Starting phenix.real_space_refine on Sat Jun 6 15:42:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.map" model { file = "/net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oh4_70483/06_2026/9oh4_70483.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 164 5.49 5 S 52 5.16 5 C 9198 2.51 5 N 2620 2.21 5 O 3136 1.98 5 H 13863 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29037 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5954 Classifications: {'peptide': 357} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 341} Chain: "B" Number of atoms: 5954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5954 Classifications: {'peptide': 357} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 341} Chain: "C" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5953 Classifications: {'peptide': 357} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 341} Chain: "D" Number of atoms: 5954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5954 Classifications: {'peptide': 357} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 341} Chain: "E" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1306 Classifications: {'DNA': 41} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 40} Chain: "F" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1303 Classifications: {'DNA': 41} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 40} Chain: "G" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1306 Classifications: {'DNA': 41} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1303 Classifications: {'DNA': 41} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3924 SG CYS A 384 34.479 124.954 43.431 1.00 39.98 S ATOM 3934 SG CYS A 385 32.530 123.545 40.401 1.00 41.86 S ATOM 4020 SG CYS A 392 34.904 126.445 39.986 1.00 45.49 S ATOM 9878 SG CYS B 384 41.938 121.440 57.482 1.00 42.41 S ATOM 9888 SG CYS B 385 44.580 121.776 60.840 1.00 43.17 S ATOM 9974 SG CYS B 392 42.869 124.269 60.330 1.00 44.60 S ATOM 15831 SG CYS C 384 42.921 26.483 43.106 1.00 45.21 S ATOM 15841 SG CYS C 385 45.903 26.765 40.754 1.00 45.26 S ATOM 15927 SG CYS C 392 43.165 24.947 39.977 1.00 46.12 S ATOM 21785 SG CYS D 384 35.967 27.339 58.766 1.00 43.09 S ATOM 21795 SG CYS D 385 33.342 28.873 61.164 1.00 44.62 S ATOM 21881 SG CYS D 392 36.231 26.949 62.541 1.00 47.88 S Time building chain proxies: 5.66, per 1000 atoms: 0.19 Number of scatterers: 29037 At special positions: 0 Unit cell: (79.05, 151.59, 101.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 52 16.00 P 164 15.00 O 3136 8.00 N 2620 7.00 C 9198 6.00 H 13863 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 753.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 385 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 384 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 378 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 392 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 384 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 385 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 378 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 392 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 385 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 384 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 392 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 384 " Number of angles added : 9 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 48.7% alpha, 7.2% beta 80 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.801A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.716A pdb=" N HIS A 250 " --> pdb=" O PRO A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 275 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.640A pdb=" N MET A 401 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.675A pdb=" N VAL A 423 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 433 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.637A pdb=" N ASP A 441 " --> pdb=" O SER A 438 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 160 through 184 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.795A pdb=" N TYR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.134A pdb=" N HIS B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'B' and resid 367 through 377 Processing helix chain 'B' and resid 393 through 412 removed outlier: 4.531A pdb=" N LEU B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET B 401 " --> pdb=" O CYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 434 removed outlier: 3.669A pdb=" N VAL B 423 " --> pdb=" O CYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 444 through 463 removed outlier: 3.700A pdb=" N PHE B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 160 through 185 Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.644A pdb=" N HIS C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 251 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.521A pdb=" N MET C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.894A pdb=" N ARG C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 removed outlier: 4.053A pdb=" N THR C 362 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 377 Processing helix chain 'C' and resid 393 through 412 removed outlier: 3.703A pdb=" N LEU C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 434 removed outlier: 3.874A pdb=" N VAL C 423 " --> pdb=" O CYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 444 through 462 Processing helix chain 'C' and resid 482 through 499 Processing helix chain 'C' and resid 500 through 505 removed outlier: 6.128A pdb=" N ILE C 503 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 160 through 185 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 258 through 277 removed outlier: 4.093A pdb=" N MET D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 332 through 341 removed outlier: 4.338A pdb=" N VAL D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 361 Processing helix chain 'D' and resid 367 through 377 Processing helix chain 'D' and resid 393 through 412 removed outlier: 3.910A pdb=" N MET D 401 " --> pdb=" O CYS D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.516A pdb=" N ASP D 416 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA D 417 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 434 removed outlier: 3.959A pdb=" N VAL D 423 " --> pdb=" O CYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 444 through 463 Processing helix chain 'D' and resid 482 through 499 Processing helix chain 'D' and resid 501 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA2, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.641A pdb=" N VAL B 214 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 311 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE B 216 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 313 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 218 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 310 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 314 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 345 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 211 through 215 removed outlier: 7.400A pdb=" N PHE C 212 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE C 309 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 214 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 308 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'D' and resid 193 through 196 removed outlier: 8.121A pdb=" N LEU D 310 " --> pdb=" O PRO D 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 224 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 284 521 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 194 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13843 1.04 - 1.23: 578 1.23 - 1.43: 6460 1.43 - 1.63: 8742 1.63 - 1.83: 72 Bond restraints: 29695 Sorted by residual: bond pdb=" N HIS C 378 " pdb=" CA HIS C 378 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.16e-02 7.43e+03 1.07e+01 bond pdb=" CG HIS C 378 " pdb=" CD2 HIS C 378 " ideal model delta sigma weight residual 1.354 1.319 0.035 1.10e-02 8.26e+03 9.94e+00 bond pdb=" N ILE C 380 " pdb=" CA ILE C 380 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.14e-02 7.69e+03 5.50e+00 bond pdb=" N ASN C 376 " pdb=" CA ASN C 376 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.35e-02 5.49e+03 5.31e+00 bond pdb=" CE1 HIS C 378 " pdb=" NE2 HIS C 378 " ideal model delta sigma weight residual 1.321 1.298 0.023 1.00e-02 1.00e+04 5.20e+00 ... (remaining 29690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 51746 2.10 - 4.20: 1563 4.20 - 6.30: 608 6.30 - 8.40: 13 8.40 - 10.51: 6 Bond angle restraints: 53936 Sorted by residual: angle pdb=" CB HIS C 378 " pdb=" CG HIS C 378 " pdb=" CD2 HIS C 378 " ideal model delta sigma weight residual 131.20 120.82 10.38 1.30e+00 5.92e-01 6.38e+01 angle pdb=" CB HIS C 378 " pdb=" CG HIS C 378 " pdb=" ND1 HIS C 378 " ideal model delta sigma weight residual 122.70 132.65 -9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" C LYS D 451 " pdb=" CA LYS D 451 " pdb=" CB LYS D 451 " ideal model delta sigma weight residual 110.81 103.02 7.79 1.60e+00 3.91e-01 2.37e+01 angle pdb=" CA HIS C 378 " pdb=" CB HIS C 378 " pdb=" CG HIS C 378 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N LYS D 451 " pdb=" CA LYS D 451 " pdb=" CB LYS D 451 " ideal model delta sigma weight residual 109.94 116.63 -6.69 1.49e+00 4.50e-01 2.01e+01 ... (remaining 53931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9993 17.81 - 35.62: 1864 35.62 - 53.43: 1025 53.43 - 71.24: 343 71.24 - 89.04: 38 Dihedral angle restraints: 13263 sinusoidal: 8236 harmonic: 5027 Sorted by residual: dihedral pdb=" CA ASN A 300 " pdb=" C ASN A 300 " pdb=" N PRO A 301 " pdb=" CA PRO A 301 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA MET A 430 " pdb=" C MET A 430 " pdb=" N TRP A 431 " pdb=" CA TRP A 431 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN D 300 " pdb=" C ASN D 300 " pdb=" N PRO D 301 " pdb=" CA PRO D 301 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 13260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2365 0.117 - 0.234: 22 0.234 - 0.352: 0 0.352 - 0.469: 0 0.469 - 0.586: 5 Chirality restraints: 2392 Sorted by residual: chirality pdb=" P DT H 36 " pdb=" OP1 DT H 36 " pdb=" OP2 DT H 36 " pdb=" O5' DT H 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" P DG H 39 " pdb=" OP1 DG H 39 " pdb=" OP2 DG H 39 " pdb=" O5' DG H 39 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" P DT H 38 " pdb=" OP1 DT H 38 " pdb=" OP2 DT H 38 " pdb=" O5' DT H 38 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.13e+00 ... (remaining 2389 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 376 " 0.128 2.00e-02 2.50e+03 1.36e-01 2.77e+02 pdb=" CG ASN C 376 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 376 " -0.120 2.00e-02 2.50e+03 pdb=" ND2 ASN C 376 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 376 " -0.198 2.00e-02 2.50e+03 pdb="HD22 ASN C 376 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 377 " 0.121 2.00e-02 2.50e+03 1.34e-01 2.71e+02 pdb=" CG ASN C 377 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN C 377 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN C 377 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 377 " -0.199 2.00e-02 2.50e+03 pdb="HD22 ASN C 377 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 378 " 0.014 2.00e-02 2.50e+03 3.43e-02 2.64e+01 pdb=" CG HIS C 378 " 0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS C 378 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 HIS C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 378 " 0.054 2.00e-02 2.50e+03 pdb=" NE2 HIS C 378 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS C 378 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS C 378 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS C 378 " 0.002 2.00e-02 2.50e+03 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.08: 533 2.08 - 2.71: 45840 2.71 - 3.34: 83696 3.34 - 3.97: 106212 3.97 - 4.60: 163523 Nonbonded interactions: 399804 Sorted by model distance: nonbonded pdb=" H1' DA E 11 " pdb=" H5' DA E 12 " model vdw 1.445 2.440 nonbonded pdb="H2'' DA E 19 " pdb=" H5' DC E 20 " model vdw 1.495 2.440 nonbonded pdb="H2'' DT H 8 " pdb=" H71 DT H 9 " model vdw 1.537 2.440 nonbonded pdb=" H2' DA G 34 " pdb=" H72 DT G 35 " model vdw 1.552 2.440 nonbonded pdb="H2'' DT F 14 " pdb=" H72 DT F 15 " model vdw 1.556 2.440 ... (remaining 399799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 149 through 377 or (resid 378 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 379 through 601)) selection = (chain 'B' and (resid 149 through 377 or (resid 378 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 379 through 601)) selection = chain 'C' selection = (chain 'D' and (resid 149 through 377 or (resid 378 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 379 through 601)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 4.650 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: 0.120 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.823 15847 Z= 0.207 Angle : 0.621 18.812 22011 Z= 0.347 Chirality : 0.043 0.586 2392 Planarity : 0.005 0.099 2220 Dihedral : 24.630 88.862 6520 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.37 % Favored : 90.49 % Rotamer: Outliers : 4.85 % Allowed : 28.56 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1420 helix: 0.02 (0.22), residues: 568 sheet: -2.13 (0.39), residues: 180 loop : -1.33 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.015 0.001 TYR B 373 PHE 0.013 0.001 PHE D 266 TRP 0.010 0.001 TRP A 363 HIS 0.056 0.002 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (15832) covalent geometry : angle 0.59784 / 0.34 (22002) hydrogen bonds : bond 0.11557 / 7.96 ( 715) hydrogen bonds : angle 6.63559 / 4.72 ( 1819) metal coordination : bond 0.22019 / 10.30 ( 15) metal coordination : angle 8.25204 / 3.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8328 (tt) cc_final: 0.7529 (mp) REVERT: A 326 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 364 ARG cc_start: 0.4176 (mtt180) cc_final: 0.3210 (ttp-170) REVERT: A 401 MET cc_start: 0.4622 (ttt) cc_final: 0.4207 (ttt) REVERT: A 429 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5363 (m-70) REVERT: A 468 TYR cc_start: 0.5904 (t80) cc_final: 0.5630 (t80) REVERT: B 288 LYS cc_start: 0.6370 (tmmt) cc_final: 0.6150 (tptt) REVERT: B 411 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5900 (mp0) REVERT: B 467 HIS cc_start: 0.3423 (OUTLIER) cc_final: 0.2904 (t-170) REVERT: C 238 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5665 (ptpt) REVERT: C 296 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7506 (mt) REVERT: C 326 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6665 (tp) REVERT: C 375 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8143 (tt) REVERT: D 177 ARG cc_start: 0.7622 (tpt-90) cc_final: 0.7396 (ttt-90) REVERT: D 306 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8029 (p) REVERT: D 373 TYR cc_start: 0.8661 (t80) cc_final: 0.8418 (t80) outliers start: 64 outliers final: 54 residues processed: 198 average time/residue: 0.3252 time to fit residues: 91.1100 Evaluate side-chains 203 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.204295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.173126 restraints weight = 61916.251| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.35 r_work: 0.4212 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15847 Z= 0.196 Angle : 0.603 10.838 22011 Z= 0.340 Chirality : 0.040 0.166 2392 Planarity : 0.005 0.098 2220 Dihedral : 25.352 85.270 3495 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.21 % Favored : 89.65 % Rotamer: Outliers : 5.30 % Allowed : 28.56 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.23), residues: 1420 helix: 0.54 (0.21), residues: 572 sheet: -2.58 (0.34), residues: 208 loop : -1.41 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.009 0.001 TYR B 373 PHE 0.013 0.001 PHE B 189 TRP 0.011 0.002 TRP D 363 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (15832) covalent geometry : angle 0.59440 / 0.34 (22002) hydrogen bonds : bond 0.05201 / 3.64 ( 715) hydrogen bonds : angle 4.78074 / 3.39 ( 1819) metal coordination : bond 0.02361 / 0.96 ( 15) metal coordination : angle 4.90567 / 2.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 142 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8503 (tt) cc_final: 0.7664 (mp) REVERT: A 364 ARG cc_start: 0.4162 (mtt180) cc_final: 0.3140 (ttp-170) REVERT: A 429 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5705 (m-70) REVERT: A 461 ARG cc_start: 0.7561 (ttp80) cc_final: 0.5407 (mmp-170) REVERT: A 468 TYR cc_start: 0.6184 (t80) cc_final: 0.5851 (t80) REVERT: B 288 LYS cc_start: 0.6404 (tmmt) cc_final: 0.6101 (tptt) REVERT: B 467 HIS cc_start: 0.3622 (OUTLIER) cc_final: 0.3108 (t-170) REVERT: D 306 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8370 (p) REVERT: D 358 PHE cc_start: 0.7001 (m-80) cc_final: 0.6658 (m-80) REVERT: D 373 TYR cc_start: 0.8551 (t80) cc_final: 0.8290 (t80) REVERT: D 445 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5346 (tt) outliers start: 70 outliers final: 56 residues processed: 205 average time/residue: 0.3131 time to fit residues: 91.7958 Evaluate side-chains 201 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 141 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 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 = 0.4636 r_free = 0.4636 target = 0.203831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.172590 restraints weight = 62072.143| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.32 r_work: 0.4165 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 15847 Z= 0.187 Angle : 0.597 12.682 22011 Z= 0.337 Chirality : 0.041 0.166 2392 Planarity : 0.005 0.098 2220 Dihedral : 25.080 86.254 3438 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.00 % Favored : 89.86 % Rotamer: Outliers : 5.91 % Allowed : 28.79 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1420 helix: 0.75 (0.21), residues: 572 sheet: -2.54 (0.36), residues: 180 loop : -1.58 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.010 0.001 TYR B 200 PHE 0.013 0.001 PHE A 345 TRP 0.012 0.002 TRP C 363 HIS 0.005 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (15832) covalent geometry : angle 0.58743 / 0.34 (22002) hydrogen bonds : bond 0.04695 / 3.24 ( 715) hydrogen bonds : angle 4.55628 / 3.24 ( 1819) metal coordination : bond 0.03057 / 1.20 ( 15) metal coordination : angle 5.35009 / 2.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 142 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: A 296 LEU cc_start: 0.8514 (tt) cc_final: 0.7694 (mp) REVERT: A 364 ARG cc_start: 0.4292 (mtt180) cc_final: 0.3246 (ttp-170) REVERT: A 429 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.5716 (m-70) REVERT: A 468 TYR cc_start: 0.6109 (t80) cc_final: 0.5780 (t80) REVERT: D 306 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (p) REVERT: D 358 PHE cc_start: 0.7010 (m-80) cc_final: 0.6630 (m-80) REVERT: D 373 TYR cc_start: 0.8559 (t80) cc_final: 0.8308 (t80) outliers start: 78 outliers final: 63 residues processed: 212 average time/residue: 0.3010 time to fit residues: 92.0327 Evaluate side-chains 204 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 138 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.206326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.175146 restraints weight = 61489.003| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.40 r_work: 0.4194 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15847 Z= 0.142 Angle : 0.569 9.492 22011 Z= 0.321 Chirality : 0.039 0.169 2392 Planarity : 0.004 0.096 2220 Dihedral : 24.852 85.061 3428 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.41 % Rotamer: Outliers : 4.77 % Allowed : 28.48 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1420 helix: 1.03 (0.22), residues: 576 sheet: -2.29 (0.38), residues: 180 loop : -1.45 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.010 0.001 TYR C 373 PHE 0.010 0.001 PHE D 266 TRP 0.008 0.001 TRP B 363 HIS 0.005 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15832) covalent geometry : angle 0.55903 / 0.32 (22002) hydrogen bonds : bond 0.04163 / 2.93 ( 715) hydrogen bonds : angle 4.23298 / 3.01 ( 1819) metal coordination : bond 0.02390 / 0.85 ( 15) metal coordination : angle 5.17155 / 2.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: A 296 LEU cc_start: 0.8487 (tt) cc_final: 0.7697 (mp) REVERT: A 364 ARG cc_start: 0.4251 (mtt180) cc_final: 0.3233 (ttp-170) REVERT: A 429 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5668 (m-70) REVERT: A 468 TYR cc_start: 0.6129 (t80) cc_final: 0.5846 (t80) REVERT: B 176 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: B 288 LYS cc_start: 0.6549 (tmmt) cc_final: 0.6257 (tptt) REVERT: B 337 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6954 (ttt-90) REVERT: B 467 HIS cc_start: 0.3593 (OUTLIER) cc_final: 0.3071 (t-170) REVERT: D 306 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8198 (p) REVERT: D 358 PHE cc_start: 0.6902 (m-80) cc_final: 0.6583 (m-80) REVERT: D 373 TYR cc_start: 0.8505 (t80) cc_final: 0.8294 (t80) REVERT: D 445 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5631 (tt) REVERT: D 489 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6701 (mm) outliers start: 63 outliers final: 47 residues processed: 205 average time/residue: 0.3204 time to fit residues: 93.3787 Evaluate side-chains 196 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 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 = 0.4634 r_free = 0.4634 target = 0.203721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.172465 restraints weight = 62122.802| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.32 r_work: 0.4159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 15847 Z= 0.188 Angle : 0.598 11.304 22011 Z= 0.338 Chirality : 0.041 0.166 2392 Planarity : 0.005 0.096 2220 Dihedral : 24.851 85.127 3421 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.28 % Favored : 89.58 % Rotamer: Outliers : 6.44 % Allowed : 27.20 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1420 helix: 0.94 (0.21), residues: 576 sheet: -2.53 (0.34), residues: 208 loop : -1.44 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.010 0.001 TYR B 200 PHE 0.019 0.001 PHE B 412 TRP 0.012 0.002 TRP C 363 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (15832) covalent geometry : angle 0.58837 / 0.34 (22002) hydrogen bonds : bond 0.04588 / 3.22 ( 715) hydrogen bonds : angle 4.36708 / 3.12 ( 1819) metal coordination : bond 0.03268 / 1.23 ( 15) metal coordination : angle 5.39640 / 2.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 145 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6118 (tm-30) REVERT: A 296 LEU cc_start: 0.8561 (tt) cc_final: 0.7737 (mp) REVERT: A 364 ARG cc_start: 0.4287 (mtt180) cc_final: 0.3258 (ttp-170) REVERT: A 429 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.5729 (m-70) REVERT: A 468 TYR cc_start: 0.6089 (t80) cc_final: 0.5776 (t80) REVERT: B 288 LYS cc_start: 0.6549 (tmmt) cc_final: 0.6247 (tptt) REVERT: B 411 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5677 (mp0) REVERT: C 238 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5765 (ptpt) REVERT: C 296 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7700 (mt) REVERT: D 306 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (p) REVERT: D 358 PHE cc_start: 0.6932 (m-80) cc_final: 0.6653 (m-80) REVERT: D 373 TYR cc_start: 0.8568 (t80) cc_final: 0.8335 (t80) REVERT: D 445 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5634 (tt) outliers start: 85 outliers final: 69 residues processed: 219 average time/residue: 0.3142 time to fit residues: 98.5026 Evaluate side-chains 217 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.204045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.172375 restraints weight = 61614.753| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.38 r_work: 0.4170 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 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 0.117 15847 Z= 0.180 Angle : 0.594 11.679 22011 Z= 0.336 Chirality : 0.041 0.167 2392 Planarity : 0.005 0.095 2220 Dihedral : 24.837 85.160 3417 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.44 % Favored : 90.42 % Rotamer: Outliers : 6.74 % Allowed : 27.35 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1420 helix: 0.97 (0.21), residues: 576 sheet: -2.46 (0.36), residues: 180 loop : -1.55 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.009 0.001 TYR B 200 PHE 0.012 0.001 PHE A 345 TRP 0.011 0.002 TRP C 363 HIS 0.003 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (15832) covalent geometry : angle 0.58470 / 0.34 (22002) hydrogen bonds : bond 0.04470 / 3.15 ( 715) hydrogen bonds : angle 4.32957 / 3.09 ( 1819) metal coordination : bond 0.03238 / 1.18 ( 15) metal coordination : angle 5.12111 / 2.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 142 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: A 296 LEU cc_start: 0.8496 (tt) cc_final: 0.7664 (mp) REVERT: A 364 ARG cc_start: 0.4276 (mtt180) cc_final: 0.3187 (ttp-170) REVERT: A 429 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.5734 (m-70) REVERT: A 468 TYR cc_start: 0.6175 (t80) cc_final: 0.5858 (t80) REVERT: B 288 LYS cc_start: 0.6650 (tmmt) cc_final: 0.6357 (tptt) REVERT: B 411 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5673 (mp0) REVERT: B 467 HIS cc_start: 0.3575 (OUTLIER) cc_final: 0.3037 (t-170) REVERT: C 238 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5756 (ptpt) REVERT: C 296 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7624 (mt) REVERT: C 384 CYS cc_start: 0.6110 (t) cc_final: 0.5855 (t) REVERT: D 306 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8367 (p) REVERT: D 358 PHE cc_start: 0.6934 (m-80) cc_final: 0.6655 (m-80) REVERT: D 445 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5603 (tt) outliers start: 89 outliers final: 70 residues processed: 219 average time/residue: 0.3141 time to fit residues: 98.3523 Evaluate side-chains 217 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 139 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.203140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.171638 restraints weight = 61943.232| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.33 r_work: 0.4150 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 15847 Z= 0.193 Angle : 0.606 10.509 22011 Z= 0.344 Chirality : 0.041 0.165 2392 Planarity : 0.005 0.094 2220 Dihedral : 24.849 85.403 3414 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.35 % Favored : 89.51 % Rotamer: Outliers : 7.05 % Allowed : 27.65 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1420 helix: 0.86 (0.21), residues: 576 sheet: -2.58 (0.36), residues: 180 loop : -1.61 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.011 0.001 TYR B 200 PHE 0.013 0.001 PHE D 345 TRP 0.012 0.002 TRP C 363 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (15832) covalent geometry : angle 0.59790 / 0.34 (22002) hydrogen bonds : bond 0.04671 / 3.30 ( 715) hydrogen bonds : angle 4.39589 / 3.13 ( 1819) metal coordination : bond 0.03587 / 1.31 ( 15) metal coordination : angle 4.86498 / 2.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: A 296 LEU cc_start: 0.8562 (tt) cc_final: 0.7725 (mp) REVERT: A 364 ARG cc_start: 0.4309 (mtt180) cc_final: 0.3234 (ttp-170) REVERT: A 429 HIS cc_start: 0.6655 (OUTLIER) cc_final: 0.5703 (m-70) REVERT: A 468 TYR cc_start: 0.6111 (t80) cc_final: 0.5882 (t80) REVERT: B 288 LYS cc_start: 0.6626 (tmmt) cc_final: 0.6319 (tptt) REVERT: B 411 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5728 (mp0) REVERT: B 467 HIS cc_start: 0.3638 (OUTLIER) cc_final: 0.3113 (t-170) REVERT: C 238 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5778 (ptpt) REVERT: C 296 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7717 (mt) REVERT: D 306 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8392 (p) REVERT: D 358 PHE cc_start: 0.6965 (m-80) cc_final: 0.6694 (m-80) REVERT: D 445 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5597 (tt) outliers start: 93 outliers final: 74 residues processed: 222 average time/residue: 0.3178 time to fit residues: 100.4898 Evaluate side-chains 220 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 138 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.202347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.170867 restraints weight = 59173.903| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.17 r_work: 0.4165 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 15847 Z= 0.160 Angle : 0.583 9.545 22011 Z= 0.331 Chirality : 0.040 0.145 2392 Planarity : 0.004 0.032 2220 Dihedral : 24.786 84.826 3414 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.21 % Allowed : 28.26 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1420 helix: 0.99 (0.21), residues: 576 sheet: -2.14 (0.42), residues: 152 loop : -1.58 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.010 0.001 TYR B 200 PHE 0.011 0.001 PHE C 473 TRP 0.010 0.001 TRP A 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15832) covalent geometry : angle 0.57722 / 0.33 (22002) hydrogen bonds : bond 0.04341 / 3.08 ( 715) hydrogen bonds : angle 4.27410 / 3.04 ( 1819) metal coordination : bond 0.02972 / 1.05 ( 15) metal coordination : angle 4.25109 / 1.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 145 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: A 296 LEU cc_start: 0.8468 (tt) cc_final: 0.7634 (mp) REVERT: A 364 ARG cc_start: 0.4378 (mtt180) cc_final: 0.3327 (ttp-170) REVERT: A 429 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.5744 (m-70) REVERT: A 468 TYR cc_start: 0.6090 (t80) cc_final: 0.5777 (t80) REVERT: B 288 LYS cc_start: 0.6624 (tmmt) cc_final: 0.6369 (tptt) REVERT: B 411 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: B 467 HIS cc_start: 0.3751 (OUTLIER) cc_final: 0.3249 (t-170) REVERT: C 238 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5759 (ptpt) REVERT: D 177 ARG cc_start: 0.7771 (tpt-90) cc_final: 0.7533 (ttt-90) REVERT: D 306 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8330 (p) REVERT: D 358 PHE cc_start: 0.6910 (m-80) cc_final: 0.6653 (m-80) REVERT: D 445 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5571 (tt) outliers start: 82 outliers final: 66 residues processed: 216 average time/residue: 0.3168 time to fit residues: 97.5800 Evaluate side-chains 216 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.204487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.173151 restraints weight = 58654.757| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.19 r_work: 0.4165 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 15847 Z= 0.138 Angle : 0.566 9.369 22011 Z= 0.321 Chirality : 0.039 0.141 2392 Planarity : 0.003 0.059 2220 Dihedral : 24.598 82.756 3414 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.00 % Allowed : 29.85 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1420 helix: 1.30 (0.22), residues: 572 sheet: -1.98 (0.43), residues: 152 loop : -1.50 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.008 0.001 TYR B 200 PHE 0.012 0.001 PHE D 266 TRP 0.010 0.001 TRP A 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15832) covalent geometry : angle 0.56047 / 0.32 (22002) hydrogen bonds : bond 0.04038 / 2.87 ( 715) hydrogen bonds : angle 4.13059 / 2.94 ( 1819) metal coordination : bond 0.03035 / 1.07 ( 15) metal coordination : angle 3.82341 / 1.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 296 LEU cc_start: 0.8410 (tt) cc_final: 0.7613 (mp) REVERT: A 326 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6714 (tp) REVERT: A 364 ARG cc_start: 0.4340 (mtt180) cc_final: 0.3333 (ttp-170) REVERT: A 429 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.5719 (m-70) REVERT: A 468 TYR cc_start: 0.6038 (t80) cc_final: 0.5725 (t80) REVERT: B 288 LYS cc_start: 0.6572 (tmmt) cc_final: 0.6326 (tptt) REVERT: B 373 TYR cc_start: 0.8611 (t80) cc_final: 0.8218 (t80) REVERT: B 411 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: B 467 HIS cc_start: 0.3564 (OUTLIER) cc_final: 0.3063 (t-170) REVERT: C 238 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5763 (ptpt) REVERT: C 384 CYS cc_start: 0.5972 (t) cc_final: 0.5754 (t) REVERT: D 177 ARG cc_start: 0.7786 (tpt-90) cc_final: 0.7576 (ttt-90) REVERT: D 306 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8180 (p) REVERT: D 445 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5608 (tt) outliers start: 66 outliers final: 51 residues processed: 207 average time/residue: 0.3212 time to fit residues: 94.2463 Evaluate side-chains 199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.204075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.172768 restraints weight = 59080.841| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.17 r_work: 0.4140 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 15847 Z= 0.148 Angle : 0.570 8.622 22011 Z= 0.323 Chirality : 0.039 0.144 2392 Planarity : 0.003 0.046 2220 Dihedral : 24.543 81.637 3413 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.85 % Allowed : 30.15 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1420 helix: 1.32 (0.22), residues: 572 sheet: -2.06 (0.40), residues: 180 loop : -1.42 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 180 TYR 0.009 0.001 TYR D 373 PHE 0.013 0.001 PHE C 473 TRP 0.008 0.001 TRP B 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15832) covalent geometry : angle 0.56525 / 0.32 (22002) hydrogen bonds : bond 0.04137 / 2.95 ( 715) hydrogen bonds : angle 4.15389 / 2.95 ( 1819) metal coordination : bond 0.03015 / 1.05 ( 15) metal coordination : angle 3.58391 / 1.60 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 296 LEU cc_start: 0.8462 (tt) cc_final: 0.7653 (mp) REVERT: A 364 ARG cc_start: 0.4327 (mtt180) cc_final: 0.3337 (ttp-170) REVERT: A 429 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.5710 (m-70) REVERT: A 468 TYR cc_start: 0.6061 (t80) cc_final: 0.5766 (t80) REVERT: B 288 LYS cc_start: 0.6538 (tmmt) cc_final: 0.6296 (tptt) REVERT: B 373 TYR cc_start: 0.8599 (t80) cc_final: 0.8223 (t80) REVERT: B 411 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5667 (mp0) REVERT: B 467 HIS cc_start: 0.3651 (OUTLIER) cc_final: 0.3140 (t-170) REVERT: C 238 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5771 (ptpt) REVERT: C 296 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (mt) REVERT: C 384 CYS cc_start: 0.6009 (t) cc_final: 0.5782 (t) REVERT: D 177 ARG cc_start: 0.7793 (tpt-90) cc_final: 0.7588 (ttt-90) REVERT: D 306 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8303 (p) REVERT: D 358 PHE cc_start: 0.6889 (m-80) cc_final: 0.6633 (m-80) REVERT: D 445 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5642 (tt) outliers start: 64 outliers final: 54 residues processed: 199 average time/residue: 0.3187 time to fit residues: 90.0248 Evaluate side-chains 202 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 397 CYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.204762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.172524 restraints weight = 59146.994| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.32 r_work: 0.4141 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 15847 Z= 0.141 Angle : 0.564 8.419 22011 Z= 0.320 Chirality : 0.039 0.143 2392 Planarity : 0.003 0.038 2220 Dihedral : 24.474 80.495 3412 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.77 % Allowed : 30.15 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1420 helix: 1.39 (0.22), residues: 572 sheet: -1.95 (0.43), residues: 152 loop : -1.45 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.008 0.001 TYR B 200 PHE 0.012 0.001 PHE C 473 TRP 0.009 0.001 TRP A 363 HIS 0.003 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15832) covalent geometry : angle 0.55936 / 0.32 (22002) hydrogen bonds : bond 0.04060 / 2.89 ( 715) hydrogen bonds : angle 4.11404 / 2.93 ( 1819) metal coordination : bond 0.02837 / 0.98 ( 15) metal coordination : angle 3.47684 / 1.55 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6852.12 seconds wall clock time: 117 minutes 13.25 seconds (7033.25 seconds total)