc_start: 0.7270 (p90) cc_final: 0.7040 (p90) REVERT: B 184 PHE cc_start: 0.8001 (m-80) cc_final: 0.7742 (m-80) REVERT: B 199 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 427 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 454 TYR cc_start: 0.8147 (m-80) cc_final: 0.7759 (m-80) REVERT: B 520 ASP cc_start: 0.7393 (t0) cc_final: 0.7167 (t0) REVERT: B 521 CYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6759 (m) outliers start: 45 outliers final: 21 residues processed: 247 average time/residue: 0.2775 time to fit residues: 88.4253 Evaluate side-chains 242 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN 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 338 PHE Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 393 TYR 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 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 427 LEU Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 521 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 95 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4099 r_free = 0.4099 target = 0.166029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141580 restraints weight = 11518.062| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.35 r_work: 0.3637 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8361 Z= 0.155 Angle : 0.611 8.191 11383 Z= 0.313 Chirality : 0.043 0.163 1256 Planarity : 0.005 0.065 1467 Dihedral : 5.288 61.605 1156 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.69 % Allowed : 24.53 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.26), residues: 1016 helix: 0.37 (0.28), residues: 342 sheet: -1.72 (0.41), residues: 147 loop : -1.68 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 303 HIS 0.012 0.001 HIS B 488 PHE 0.011 0.001 PHE A 77 TYR 0.016 0.001 TYR B 394 ARG 0.006 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 292) hydrogen bonds : angle 5.23824 ( 834) SS BOND : bond 0.00423 ( 17) SS BOND : angle 0.94213 ( 34) glycosidic custom : bond 0.00095 ( 1) glycosidic custom : angle 1.12961 ( 3) covalent geometry : bond 0.00357 ( 8343) covalent geometry : angle 0.60904 (11346) *********************** 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 267 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7630 (m-80) cc_final: 0.7270 (m-10) REVERT: A 145 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6601 (pp20) REVERT: A 222 LEU cc_start: 0.8407 (mt) cc_final: 0.8201 (mp) REVERT: A 238 GLU cc_start: 0.7101 (tp30) cc_final: 0.6813 (mm-30) REVERT: A 248 ASN cc_start: 0.8437 (t0) cc_final: 0.7565 (t0) REVERT: A 255 GLN cc_start: 0.7122 (tm-30) cc_final: 0.6818 (tm-30) REVERT: A 291 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: A 321 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7160 (m) REVERT: A 322 PHE cc_start: 0.7739 (m-80) cc_final: 0.7422 (m-80) REVERT: A 338 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6367 (t80) REVERT: A 400 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6395 (t-90) REVERT: A 457 ARG cc_start: 0.7306 (mmp-170) cc_final: 0.6961 (mmp-170) REVERT: A 511 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7669 (m90) REVERT: B 131 TYR cc_start: 0.7276 (p90) cc_final: 0.7034 (p90) REVERT: B 454 TYR cc_start: 0.8160 (m-80) cc_final: 0.7770 (m-80) REVERT: B 520 ASP cc_start: 0.7369 (t0) cc_final: 0.7130 (t0) outliers start: 51 outliers final: 29 residues processed: 250 average time/residue: 0.3568 time to fit residues: 115.7152 Evaluate side-chains 251 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 ILE 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 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 450 VAL Chi-restraints excluded: chain B residue 517 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 13 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4091 r_free = 0.4091 target = 0.165374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140547 restraints weight = 11522.737| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.39 r_work: 0.3652 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.004 0.038 8361 Z= 0.190 Angle : 0.623 8.009 11383 Z= 0.321 Chirality : 0.044 0.151 1256 Planarity : 0.005 0.062 1467 Dihedral : 5.367 60.410 1156 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.02 % Allowed : 24.64 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 1016 helix: 0.26 (0.28), residues: 340 sheet: -1.56 (0.42), residues: 147 loop : -1.62 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.016 0.002 PHE B 100 TYR 0.016 0.001 TYR B 394 ARG 0.008 0.001 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 292) hydrogen bonds : angle 5.16790 ( 834) SS BOND : bond 0.00412 ( 17) SS BOND : angle 1.01632 ( 34) glycosidic custom : bond 0.00069 ( 1) glycosidic custom : angle 0.83507 ( 3) covalent geometry : bond 0.00436 ( 8343) covalent geometry : angle 0.62095 (11346) *********************** 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 275 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7700 (m-80) cc_final: 0.7437 (m-80) REVERT: A 159 LEU cc_start: 0.7986 (tt) cc_final: 0.7699 (tt) REVERT: A 248 ASN cc_start: 0.8457 (t0) cc_final: 0.7598 (t0) REVERT: A 255 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 321 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7196 (m) REVERT: A 322 PHE cc_start: 0.7811 (m-80) cc_final: 0.7413 (m-80) REVERT: A 338 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6302 (t80) REVERT: A 400 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6482 (t-90) REVERT: A 449 GLU cc_start: 0.7134 (tp30) cc_final: 0.6618 (tp30) REVERT: A 468 TYR cc_start: 0.7236 (t80) cc_final: 0.7032 (t80) REVERT: A 511 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7717 (m90) REVERT: B 131 TYR cc_start: 0.7302 (p90) cc_final: 0.7023 (p90) REVERT: B 199 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 258 ASP cc_start: 0.6843 (m-30) cc_final: 0.6477 (m-30) REVERT: B 419 ASP cc_start: 0.7880 (p0) cc_final: 0.7674 (p0) REVERT: B 520 ASP cc_start: 0.7318 (t0) cc_final: 0.7063 (t0) outliers start: 54 outliers final: 33 residues processed: 256 average time/residue: 0.2939 time to fit residues: 97.8341 Evaluate side-chains 249 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 321 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 358 THR 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 24 CYS 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 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 450 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 519 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 ** 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 = 0.4099 r_free = 0.4099 target = 0.166070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141641 restraints weight = 11358.251| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.35 r_work: 0.3640 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1783 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= 0.160 Angle : 0.618 9.536 11383 Z= 0.314 Chirality : 0.044 0.142 1256 Planarity : 0.005 0.060 1467 Dihedral : 5.339 59.889 1156 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 1016 helix: 0.26 (0.28), residues: 340 sheet: -1.42 (0.42), residues: 147 loop : -1.54 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.015 0.001 PHE B 100 TYR 0.017 0.001 TYR B 394 ARG 0.007 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 292) hydrogen bonds : angle 5.06770 ( 834) SS BOND : bond 0.00289 ( 17) SS BOND : angle 1.03468 ( 34) glycosidic custom : bond 0.00013 ( 1) glycosidic custom : angle 0.68939 ( 3) covalent geometry : bond 0.00369 ( 8343) covalent geometry : angle 0.61622 (11346) *********************** 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 262 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7722 (m-80) cc_final: 0.7467 (m-80) REVERT: A 159 LEU cc_start: 0.8125 (tt) cc_final: 0.7863 (tt) REVERT: A 248 ASN cc_start: 0.8453 (t0) cc_final: 0.7925 (t0) REVERT: A 255 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 321 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7109 (m) REVERT: A 322 PHE cc_start: 0.7786 (m-80) cc_final: 0.7417 (m-80) REVERT: A 338 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6365 (t80) REVERT: A 400 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6557 (t-90) REVERT: A 449 GLU cc_start: 0.7166 (tp30) cc_final: 0.6626 (tp30) REVERT: A 511 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7714 (m90) REVERT: A 516 GLU cc_start: 0.6197 (tm-30) cc_final: 0.5563 (tm-30) REVERT: B 72 TRP cc_start: 0.7690 (m-10) cc_final: 0.7341 (m-10) REVERT: B 131 TYR cc_start: 0.7257 (p90) cc_final: 0.6987 (p90) REVERT: B 199 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7398 (mm-30) REVERT: B 258 ASP cc_start: 0.6795 (m-30) cc_final: 0.6453 (m-30) REVERT: B 291 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6342 (mtm-85) REVERT: B 520 ASP cc_start: 0.7314 (t0) cc_final: 0.7045 (t0) outliers start: 46 outliers final: 33 residues processed: 246 average time/residue: 0.3039 time to fit residues: 96.1316 Evaluate side-chains 250 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 321 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 209 VAL Chi-restraints excluded: chain B residue 243 VAL 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 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139790 restraints weight = 11429.969| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.37 r_work: 0.3630 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1840 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= 0.216 Angle : 0.667 10.859 11383 Z= 0.338 Chirality : 0.046 0.189 1256 Planarity : 0.005 0.062 1467 Dihedral : 5.473 59.591 1156 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.13 % Allowed : 26.76 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.26), residues: 1016 helix: 0.22 (0.28), residues: 342 sheet: -1.50 (0.41), residues: 147 loop : -1.55 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.016 0.002 PHE B 100 TYR 0.018 0.002 TYR B 394 ARG 0.008 0.001 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 292) hydrogen bonds : angle 5.05099 ( 834) SS BOND : bond 0.00506 ( 17) SS BOND : angle 1.31853 ( 34) glycosidic custom : bond 0.00046 ( 1) glycosidic custom : angle 0.63133 ( 3) covalent geometry : bond 0.00496 ( 8343) covalent geometry : angle 0.66381 (11346) *********************** 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 276 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 1.382 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: 0.7757 (m-80) cc_final: 0.7547 (m-80) REVERT: A 159 LEU cc_start: 0.8107 (tt) cc_final: 0.7851 (tt) REVERT: A 218 ASP cc_start: 0.8139 (t0) cc_final: 0.7593 (t0) REVERT: A 248 ASN cc_start: 0.8454 (t0) cc_final: 0.7953 (t0) REVERT: A 255 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6937 (tm-30) REVERT: A 338 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6357 (t80) REVERT: A 400 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6589 (t-90) REVERT: A 449 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6653 (tp30) REVERT: A 511 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7766 (m90) REVERT: B 64 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7591 (mtm180) REVERT: B 65 PHE cc_start: 0.7485 (t80) cc_final: 0.7125 (t80) REVERT: B 72 TRP cc_start: 0.7699 (m-10) cc_final: 0.7334 (m-10) REVERT: B 131 TYR cc_start: 0.7348 (p90) cc_final: 0.7043 (p90) REVERT: B 185 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6662 (ptt180) REVERT: B 258 ASP cc_start: 0.6846 (m-30) cc_final: 0.6488 (m-30) REVERT: B 291 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6473 (mtm-85) REVERT: B 449 ASN cc_start: 0.7657 (m-40) cc_final: 0.7393 (m-40) REVERT: B 482 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6854 (mtp85) REVERT: B 520 ASP cc_start: 0.7443 (t0) cc_final: 0.7155 (t0) outliers start: 55 outliers final: 39 residues processed: 252 average time/residue: 0.3257 time to fit residues: 107.5211 Evaluate side-chains 260 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 321 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 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 185 ARG 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 508 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141830 restraints weight = 11502.207| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.38 r_work: 0.3668 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8361 Z= 0.155 Angle : 0.651 10.868 11383 Z= 0.328 Chirality : 0.045 0.258 1256 Planarity : 0.005 0.059 1467 Dihedral : 5.374 58.644 1156 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1016 helix: 0.29 (0.28), residues: 342 sheet: -1.40 (0.42), residues: 147 loop : -1.50 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.014 0.001 PHE A 322 TYR 0.017 0.001 TYR B 394 ARG 0.010 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 292) hydrogen bonds : angle 4.94122 ( 834) SS BOND : bond 0.00363 ( 17) SS BOND : angle 1.32700 ( 34) glycosidic custom : bond 0.00003 ( 1) glycosidic custom : angle 0.57524 ( 3) covalent geometry : bond 0.00361 ( 8343) covalent geometry : angle 0.64758 (11346) *********************** 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 261 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.6626 (tt0) cc_final: 0.6183 (pt0) REVERT: A 159 LEU cc_start: 0.8097 (tt) cc_final: 0.7833 (tt) REVERT: A 218 ASP cc_start: 0.8129 (t0) cc_final: 0.7601 (t0) REVERT: A 238 GLU cc_start: 0.7052 (tp30) cc_final: 0.6676 (mp0) REVERT: A 248 ASN cc_start: 0.8448 (t0) cc_final: 0.7956 (t0) REVERT: A 255 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 338 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6278 (t80) REVERT: A 400 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6531 (t-90) REVERT: A 449 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: A 511 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7728 (m90) REVERT: A 516 GLU cc_start: 0.6651 (tm-30) cc_final: 0.5910 (tm-30) REVERT: B 64 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7495 (mtp85) REVERT: B 131 TYR cc_start: 0.7313 (p90) cc_final: 0.6971 (p90) REVERT: B 199 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 258 ASP cc_start: 0.6775 (m-30) cc_final: 0.6441 (m-30) REVERT: B 291 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6429 (mtm-85) REVERT: B 482 ARG cc_start: 0.7068 (mtp85) cc_final: 0.6854 (mtp85) REVERT: B 520 ASP cc_start: 0.7334 (t0) cc_final: 0.7034 (t0) outliers start: 48 outliers final: 37 residues processed: 242 average time/residue: 0.3676 time to fit residues: 116.5211 Evaluate side-chains 250 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 321 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 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 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 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 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 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 247 GLN ** A 283 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140808 restraints weight = 11443.234| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.41 r_work: 0.3648 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2004 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= 0.189 Angle : 0.666 10.619 11383 Z= 0.337 Chirality : 0.045 0.236 1256 Planarity : 0.005 0.059 1467 Dihedral : 5.430 58.199 1156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.91 % Allowed : 27.76 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.26), residues: 1016 helix: 0.25 (0.28), residues: 341 sheet: -1.56 (0.41), residues: 152 loop : -1.46 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 303 HIS 0.010 0.001 HIS B 488 PHE 0.023 0.002 PHE A 322 TYR 0.019 0.001 TYR B 394 ARG 0.009 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 292) hydrogen bonds : angle 4.95898 ( 834) SS BOND : bond 0.00360 ( 17) SS BOND : angle 1.16639 ( 34) glycosidic custom : bond 0.00013 ( 1) glycosidic custom : angle 0.57353 ( 3) covalent geometry : bond 0.00439 ( 8343) covalent geometry : angle 0.66383 (11346) *********************** 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 267 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8139 (tt) cc_final: 0.7893 (tt) REVERT: A 201 PHE cc_start: 0.8273 (m-10) cc_final: 0.7734 (m-80) REVERT: A 218 ASP cc_start: 0.8141 (t0) cc_final: 0.7606 (t0) REVERT: A 238 GLU cc_start: 0.7049 (tp30) cc_final: 0.6739 (mp0) REVERT: A 248 ASN cc_start: 0.8418 (t0) cc_final: 0.8073 (m110) REVERT: A 255 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 338 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6320 (t80) REVERT: A 400 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6594 (t-90) REVERT: A 449 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6303 (mt-10) REVERT: A 511 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7764 (m90) REVERT: B 72 TRP cc_start: 0.7723 (m-10) cc_final: 0.7407 (m-10) REVERT: B 131 TYR cc_start: 0.7310 (p90) cc_final: 0.6990 (p90) REVERT: B 159 PHE cc_start: 0.7907 (t80) cc_final: 0.7535 (t80) REVERT: B 185 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6667 (ptt180) REVERT: B 199 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 258 ASP cc_start: 0.6877 (m-30) cc_final: 0.6492 (m-30) REVERT: B 291 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6468 (mtm-85) REVERT: B 504 GLN cc_start: 0.7974 (mt0) cc_final: 0.7065 (mp10) REVERT: B 520 ASP cc_start: 0.7313 (t0) cc_final: 0.7046 (t0) outliers start: 53 outliers final: 38 residues processed: 246 average time/residue: 0.2505 time to fit residues: 78.9717 Evaluate side-chains 248 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 321 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 56 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144036 restraints weight = 11571.584| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.23 r_work: 0.3666 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8361 Z= 0.139 Angle : 0.648 10.537 11383 Z= 0.327 Chirality : 0.043 0.175 1256 Planarity : 0.005 0.058 1467 Dihedral : 5.314 57.586 1156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.91 % Allowed : 28.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.27), residues: 1016 helix: 0.40 (0.28), residues: 350 sheet: -1.48 (0.41), residues: 152 loop : -1.34 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.014 0.001 PHE B 100 TYR 0.022 0.001 TYR A 28 ARG 0.010 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 292) hydrogen bonds : angle 4.77947 ( 834) SS BOND : bond 0.00348 ( 17) SS BOND : angle 1.10015 ( 34) glycosidic custom : bond 0.00035 ( 1) glycosidic custom : angle 0.54187 ( 3) covalent geometry : bond 0.00327 ( 8343) covalent geometry : angle 0.64600 (11346) *********************** 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 254 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8179 (tt) cc_final: 0.7956 (tt) REVERT: A 201 PHE cc_start: 0.8237 (m-10) cc_final: 0.7742 (m-80) REVERT: A 218 ASP cc_start: 0.8328 (t0) cc_final: 0.7867 (t0) REVERT: A 248 ASN cc_start: 0.8485 (t0) cc_final: 0.8172 (m110) REVERT: A 249 MET cc_start: 0.6482 (mmm) cc_final: 0.6075 (mmm) REVERT: A 255 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7064 (tm-30) REVERT: A 290 ARG cc_start: 0.7436 (mtm110) cc_final: 0.7155 (ptp-110) REVERT: A 338 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6323 (t80) REVERT: A 400 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6551 (t-90) REVERT: A 449 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: A 511 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7765 (m90) REVERT: B 64 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7651 (mtp85) REVERT: B 131 TYR cc_start: 0.7343 (p90) cc_final: 0.7019 (p90) REVERT: B 185 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6757 (ptt90) REVERT: B 199 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 258 ASP cc_start: 0.6957 (m-30) cc_final: 0.6615 (m-30) REVERT: B 291 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6480 (mtm-85) REVERT: B 454 TYR cc_start: 0.8228 (m-80) cc_final: 0.7904 (m-80) REVERT: B 482 ARG cc_start: 0.7210 (mtp85) cc_final: 0.6976 (mtp85) REVERT: B 520 ASP cc_start: 0.7392 (t0) cc_final: 0.7093 (t0) outliers start: 44 outliers final: 36 residues processed: 237 average time/residue: 0.2619 time to fit residues: 79.3212 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 : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 ASN 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 321 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141956 restraints weight = 11399.583| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.34 r_work: 0.3664 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8361 Z= 0.196 Angle : 0.684 10.601 11383 Z= 0.346 Chirality : 0.045 0.210 1256 Planarity : 0.005 0.065 1467 Dihedral : 5.404 57.481 1156 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.68 % Allowed : 28.76 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.27), residues: 1016 helix: 0.37 (0.28), residues: 343 sheet: -1.58 (0.41), residues: 152 loop : -1.42 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 303 HIS 0.011 0.001 HIS B 488 PHE 0.017 0.002 PHE B 100 TYR 0.018 0.002 TYR A 28 ARG 0.015 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 292) hydrogen bonds : angle 4.91587 ( 834) SS BOND : bond 0.00369 ( 17) SS BOND : angle 0.99279 ( 34) glycosidic custom : bond 0.00003 ( 1) glycosidic custom : angle 0.54136 ( 3) covalent geometry : bond 0.00455 ( 8343) covalent geometry : angle 0.68289 (11346) ********************** 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 252 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8131 (tt) cc_final: 0.7882 (tt) REVERT: A 218 ASP cc_start: 0.8072 (t0) cc_final: 0.7126 (t0) REVERT: A 222 LEU cc_start: 0.8284 (mp) cc_final: 0.8018 (mp) REVERT: A 248 ASN cc_start: 0.8410 (t0) cc_final: 0.8185 (m110) REVERT: A 255 GLN cc_start: 0.7279 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 287 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5992 (pm20) REVERT: A 322 PHE cc_start: 0.7856 (m-80) cc_final: 0.7540 (m-80) REVERT: A 338 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6332 (t80) REVERT: A 400 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6594 (t-90) REVERT: A 449 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6602 (tp30) REVERT: A 511 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7771 (m90) REVERT: B 72 TRP cc_start: 0.7717 (m-10) cc_final: 0.7441 (m-10) REVERT: B 131 TYR cc_start: 0.7271 (p90) cc_final: 0.6946 (p90) REVERT: B 185 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6663 (ptt180) REVERT: B 199 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 258 ASP cc_start: 0.6873 (m-30) cc_final: 0.6510 (m-30) REVERT: B 291 ARG cc_start: 0.6890 (mtm-85) cc_final: 0.6400 (mtm-85) REVERT: B 482 ARG cc_start: 0.7096 (mtp85) cc_final: 0.6860 (mtp85) REVERT: B 504 GLN cc_start: 0.7841 (mt0) cc_final: 0.7068 (mp10) REVERT: B 520 ASP cc_start: 0.7278 (t0) cc_final: 0.6987 (t0) outliers start: 42 outliers final: 33 residues processed: 237 average time/residue: 0.2616 time to fit residues: 79.2606 Evaluate side-chains 246 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 321 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 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 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 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 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 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 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 29 optimal weight: 0.0370 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 68 optimal weight: 0.0570 chunk 21 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.1354 ------------------------------------------------------------------------------- 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 ** 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 = 0.4153 r_free = 0.4153 target = 0.170010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146911 restraints weight = 11453.570| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.21 r_work: 0.3722 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8361 Z= 0.128 Angle : 0.654 10.765 11383 Z= 0.329 Chirality : 0.043 0.168 1256 Planarity : 0.005 0.059 1467 Dihedral : 5.200 55.962 1156 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.57 % Allowed : 29.99 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.27), residues: 1016 helix: 0.54 (0.28), residues: 343 sheet: -1.69 (0.40), residues: 151 loop : -1.34 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP B 303 HIS 0.010 0.001 HIS B 488 PHE 0.014 0.001 PHE B 100 TYR 0.019 0.001 TYR A 28 ARG 0.013 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 292) hydrogen bonds : angle 4.66222 ( 834) SS BOND : bond 0.00301 ( 17) SS BOND : angle 1.00875 ( 34) glycosidic custom : bond 0.00070 ( 1) glycosidic custom : angle 0.53479 ( 3) covalent geometry : bond 0.00298 ( 8343) covalent geometry : angle 0.65305 (11346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4999.46 seconds wall clock time: 91 minutes 49.65 seconds (5509.65 seconds total)