Starting phenix.real_space_refine on Sun Jul 5 19:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oh4_70483/07_2026/9oh4_70483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oh4_70483/07_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_70483/07_2026/9oh4_70483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oh4_70483/07_2026/9oh4_70483.map" model { file = "/net/cci-nas-00/data/ceres_data/9oh4_70483/07_2026/9oh4_70483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oh4_70483/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.43, per 1000 atoms: 0.15 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: 2.79 Conformation dependent library (CDL) restraints added in 673.1 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: 4.79 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: 6.45 Time building geometry restraints manager: 3.80 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=" C3' DT F 8 " pdb=" C2' DT F 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+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=" C3' DA F 27 " pdb=" C2' DA F 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.90e+00 bond pdb=" C3' DA H 27 " pdb=" C2' DA H 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 ... (remaining 29690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 51578 2.10 - 4.20: 1731 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 - 0.119: 2366 0.119 - 0.238: 21 0.238 - 0.358: 0 0.358 - 0.477: 0 0.477 - 0.596: 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 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.89e+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 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.61e+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 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.41e+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: 4.870 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 36.020 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 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= 0.376 Angle : 0.696 18.812 22011 Z= 0.514 Chirality : 0.049 0.596 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 0.00451 / 0.36 (15832) covalent geometry : angle 0.67543 / 0.51 (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 : 0.507 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: 0.2881 time to fit residues: 82.0848 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 : 0.737 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.205181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.173727 restraints weight = 61879.843| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.40 r_work: 0.4172 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15847 Z= 0.186 Angle : 0.622 10.117 22011 Z= 0.356 Chirality : 0.039 0.167 2392 Planarity : 0.005 0.099 2220 Dihedral : 25.607 85.199 3495 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.28 % Favored : 89.58 % Rotamer: Outliers : 4.70 % Allowed : 28.79 % Favored : 66.52 % 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: -1.33 (0.23), residues: 1420 helix: 0.42 (0.21), residues: 576 sheet: -2.56 (0.34), residues: 208 loop : -1.45 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.007 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 A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (15832) covalent geometry : angle 0.61315 / 0.36 (22002) hydrogen bonds : bond 0.06579 / 4.71 ( 715) hydrogen bonds : angle 5.07036 / 3.59 ( 1819) metal coordination : bond 0.02033 / 0.79 ( 15) metal coordination : angle 5.16168 / 2.16 ( 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 201 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 0.647 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: 0.8509 (tt) cc_final: 0.7681 (mp) REVERT: A 364 ARG cc_start: 0.4164 (mtt180) cc_final: 0.3196 (ttp-170) REVERT: A 429 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.5623 (m-70) REVERT: A 461 ARG cc_start: 0.7736 (ttp80) cc_final: 0.5575 (mmp-170) REVERT: A 468 TYR cc_start: 0.6097 (t80) cc_final: 0.5787 (t80) REVERT: B 288 LYS cc_start: 0.6296 (tmmt) cc_final: 0.5986 (tptt) REVERT: B 467 HIS cc_start: 0.3683 (OUTLIER) cc_final: 0.3169 (t-170) REVERT: D 306 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8301 (p) REVERT: D 343 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: D 358 PHE cc_start: 0.6924 (m-80) cc_final: 0.6534 (m-80) REVERT: D 373 TYR cc_start: 0.8530 (t80) cc_final: 0.8255 (t80) outliers start: 62 outliers final: 52 residues processed: 196 average time/residue: 0.2669 time to fit residues: 76.2173 Evaluate side-chains 193 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 197 THR 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 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 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 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 489 LEU 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 329 GLN Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 397 CYS 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 329 GLN Chi-restraints excluded: chain D residue 343 GLU 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 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: 1.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.204989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.173366 restraints weight = 61819.223| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.40 r_work: 0.4172 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 15847 Z= 0.165 Angle : 0.587 12.213 22011 Z= 0.337 Chirality : 0.039 0.166 2392 Planarity : 0.005 0.097 2220 Dihedral : 25.476 85.679 3445 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % Rotamer: Outliers : 5.68 % Allowed : 27.95 % 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: -1.08 (0.23), residues: 1420 helix: 0.76 (0.22), residues: 572 sheet: -2.45 (0.35), residues: 208 loop : -1.42 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 337 TYR 0.008 0.001 TYR B 200 PHE 0.012 0.001 PHE A 345 TRP 0.011 0.002 TRP C 363 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (15832) covalent geometry : angle 0.57782 / 0.34 (22002) hydrogen bonds : bond 0.05472 / 3.81 ( 715) hydrogen bonds : angle 4.62733 / 3.28 ( 1819) metal coordination : bond 0.02982 / 1.20 ( 15) metal coordination : angle 5.21482 / 2.24 ( 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 216 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 141 time to evaluate : 0.680 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: 0.6449 (OUTLIER) cc_final: 0.5935 (tm-30) REVERT: A 296 LEU cc_start: 0.8486 (tt) cc_final: 0.7666 (mp) REVERT: A 364 ARG cc_start: 0.4184 (mtt180) cc_final: 0.3212 (ttp-170) REVERT: A 429 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.5657 (m-70) REVERT: A 461 ARG cc_start: 0.7578 (ttp80) cc_final: 0.5465 (mmp-170) REVERT: A 468 TYR cc_start: 0.6156 (t80) cc_final: 0.5840 (t80) REVERT: B 288 LYS cc_start: 0.6368 (tmmt) cc_final: 0.6072 (tptt) REVERT: B 467 HIS cc_start: 0.3634 (OUTLIER) cc_final: 0.3128 (t-170) REVERT: C 384 CYS cc_start: 0.6106 (t) cc_final: 0.5882 (t) REVERT: D 306 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8254 (p) REVERT: D 358 PHE cc_start: 0.6993 (m-80) cc_final: 0.6618 (m-80) REVERT: D 373 TYR cc_start: 0.8515 (t80) cc_final: 0.8293 (t80) outliers start: 75 outliers final: 60 residues processed: 208 average time/residue: 0.2775 time to fit residues: 84.1701 Evaluate side-chains 203 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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 B residue 155 ASP 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 329 GLN 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 427 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 467 HIS 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 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 370 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 397 CYS 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 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: 0.7980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.206385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.175293 restraints weight = 61672.987| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.37 r_work: 0.4192 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 15847 Z= 0.140 Angle : 0.570 11.048 22011 Z= 0.326 Chirality : 0.039 0.179 2392 Planarity : 0.004 0.096 2220 Dihedral : 25.329 85.205 3434 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % Rotamer: Outliers : 5.76 % Allowed : 27.42 % Favored : 66.82 % 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: -0.84 (0.23), residues: 1420 helix: 1.03 (0.22), residues: 572 sheet: -2.26 (0.39), residues: 180 loop : -1.47 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.008 0.001 TYR B 200 PHE 0.011 0.001 PHE C 473 TRP 0.008 0.001 TRP B 363 HIS 0.006 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (15832) covalent geometry : angle 0.56290 / 0.33 (22002) hydrogen bonds : bond 0.04994 / 3.49 ( 715) hydrogen bonds : angle 4.36762 / 3.10 ( 1819) metal coordination : bond 0.02647 / 0.91 ( 15) metal coordination : angle 4.42109 / 1.96 ( 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 220 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 144 time to evaluate : 0.710 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: 0.6559 (OUTLIER) cc_final: 0.5975 (tm-30) REVERT: A 296 LEU cc_start: 0.8472 (tt) cc_final: 0.7673 (mp) REVERT: A 364 ARG cc_start: 0.4196 (mtt180) cc_final: 0.3170 (ttp-170) REVERT: A 429 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.5670 (m-70) REVERT: A 461 ARG cc_start: 0.7502 (ttp80) cc_final: 0.5467 (mmt-90) REVERT: A 468 TYR cc_start: 0.6070 (t80) cc_final: 0.5789 (t80) REVERT: B 288 LYS cc_start: 0.6344 (tmmt) cc_final: 0.6030 (tptt) REVERT: B 467 HIS cc_start: 0.3605 (OUTLIER) cc_final: 0.3045 (t-170) REVERT: C 227 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5442 (pm20) REVERT: C 238 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5725 (ptpt) REVERT: C 296 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7584 (mt) REVERT: D 306 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8206 (p) REVERT: D 358 PHE cc_start: 0.6915 (m-80) cc_final: 0.6556 (m-80) outliers start: 76 outliers final: 59 residues processed: 211 average time/residue: 0.3001 time to fit residues: 90.7544 Evaluate side-chains 203 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 137 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 453 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 377 ASN 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 489 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 227 GLU 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 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 196 ASN 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 329 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 375 LEU 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=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: 0.9990 chunk 132 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4639 r_free = 0.4639 target = 0.204335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172618 restraints weight = 61883.630| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.40 r_work: 0.4162 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 15847 Z= 0.179 Angle : 0.591 12.219 22011 Z= 0.339 Chirality : 0.039 0.166 2392 Planarity : 0.005 0.096 2220 Dihedral : 25.335 85.121 3432 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.79 % Favored : 90.07 % Rotamer: Outliers : 5.91 % Allowed : 27.50 % 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: -1.00 (0.23), residues: 1420 helix: 0.94 (0.21), residues: 572 sheet: -2.50 (0.34), residues: 208 loop : -1.47 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.008 0.001 TYR B 200 PHE 0.014 0.001 PHE C 473 TRP 0.012 0.002 TRP C 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (15832) covalent geometry : angle 0.58288 / 0.34 (22002) hydrogen bonds : bond 0.05062 / 3.54 ( 715) hydrogen bonds : angle 4.44153 / 3.16 ( 1819) metal coordination : bond 0.03603 / 1.33 ( 15) metal coordination : angle 4.95242 / 2.22 ( 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 215 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 0.745 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: 0.6439 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: A 296 LEU cc_start: 0.8549 (tt) cc_final: 0.7739 (mp) REVERT: A 364 ARG cc_start: 0.4275 (mtt180) cc_final: 0.3318 (ttp-170) REVERT: A 429 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.5703 (m-70) REVERT: A 468 TYR cc_start: 0.6189 (t80) cc_final: 0.5873 (t80) REVERT: A 489 LEU cc_start: 0.5052 (tp) cc_final: 0.4825 (tp) REVERT: B 288 LYS cc_start: 0.6417 (tmmt) cc_final: 0.6123 (tptt) REVERT: B 411 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: C 296 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7679 (mt) REVERT: C 326 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6862 (tp) REVERT: D 306 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 358 PHE cc_start: 0.6975 (m-80) cc_final: 0.6608 (m-80) REVERT: D 445 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5821 (tt) outliers start: 78 outliers final: 69 residues processed: 205 average time/residue: 0.2723 time to fit residues: 82.0627 Evaluate side-chains 212 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 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 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 489 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 237 VAL 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 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 397 CYS Chi-restraints excluded: chain D residue 438 SER 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 477 SER Chi-restraints excluded: chain D residue 489 LEU 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: 10.0000 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.203913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.172536 restraints weight = 61766.675| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.34 r_work: 0.4162 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15847 Z= 0.180 Angle : 0.597 9.951 22011 Z= 0.341 Chirality : 0.039 0.163 2392 Planarity : 0.004 0.095 2220 Dihedral : 25.335 85.383 3430 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.79 % 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 : 1.67 % 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: -1.06 (0.23), residues: 1420 helix: 0.86 (0.21), residues: 576 sheet: -2.53 (0.34), residues: 208 loop : -1.49 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 364 TYR 0.009 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 0.00376 / 0.18 (15832) covalent geometry : angle 0.58816 / 0.34 (22002) hydrogen bonds : bond 0.05078 / 3.56 ( 715) hydrogen bonds : angle 4.42941 / 3.16 ( 1819) metal coordination : bond 0.01841 / 0.77 ( 15) metal coordination : angle 5.04144 / 2.08 ( 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 224 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 139 time to evaluate : 0.918 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 296 LEU cc_start: 0.8531 (tt) cc_final: 0.7698 (mp) REVERT: A 364 ARG cc_start: 0.4305 (mtt180) cc_final: 0.3256 (ttp-170) REVERT: A 429 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.5696 (m-70) REVERT: A 468 TYR cc_start: 0.6102 (t80) cc_final: 0.5788 (t80) REVERT: A 489 LEU cc_start: 0.5127 (tp) cc_final: 0.4890 (tp) REVERT: B 288 LYS cc_start: 0.6360 (tmmt) cc_final: 0.6078 (tptt) REVERT: B 411 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5717 (mp0) REVERT: B 467 HIS cc_start: 0.3616 (OUTLIER) cc_final: 0.3071 (t-170) REVERT: C 238 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5850 (ptpt) REVERT: C 296 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 326 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6913 (tp) REVERT: D 306 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8413 (p) REVERT: D 358 PHE cc_start: 0.7006 (m-80) cc_final: 0.6627 (m-80) REVERT: D 445 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5798 (tt) outliers start: 85 outliers final: 69 residues processed: 214 average time/residue: 0.2731 time to fit residues: 85.5206 Evaluate side-chains 215 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 138 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 326 LEU 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 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 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 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 195 LEU 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 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 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 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 477 SER 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: 1.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4645 r_free = 0.4645 target = 0.205018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.173466 restraints weight = 61679.580| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.39 r_work: 0.4177 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 15847 Z= 0.150 Angle : 0.577 11.854 22011 Z= 0.330 Chirality : 0.039 0.145 2392 Planarity : 0.003 0.030 2220 Dihedral : 25.269 85.194 3425 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.29 % Allowed : 27.27 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -0.91 (0.23), residues: 1420 helix: 0.99 (0.21), residues: 576 sheet: -2.33 (0.38), residues: 180 loop : -1.53 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 299 TYR 0.009 0.001 TYR B 200 PHE 0.012 0.001 PHE A 345 TRP 0.009 0.001 TRP C 363 HIS 0.015 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (15832) covalent geometry : angle 0.56922 / 0.33 (22002) hydrogen bonds : bond 0.04821 / 3.39 ( 715) hydrogen bonds : angle 4.30525 / 3.08 ( 1819) metal coordination : bond 0.03437 / 1.25 ( 15) metal coordination : angle 4.65880 / 2.06 ( 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 224 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 141 time to evaluate : 0.724 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 296 LEU cc_start: 0.8465 (tt) cc_final: 0.7652 (mp) REVERT: A 364 ARG cc_start: 0.4255 (mtt180) cc_final: 0.3176 (ttp-170) REVERT: A 429 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5710 (m-70) REVERT: A 468 TYR cc_start: 0.6157 (t80) cc_final: 0.5844 (t80) REVERT: A 489 LEU cc_start: 0.5094 (tp) cc_final: 0.4872 (tp) REVERT: B 288 LYS cc_start: 0.6583 (tmmt) cc_final: 0.6277 (tptt) REVERT: B 411 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5655 (mp0) REVERT: B 467 HIS cc_start: 0.3578 (OUTLIER) cc_final: 0.3054 (t-170) REVERT: C 238 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5790 (ptpt) REVERT: C 296 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7616 (mt) REVERT: C 326 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6843 (tp) REVERT: D 306 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8240 (p) REVERT: D 358 PHE cc_start: 0.6971 (m-80) cc_final: 0.6618 (m-80) REVERT: D 445 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5679 (tt) outliers start: 83 outliers final: 69 residues processed: 213 average time/residue: 0.2866 time to fit residues: 88.7291 Evaluate side-chains 216 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 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 B residue 155 ASP 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 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 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 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 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 237 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 306 VAL 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 405 LEU Chi-restraints excluded: chain D residue 438 SER 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 477 SER 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: 0.6980 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.205898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.174505 restraints weight = 61635.015| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.41 r_work: 0.4192 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15847 Z= 0.137 Angle : 0.566 9.162 22011 Z= 0.325 Chirality : 0.039 0.141 2392 Planarity : 0.003 0.030 2220 Dihedral : 25.213 84.561 3423 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 5.91 % Allowed : 27.73 % 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: -0.80 (0.23), residues: 1420 helix: 1.09 (0.21), residues: 576 sheet: -2.23 (0.39), residues: 180 loop : -1.50 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.009 0.001 TYR B 200 PHE 0.012 0.001 PHE D 418 TRP 0.009 0.001 TRP B 363 HIS 0.005 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (15832) covalent geometry : angle 0.55910 / 0.32 (22002) hydrogen bonds : bond 0.04626 / 3.27 ( 715) hydrogen bonds : angle 4.20946 / 3.00 ( 1819) metal coordination : bond 0.01833 / 0.66 ( 15) metal coordination : angle 4.27404 / 1.78 ( 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 219 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 141 time to evaluate : 0.691 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 296 LEU cc_start: 0.8466 (tt) cc_final: 0.7673 (mp) REVERT: A 364 ARG cc_start: 0.4214 (mtt180) cc_final: 0.3143 (ttp-170) REVERT: A 429 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5719 (m-70) REVERT: A 468 TYR cc_start: 0.6109 (t80) cc_final: 0.5821 (t80) REVERT: A 489 LEU cc_start: 0.5057 (tp) cc_final: 0.4844 (tp) REVERT: B 288 LYS cc_start: 0.6495 (tmmt) cc_final: 0.6186 (tptt) REVERT: B 337 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6960 (ttt-90) REVERT: B 411 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: B 467 HIS cc_start: 0.3618 (OUTLIER) cc_final: 0.3104 (t-170) REVERT: C 238 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5790 (ptpt) REVERT: C 296 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (mt) REVERT: D 306 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8277 (p) REVERT: D 358 PHE cc_start: 0.6805 (m-80) cc_final: 0.6537 (m-80) REVERT: D 445 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5642 (tt) outliers start: 78 outliers final: 65 residues processed: 208 average time/residue: 0.2976 time to fit residues: 90.1371 Evaluate side-chains 211 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 326 LEU 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 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 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 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 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 489 LEU 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 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 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 291 SER Chi-restraints excluded: chain D residue 306 VAL 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 405 LEU Chi-restraints excluded: chain D residue 438 SER 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 491 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4659 r_free = 0.4659 target = 0.206472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.175187 restraints weight = 61403.107| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.40 r_work: 0.4237 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15847 Z= 0.134 Angle : 0.563 11.140 22011 Z= 0.322 Chirality : 0.038 0.141 2392 Planarity : 0.003 0.029 2220 Dihedral : 25.165 83.764 3422 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 5.61 % Allowed : 28.11 % Favored : 66.29 % 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: -0.74 (0.23), residues: 1420 helix: 1.17 (0.21), residues: 576 sheet: -2.23 (0.39), residues: 180 loop : -1.48 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.009 0.001 TYR D 373 PHE 0.013 0.001 PHE D 418 TRP 0.009 0.001 TRP A 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (15832) covalent geometry : angle 0.55550 / 0.32 (22002) hydrogen bonds : bond 0.04518 / 3.20 ( 715) hydrogen bonds : angle 4.16446 / 2.97 ( 1819) metal coordination : bond 0.02482 / 0.88 ( 15) metal coordination : angle 4.52206 / 1.95 ( 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 223 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 0.789 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: symmetry clash REVERT: A 296 LEU cc_start: 0.8465 (tt) cc_final: 0.7671 (mp) REVERT: A 364 ARG cc_start: 0.4227 (mtt180) cc_final: 0.3130 (ttp-170) REVERT: A 429 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5683 (m-70) REVERT: A 468 TYR cc_start: 0.6120 (t80) cc_final: 0.5837 (t80) REVERT: B 288 LYS cc_start: 0.6567 (tmmt) cc_final: 0.6286 (tptt) REVERT: B 323 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7081 (tppt) REVERT: B 337 ARG cc_start: 0.7233 (ttt-90) cc_final: 0.6982 (ttt-90) REVERT: B 411 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5612 (mp0) REVERT: B 467 HIS cc_start: 0.3558 (OUTLIER) cc_final: 0.3043 (t-170) REVERT: C 238 LYS cc_start: 0.6476 (OUTLIER) cc_final: 0.5802 (ptpt) REVERT: C 296 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7569 (mt) REVERT: D 177 ARG cc_start: 0.7828 (tpt-90) cc_final: 0.7580 (ttt-90) REVERT: D 306 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8266 (p) REVERT: D 358 PHE cc_start: 0.6795 (m-80) cc_final: 0.6531 (m-80) REVERT: D 445 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5640 (tt) outliers start: 74 outliers final: 61 residues processed: 214 average time/residue: 0.3126 time to fit residues: 96.2902 Evaluate side-chains 213 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 144 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 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 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 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 323 LYS 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 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 489 LEU 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 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 427 ILE 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 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 397 CYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 405 LEU 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 44 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.206928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.176008 restraints weight = 63921.664| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.45 r_work: 0.4202 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 15847 Z= 0.134 Angle : 0.561 8.036 22011 Z= 0.322 Chirality : 0.039 0.141 2392 Planarity : 0.003 0.029 2220 Dihedral : 25.127 83.149 3417 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.38 % Allowed : 28.41 % Favored : 66.21 % 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: -0.63 (0.23), residues: 1420 helix: 1.23 (0.21), residues: 576 sheet: -1.93 (0.43), residues: 152 loop : -1.53 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.009 0.001 TYR B 200 PHE 0.013 0.001 PHE D 418 TRP 0.008 0.001 TRP A 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (15832) covalent geometry : angle 0.55565 / 0.32 (22002) hydrogen bonds : bond 0.04507 / 3.19 ( 715) hydrogen bonds : angle 4.14161 / 2.95 ( 1819) metal coordination : bond 0.02268 / 0.85 ( 15) metal coordination : angle 4.03139 / 1.65 ( 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 213 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 0.715 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: 0.8453 (tt) cc_final: 0.7657 (mp) REVERT: A 364 ARG cc_start: 0.4240 (mtt180) cc_final: 0.3218 (ttp-170) REVERT: A 429 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.5669 (m-70) REVERT: A 468 TYR cc_start: 0.6060 (t80) cc_final: 0.5791 (t80) REVERT: B 288 LYS cc_start: 0.6680 (tmmt) cc_final: 0.6374 (tptt) REVERT: B 323 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7151 (tppt) REVERT: B 329 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: B 337 ARG cc_start: 0.7213 (ttt-90) cc_final: 0.6975 (ttt-90) REVERT: B 411 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5611 (mp0) REVERT: B 467 HIS cc_start: 0.3622 (OUTLIER) cc_final: 0.3111 (t-170) REVERT: C 238 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5810 (ptpt) REVERT: C 296 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7604 (mt) REVERT: D 177 ARG cc_start: 0.7798 (tpt-90) cc_final: 0.7554 (ttt-90) REVERT: D 306 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8282 (p) REVERT: D 358 PHE cc_start: 0.6855 (m-80) cc_final: 0.6590 (m-80) REVERT: D 445 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5576 (tt) outliers start: 71 outliers final: 57 residues processed: 204 average time/residue: 0.3086 time to fit residues: 90.4977 Evaluate side-chains 207 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 141 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 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 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 282 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 323 LYS 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 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 489 LEU 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 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 427 ILE 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 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 397 CYS Chi-restraints excluded: chain D residue 405 LEU 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: 0.1980 chunk 16 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4666 r_free = 0.4666 target = 0.207539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.176884 restraints weight = 64287.699| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.41 r_work: 0.4210 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 15847 Z= 0.129 Angle : 0.556 10.646 22011 Z= 0.319 Chirality : 0.038 0.140 2392 Planarity : 0.003 0.029 2220 Dihedral : 25.099 82.439 3415 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.23 % Allowed : 28.64 % 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: -0.55 (0.23), residues: 1420 helix: 1.36 (0.21), residues: 572 sheet: -1.89 (0.43), residues: 152 loop : -1.51 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.008 0.001 TYR B 200 PHE 0.014 0.001 PHE D 418 TRP 0.008 0.001 TRP A 363 HIS 0.004 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (15832) covalent geometry : angle 0.54936 / 0.32 (22002) hydrogen bonds : bond 0.04417 / 3.14 ( 715) hydrogen bonds : angle 4.09484 / 2.92 ( 1819) metal coordination : bond 0.02795 / 1.01 ( 15) metal coordination : angle 4.15554 / 1.81 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6282.30 seconds wall clock time: 107 minutes 27.68 seconds (6447.68 seconds total)