Starting phenix.real_space_refine on Sun Aug 24 14:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7adk_11729/08_2025/7adk_11729.map" } resolution = 2.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 6690 2.51 5 N 1782 2.21 5 O 2128 1.98 5 H 10260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20869 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9710 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 11159 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 14, 'TRANS': 689} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.72, per 1000 atoms: 0.18 Number of scatterers: 20869 At special positions: 0 Unit cell: (98.77, 102.09, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 2128 8.00 N 1782 7.00 C 6690 6.00 H 10260 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 704.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 34.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.529A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 removed outlier: 4.335A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.932A pdb=" N LYS A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 264 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.779A pdb=" N TRP A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 291 No H-bonds generated for 'chain 'A' and resid 290 through 291' Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.814A pdb=" N SER A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 388 removed outlier: 4.354A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.523A pdb=" N TYR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.821A pdb=" N VAL A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.610A pdb=" N GLY A 588 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.747A pdb=" N GLU A 659 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 710 removed outlier: 3.668A pdb=" N LYS A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.565A pdb=" N GLU B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 3.518A pdb=" N TYR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 219 through 227 removed outlier: 4.112A pdb=" N ALA B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.791A pdb=" N ASN B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.846A pdb=" N ILE B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 removed outlier: 3.689A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 360 through 376 removed outlier: 4.395A pdb=" N ASP B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 366 " --> pdb=" O GLN B 362 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 413 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 639 through 643 removed outlier: 4.076A pdb=" N LYS B 642 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 removed outlier: 4.470A pdb=" N LYS B 656 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.786A pdb=" N TYR B 673 " --> pdb=" O TYR B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.686A pdb=" N THR B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 removed outlier: 4.063A pdb=" N ASN B 720 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 3.782A pdb=" N LYS B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 850 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 7.351A pdb=" N GLU A 140 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL A 178 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU A 142 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 379 removed outlier: 8.627A pdb=" N SER A 448 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 417 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG A 450 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 419 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LYS A 452 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 421 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET A 454 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 516 through 517 removed outlier: 5.609A pdb=" N TYR A 517 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 554 " --> pdb=" O ASP A 610 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 609 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 641 " --> pdb=" O HIS A 678 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 425 removed outlier: 3.618A pdb=" N SER B 461 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.550A pdb=" N ILE B 542 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS B 442 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B 446 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE B 428 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 836 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 535 through 537 removed outlier: 6.818A pdb=" N GLY B 535 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 727 " --> pdb=" O TYR B 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 594 through 595 removed outlier: 6.842A pdb=" N LYS B 594 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA B 772 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 785 " --> pdb=" O HIS B 775 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER B 777 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 783 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 745 " --> pdb=" O ALA B 788 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 594 through 595 removed outlier: 6.842A pdb=" N LYS B 594 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA B 772 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 770 " --> pdb=" O THR B 765 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR B 765 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 761 " --> pdb=" O TYR B 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 790 through 792 303 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 4674 1.09 - 1.27: 7446 1.27 - 1.45: 3005 1.45 - 1.64: 5938 1.64 - 1.82: 18 Bond restraints: 21081 Sorted by residual: bond pdb=" ND2 ASN A 389 " pdb="HD22 ASN A 389 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N LEU B 191 " pdb=" H LEU B 191 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH1 ARG A 316 " pdb="HH11 ARG A 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CD2 PHE A 390 " pdb=" HD2 PHE A 390 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 TYR B 660 " pdb=" HE2 TYR B 660 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 21076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 32502 3.05 - 6.09: 4451 6.09 - 9.14: 983 9.14 - 12.18: 17 12.18 - 15.23: 1 Bond angle restraints: 37954 Sorted by residual: angle pdb=" CA PHE B 229 " pdb=" CB PHE B 229 " pdb=" CG PHE B 229 " ideal model delta sigma weight residual 113.80 122.61 -8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" CA ASP B 270 " pdb=" CB ASP B 270 " pdb=" CG ASP B 270 " ideal model delta sigma weight residual 112.60 120.32 -7.72 1.00e+00 1.00e+00 5.96e+01 angle pdb=" C TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta sigma weight residual 109.95 125.18 -15.23 1.99e+00 2.53e-01 5.85e+01 angle pdb=" CA ASN B 468 " pdb=" CB ASN B 468 " pdb=" CG ASN B 468 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.66e+01 angle pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " pdb=" CG ASP A 420 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.00e+00 1.00e+00 5.35e+01 ... (remaining 37949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8905 17.72 - 35.44: 732 35.44 - 53.16: 204 53.16 - 70.89: 101 70.89 - 88.61: 18 Dihedral angle restraints: 9960 sinusoidal: 5360 harmonic: 4600 Sorted by residual: dihedral pdb=" C TYR A 284 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta harmonic sigma weight residual -122.60 -142.68 20.08 0 2.50e+00 1.60e-01 6.45e+01 dihedral pdb=" CA LYS A 497 " pdb=" C LYS A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 147.49 32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER B 421 " pdb=" C SER B 421 " pdb=" N GLU B 422 " pdb=" CA GLU B 422 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 9957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1153 0.130 - 0.260: 310 0.260 - 0.390: 47 0.390 - 0.520: 11 0.520 - 0.650: 2 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA TYR A 284 " pdb=" N TYR A 284 " pdb=" C TYR A 284 " pdb=" CB TYR A 284 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE B 666 " pdb=" CA ILE B 666 " pdb=" CG1 ILE B 666 " pdb=" CG2 ILE B 666 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CG LEU B 578 " pdb=" CB LEU B 578 " pdb=" CD1 LEU B 578 " pdb=" CD2 LEU B 578 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 1520 not shown) Planarity restraints: 3193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.232 2.00e-02 2.50e+03 1.14e-01 5.19e+02 pdb=" CG TRP A 286 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.058 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " 0.116 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 TRP A 286 " -0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP A 286 " -0.110 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 286 " 0.114 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 286 " -0.193 2.00e-02 2.50e+03 pdb=" HH2 TRP A 286 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 633 " 0.163 2.00e-02 2.50e+03 1.15e-01 3.99e+02 pdb=" CG TYR B 633 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 633 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 633 " -0.109 2.00e-02 2.50e+03 pdb=" CE1 TYR B 633 " -0.103 2.00e-02 2.50e+03 pdb=" CE2 TYR B 633 " -0.082 2.00e-02 2.50e+03 pdb=" CZ TYR B 633 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 633 " 0.244 2.00e-02 2.50e+03 pdb=" HD1 TYR B 633 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 TYR B 633 " -0.100 2.00e-02 2.50e+03 pdb=" HE1 TYR B 633 " -0.147 2.00e-02 2.50e+03 pdb=" HE2 TYR B 633 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.257 2.00e-02 2.50e+03 1.10e-01 3.60e+02 pdb=" CG TYR A 284 " -0.214 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.123 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR A 284 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 284 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 284 " 0.084 2.00e-02 2.50e+03 ... (remaining 3190 not shown) Histogram of nonbonded interaction distances: 0.21 - 1.09: 5 1.09 - 1.96: 473 1.96 - 2.84: 43121 2.84 - 3.72: 89607 3.72 - 4.60: 149497 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282703 Sorted by model distance: nonbonded pdb=" CD LYS A 484 " pdb=" HZ2 LYS B 478 " model vdw 0.207 2.200 nonbonded pdb=" HB3 LYS A 484 " pdb=" HE3 LYS B 478 " model vdw 0.542 2.440 nonbonded pdb=" HB3 LYS A 484 " pdb=" CE LYS B 478 " model vdw 0.970 2.920 nonbonded pdb=" HD2 LYS A 484 " pdb=" HZ2 LYS B 478 " model vdw 0.971 2.270 nonbonded pdb=" HG2 LYS A 484 " pdb=" HZ1 LYS B 478 " model vdw 1.003 1.816 ... (remaining 282698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.080 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 : 0.014 0.433 10822 Z= 0.916 Angle : 2.029 15.226 14569 Z= 1.353 Chirality : 0.123 0.650 1523 Planarity : 0.016 0.266 1914 Dihedral : 15.241 88.607 4082 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.43 % Allowed : 7.43 % Favored : 92.13 % Cbeta Deviations : 1.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.21), residues: 1313 helix: -3.00 (0.20), residues: 316 sheet: 0.00 (0.43), residues: 118 loop : -1.38 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 352 TYR 0.246 0.025 TYR A 284 PHE 0.107 0.015 PHE B 240 TRP 0.123 0.027 TRP A 286 HIS 0.016 0.006 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.01367 (10821) covalent geometry : angle 2.02910 (14569) hydrogen bonds : bond 0.22510 ( 303) hydrogen bonds : angle 8.46005 ( 777) Misc. bond : bond 0.43319 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 245 time to evaluate : 0.609 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 159 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8035 (mttt) REVERT: A 174 LYS cc_start: 0.7886 (tptt) cc_final: 0.7128 (ttpt) REVERT: A 222 LYS cc_start: 0.7385 (mttt) cc_final: 0.6829 (mtpt) REVERT: A 276 LYS cc_start: 0.7332 (mmmm) cc_final: 0.7035 (ttpp) REVERT: A 305 LYS cc_start: 0.6242 (pttp) cc_final: 0.6035 (mtmm) REVERT: A 391 LYS cc_start: 0.7306 (mtmm) cc_final: 0.7077 (mtmm) REVERT: A 399 SER cc_start: 0.8154 (p) cc_final: 0.7755 (m) REVERT: A 472 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6652 (ttmm) REVERT: A 475 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6729 (mm110) REVERT: A 523 ARG cc_start: 0.6912 (ttm-80) cc_final: 0.6592 (ttm-80) REVERT: A 634 GLU cc_start: 0.6893 (tt0) cc_final: 0.6320 (tm-30) REVERT: A 640 GLU cc_start: 0.7252 (tt0) cc_final: 0.6857 (mp0) REVERT: A 647 GLU cc_start: 0.6958 (mp0) cc_final: 0.6751 (mm-30) REVERT: B 165 THR cc_start: 0.7416 (t) cc_final: 0.7179 (t) REVERT: B 169 ASP cc_start: 0.7046 (m-30) cc_final: 0.6822 (m-30) REVERT: B 276 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6247 (mp0) REVERT: B 434 GLU cc_start: 0.6714 (mp0) cc_final: 0.6339 (mp0) REVERT: B 449 SER cc_start: 0.7959 (t) cc_final: 0.7410 (m) REVERT: B 507 PHE cc_start: 0.7485 (t80) cc_final: 0.7252 (t80) REVERT: B 558 TYR cc_start: 0.8202 (p90) cc_final: 0.7977 (p90) REVERT: B 642 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7918 (mtpp) REVERT: B 739 LYS cc_start: 0.6528 (mttt) cc_final: 0.6317 (mtpt) REVERT: B 828 MET cc_start: 0.7173 (ttt) cc_final: 0.6673 (mmm) REVERT: B 830 LYS cc_start: 0.7463 (pttt) cc_final: 0.7016 (pttm) outliers start: 5 outliers final: 3 residues processed: 249 average time/residue: 1.1713 time to fit residues: 315.3761 Evaluate side-chains 157 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 260 ASN A 369 ASN A 440 GLN A 458 ASN A 461 GLN A 529 ASN A 581 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 671 ASN A 711 ASN B 194 GLN B 402 GLN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN B 733 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.242688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.213512 restraints weight = 33558.114| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.93 r_work: 0.4457 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 10822 Z= 0.154 Angle : 0.693 8.523 14569 Z= 0.376 Chirality : 0.044 0.209 1523 Planarity : 0.004 0.064 1914 Dihedral : 7.369 40.012 1444 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.94 % Allowed : 13.31 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.22), residues: 1313 helix: -1.93 (0.24), residues: 332 sheet: 0.37 (0.43), residues: 116 loop : -1.36 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 356 TYR 0.051 0.002 TYR A 284 PHE 0.015 0.002 PHE B 445 TRP 0.012 0.002 TRP B 401 HIS 0.005 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00341 (10821) covalent geometry : angle 0.69292 (14569) hydrogen bonds : bond 0.04834 ( 303) hydrogen bonds : angle 5.96124 ( 777) Misc. bond : bond 0.02167 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.349 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: A 174 LYS cc_start: 0.7983 (tptt) cc_final: 0.7455 (ttpt) REVERT: A 222 LYS cc_start: 0.7506 (mttt) cc_final: 0.6987 (mtpt) REVERT: A 284 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.5315 (p90) REVERT: A 304 GLU cc_start: 0.6685 (tt0) cc_final: 0.6393 (tt0) REVERT: A 305 LYS cc_start: 0.7023 (pttp) cc_final: 0.6463 (mtmm) REVERT: A 309 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5784 (mppt) REVERT: A 397 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.5727 (mtm-85) REVERT: A 405 ASN cc_start: 0.7918 (m-40) cc_final: 0.7698 (m110) REVERT: A 441 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7499 (pttm) REVERT: A 472 LYS cc_start: 0.7432 (ttpt) cc_final: 0.7150 (ttmm) REVERT: A 475 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7463 (mm110) REVERT: A 617 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7557 (pp) REVERT: A 640 GLU cc_start: 0.7948 (tt0) cc_final: 0.7472 (mt-10) REVERT: B 192 LYS cc_start: 0.6793 (ptpt) cc_final: 0.5971 (tptt) REVERT: B 293 LYS cc_start: 0.7595 (tttt) cc_final: 0.7363 (mptm) REVERT: B 434 GLU cc_start: 0.6910 (mp0) cc_final: 0.6613 (mp0) REVERT: B 642 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8065 (mtpp) REVERT: B 688 GLU cc_start: 0.7362 (mp0) cc_final: 0.6784 (mp0) REVERT: B 830 LYS cc_start: 0.7695 (pttt) cc_final: 0.7341 (pttm) outliers start: 34 outliers final: 9 residues processed: 200 average time/residue: 1.0560 time to fit residues: 228.4492 Evaluate side-chains 149 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 445 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN A 646 ASN A 658 ASN A 663 GLN B 565 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.241736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.214040 restraints weight = 33875.552| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.83 r_work: 0.4449 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 10822 Z= 0.126 Angle : 0.599 8.543 14569 Z= 0.324 Chirality : 0.042 0.196 1523 Planarity : 0.003 0.040 1914 Dihedral : 6.347 34.893 1442 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.85 % Allowed : 16.68 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.22), residues: 1313 helix: -1.34 (0.26), residues: 334 sheet: 0.34 (0.48), residues: 111 loop : -1.35 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.055 0.002 TYR A 284 PHE 0.013 0.001 PHE B 855 TRP 0.009 0.001 TRP A 286 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00291 (10821) covalent geometry : angle 0.59906 (14569) hydrogen bonds : bond 0.03988 ( 303) hydrogen bonds : angle 5.44704 ( 777) Misc. bond : bond 0.01537 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.482 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: A 174 LYS cc_start: 0.7883 (tptt) cc_final: 0.7537 (ttpt) REVERT: A 222 LYS cc_start: 0.7528 (mttt) cc_final: 0.7024 (mtmt) REVERT: A 268 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7278 (mtmt) REVERT: A 290 ASN cc_start: 0.7210 (m-40) cc_final: 0.6685 (m110) REVERT: A 305 LYS cc_start: 0.6976 (pttp) cc_final: 0.6406 (mtmm) REVERT: A 309 LYS cc_start: 0.6360 (mtpt) cc_final: 0.5800 (mppt) REVERT: A 397 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.5786 (mtm-85) REVERT: A 472 LYS cc_start: 0.7347 (ttpt) cc_final: 0.7120 (ttmm) REVERT: A 617 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7545 (pp) REVERT: A 640 GLU cc_start: 0.8013 (tt0) cc_final: 0.7581 (mt-10) REVERT: B 177 LYS cc_start: 0.7154 (ttmt) cc_final: 0.6767 (tmmt) REVERT: B 192 LYS cc_start: 0.6845 (ptpt) cc_final: 0.5980 (tptt) REVERT: B 688 GLU cc_start: 0.7362 (mp0) cc_final: 0.6872 (mp0) REVERT: B 830 LYS cc_start: 0.7718 (pttt) cc_final: 0.7417 (pttm) outliers start: 33 outliers final: 15 residues processed: 165 average time/residue: 1.0298 time to fit residues: 185.2204 Evaluate side-chains 149 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 587 GLN B 216 ASN B 374 GLN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.234795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.206451 restraints weight = 33957.627| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.85 r_work: 0.4354 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 10822 Z= 0.212 Angle : 0.683 20.891 14569 Z= 0.367 Chirality : 0.044 0.208 1523 Planarity : 0.004 0.045 1914 Dihedral : 6.515 36.630 1442 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.03 % Allowed : 17.98 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.22), residues: 1313 helix: -1.17 (0.27), residues: 332 sheet: 0.24 (0.46), residues: 121 loop : -1.52 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 274 TYR 0.051 0.002 TYR A 284 PHE 0.019 0.002 PHE B 855 TRP 0.009 0.002 TRP B 427 HIS 0.007 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00502 (10821) covalent geometry : angle 0.68342 (14569) hydrogen bonds : bond 0.04326 ( 303) hydrogen bonds : angle 5.40284 ( 777) Misc. bond : bond 0.01832 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.569 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: A 174 LYS cc_start: 0.7895 (tptt) cc_final: 0.7615 (ttmm) REVERT: A 222 LYS cc_start: 0.7607 (mttt) cc_final: 0.7128 (mtmt) REVERT: A 268 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7348 (mtmt) REVERT: A 284 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5312 (p90) REVERT: A 305 LYS cc_start: 0.7179 (pttp) cc_final: 0.6596 (mtmm) REVERT: A 309 LYS cc_start: 0.6598 (mtpt) cc_final: 0.6006 (mppt) REVERT: A 472 LYS cc_start: 0.7371 (ttpt) cc_final: 0.7127 (ttmm) REVERT: A 617 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7702 (pp) REVERT: A 640 GLU cc_start: 0.8084 (tt0) cc_final: 0.7646 (mp0) REVERT: B 177 LYS cc_start: 0.7371 (ttmt) cc_final: 0.6875 (ttpp) REVERT: B 190 ARG cc_start: 0.5656 (ptm-80) cc_final: 0.4914 (mtp180) REVERT: B 192 LYS cc_start: 0.7116 (ptpt) cc_final: 0.6023 (tptt) REVERT: B 688 GLU cc_start: 0.7445 (mp0) cc_final: 0.6959 (mp0) REVERT: B 800 PHE cc_start: 0.6554 (m-80) cc_final: 0.6344 (m-80) REVERT: B 830 LYS cc_start: 0.7815 (pttt) cc_final: 0.7482 (pttm) outliers start: 35 outliers final: 21 residues processed: 164 average time/residue: 1.0435 time to fit residues: 186.2512 Evaluate side-chains 158 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 590 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.234607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.206615 restraints weight = 33811.837| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.83 r_work: 0.4355 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 10822 Z= 0.199 Angle : 0.703 30.911 14569 Z= 0.369 Chirality : 0.043 0.205 1523 Planarity : 0.004 0.047 1914 Dihedral : 6.400 37.037 1440 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.63 % Allowed : 18.32 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.21), residues: 1313 helix: -1.14 (0.26), residues: 332 sheet: 0.29 (0.46), residues: 118 loop : -1.63 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.050 0.002 TYR A 284 PHE 0.015 0.002 PHE B 855 TRP 0.006 0.001 TRP A 286 HIS 0.006 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00470 (10821) covalent geometry : angle 0.70291 (14569) hydrogen bonds : bond 0.04129 ( 303) hydrogen bonds : angle 5.33835 ( 777) Misc. bond : bond 0.03762 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.563 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: A 174 LYS cc_start: 0.7891 (tptt) cc_final: 0.7574 (ttmm) REVERT: A 222 LYS cc_start: 0.7638 (mttt) cc_final: 0.7129 (mtmt) REVERT: A 232 GLU cc_start: 0.4808 (mt-10) cc_final: 0.4576 (mt-10) REVERT: A 268 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7347 (mtmt) REVERT: A 283 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6572 (tp30) REVERT: A 284 TYR cc_start: 0.5705 (OUTLIER) cc_final: 0.5198 (p90) REVERT: A 305 LYS cc_start: 0.7006 (pttp) cc_final: 0.6427 (mtmm) REVERT: A 309 LYS cc_start: 0.6479 (mtpt) cc_final: 0.5936 (mppt) REVERT: A 420 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: A 472 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7034 (ttmm) REVERT: A 617 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7687 (pp) REVERT: A 640 GLU cc_start: 0.8108 (tt0) cc_final: 0.7627 (mp0) REVERT: B 177 LYS cc_start: 0.7364 (ttmt) cc_final: 0.6858 (ttpp) REVERT: B 190 ARG cc_start: 0.5665 (ptm-80) cc_final: 0.4918 (mtp180) REVERT: B 192 LYS cc_start: 0.7043 (ptpt) cc_final: 0.5946 (tptt) REVERT: B 642 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8079 (mmmt) REVERT: B 688 GLU cc_start: 0.7472 (mp0) cc_final: 0.6957 (mp0) REVERT: B 830 LYS cc_start: 0.7850 (pttt) cc_final: 0.7474 (pttm) outliers start: 42 outliers final: 27 residues processed: 168 average time/residue: 1.1288 time to fit residues: 206.6523 Evaluate side-chains 165 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 563 ASN A 590 HIS A 645 ASN A 684 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.232765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.204605 restraints weight = 33875.006| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.85 r_work: 0.4339 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4244 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 10822 Z= 0.203 Angle : 0.666 18.443 14569 Z= 0.359 Chirality : 0.043 0.202 1523 Planarity : 0.004 0.046 1914 Dihedral : 6.434 37.107 1440 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.49 % Allowed : 17.72 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.21), residues: 1313 helix: -1.13 (0.26), residues: 340 sheet: 0.39 (0.47), residues: 116 loop : -1.81 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.053 0.002 TYR A 284 PHE 0.016 0.002 PHE B 855 TRP 0.007 0.001 TRP B 427 HIS 0.007 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00475 (10821) covalent geometry : angle 0.66570 (14569) hydrogen bonds : bond 0.04085 ( 303) hydrogen bonds : angle 5.29235 ( 777) Misc. bond : bond 0.02316 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7832 (tptt) cc_final: 0.7564 (ttmm) REVERT: A 222 LYS cc_start: 0.7724 (mttt) cc_final: 0.7194 (mtpt) REVERT: A 232 GLU cc_start: 0.4844 (mt-10) cc_final: 0.4620 (mt-10) REVERT: A 268 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7361 (mtmt) REVERT: A 283 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6726 (tp30) REVERT: A 284 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5239 (p90) REVERT: A 305 LYS cc_start: 0.7065 (pttp) cc_final: 0.6445 (mtmm) REVERT: A 309 LYS cc_start: 0.6498 (mtpt) cc_final: 0.5974 (mppt) REVERT: A 420 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5980 (m-30) REVERT: A 472 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7039 (tppt) REVERT: A 617 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7717 (pp) REVERT: A 640 GLU cc_start: 0.8114 (tt0) cc_final: 0.7657 (mp0) REVERT: A 732 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.3748 (mmtt) REVERT: B 177 LYS cc_start: 0.7411 (ttmt) cc_final: 0.6896 (ttpp) REVERT: B 190 ARG cc_start: 0.5739 (ptm-80) cc_final: 0.4904 (mtp180) REVERT: B 192 LYS cc_start: 0.7206 (ptpt) cc_final: 0.6006 (tptt) REVERT: B 642 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8073 (mmmt) REVERT: B 688 GLU cc_start: 0.7520 (mp0) cc_final: 0.6966 (mp0) REVERT: B 830 LYS cc_start: 0.7845 (pttt) cc_final: 0.7446 (pttm) REVERT: B 852 GLU cc_start: 0.7695 (tt0) cc_final: 0.7347 (tt0) outliers start: 52 outliers final: 27 residues processed: 175 average time/residue: 1.0758 time to fit residues: 205.6933 Evaluate side-chains 166 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 563 ASN A 590 HIS B 176 GLN B 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.229190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.200114 restraints weight = 33616.939| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.96 r_work: 0.4293 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 10822 Z= 0.167 Angle : 0.717 37.563 14569 Z= 0.357 Chirality : 0.042 0.230 1523 Planarity : 0.004 0.044 1914 Dihedral : 6.251 35.726 1440 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.54 % Allowed : 18.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.21), residues: 1313 helix: -1.07 (0.26), residues: 347 sheet: 0.34 (0.47), residues: 118 loop : -1.80 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.052 0.002 TYR A 284 PHE 0.013 0.002 PHE B 855 TRP 0.008 0.001 TRP A 286 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00394 (10821) covalent geometry : angle 0.71692 (14569) hydrogen bonds : bond 0.03758 ( 303) hydrogen bonds : angle 5.18940 ( 777) Misc. bond : bond 0.03246 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7797 (tptt) cc_final: 0.7472 (ttmm) REVERT: A 222 LYS cc_start: 0.7735 (mttt) cc_final: 0.7133 (mtpt) REVERT: A 283 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: A 284 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5038 (p90) REVERT: A 305 LYS cc_start: 0.6918 (pttp) cc_final: 0.6310 (mtmm) REVERT: A 309 LYS cc_start: 0.6410 (mtpt) cc_final: 0.5891 (mppt) REVERT: A 472 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6902 (tppt) REVERT: A 617 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7594 (pp) REVERT: A 640 GLU cc_start: 0.8133 (tt0) cc_final: 0.7802 (mt-10) REVERT: A 732 LYS cc_start: 0.4785 (OUTLIER) cc_final: 0.3997 (mmtt) REVERT: B 177 LYS cc_start: 0.7280 (ttmt) cc_final: 0.6722 (ttpp) REVERT: B 190 ARG cc_start: 0.5570 (ptm-80) cc_final: 0.4664 (mtp180) REVERT: B 192 LYS cc_start: 0.7045 (ptpt) cc_final: 0.5846 (tptt) REVERT: B 642 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8030 (mmmt) REVERT: B 688 GLU cc_start: 0.7442 (mp0) cc_final: 0.6874 (mp0) REVERT: B 830 LYS cc_start: 0.7870 (pttt) cc_final: 0.7473 (pttm) REVERT: B 852 GLU cc_start: 0.7718 (tt0) cc_final: 0.7354 (tt0) outliers start: 41 outliers final: 27 residues processed: 170 average time/residue: 1.1131 time to fit residues: 207.5769 Evaluate side-chains 166 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 96 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 590 HIS A 663 GLN A 684 ASN B 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.229704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.198884 restraints weight = 33094.173| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.02 r_work: 0.4297 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4198 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 10822 Z= 0.155 Angle : 0.647 21.164 14569 Z= 0.340 Chirality : 0.042 0.216 1523 Planarity : 0.003 0.039 1914 Dihedral : 6.076 34.435 1440 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.63 % Allowed : 19.10 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.21), residues: 1313 helix: -0.85 (0.27), residues: 341 sheet: 0.41 (0.47), residues: 118 loop : -1.82 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.050 0.002 TYR A 284 PHE 0.012 0.001 PHE B 855 TRP 0.007 0.001 TRP A 286 HIS 0.006 0.002 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00369 (10821) covalent geometry : angle 0.64686 (14569) hydrogen bonds : bond 0.03581 ( 303) hydrogen bonds : angle 5.13561 ( 777) Misc. bond : bond 0.02754 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7802 (tptt) cc_final: 0.7510 (ttmm) REVERT: A 222 LYS cc_start: 0.7723 (mttt) cc_final: 0.7127 (mtpt) REVERT: A 268 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7322 (mtmt) REVERT: A 283 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6704 (tp30) REVERT: A 284 TYR cc_start: 0.5456 (OUTLIER) cc_final: 0.4913 (p90) REVERT: A 291 LEU cc_start: 0.7587 (mp) cc_final: 0.7348 (tp) REVERT: A 305 LYS cc_start: 0.6949 (pttp) cc_final: 0.6322 (mtmm) REVERT: A 309 LYS cc_start: 0.6392 (mtpt) cc_final: 0.5877 (mppt) REVERT: A 472 LYS cc_start: 0.7246 (ttpt) cc_final: 0.6912 (tppt) REVERT: A 475 GLN cc_start: 0.7415 (mm110) cc_final: 0.7152 (mm110) REVERT: A 617 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7604 (pp) REVERT: A 640 GLU cc_start: 0.8144 (tt0) cc_final: 0.7792 (mt-10) REVERT: A 732 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.3870 (mptt) REVERT: B 177 LYS cc_start: 0.7289 (ttmt) cc_final: 0.6729 (ttpp) REVERT: B 190 ARG cc_start: 0.5582 (ptm-80) cc_final: 0.4733 (mtp180) REVERT: B 192 LYS cc_start: 0.7045 (ptpt) cc_final: 0.5852 (tptt) REVERT: B 468 ASN cc_start: 0.8128 (p0) cc_final: 0.7631 (p0) REVERT: B 642 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8037 (mmmt) REVERT: B 688 GLU cc_start: 0.7485 (mp0) cc_final: 0.6936 (mp0) REVERT: B 830 LYS cc_start: 0.7851 (pttt) cc_final: 0.7414 (pttm) REVERT: B 852 GLU cc_start: 0.7703 (tt0) cc_final: 0.7360 (tt0) outliers start: 42 outliers final: 24 residues processed: 162 average time/residue: 1.1245 time to fit residues: 198.8179 Evaluate side-chains 163 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 563 ASN A 590 HIS A 684 ASN B 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.231498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.201422 restraints weight = 33748.712| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.97 r_work: 0.4340 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4243 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 10822 Z= 0.166 Angle : 0.632 18.718 14569 Z= 0.337 Chirality : 0.042 0.198 1523 Planarity : 0.004 0.036 1914 Dihedral : 6.061 35.028 1440 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.54 % Allowed : 19.62 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.21), residues: 1313 helix: -0.77 (0.27), residues: 341 sheet: 0.39 (0.47), residues: 118 loop : -1.86 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.050 0.002 TYR A 284 PHE 0.014 0.001 PHE B 855 TRP 0.007 0.001 TRP A 286 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00385 (10821) covalent geometry : angle 0.63200 (14569) hydrogen bonds : bond 0.03682 ( 303) hydrogen bonds : angle 5.14778 ( 777) Misc. bond : bond 0.03072 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7846 (tptt) cc_final: 0.7593 (ttmm) REVERT: A 222 LYS cc_start: 0.7718 (mttt) cc_final: 0.7088 (mtpt) REVERT: A 268 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7311 (mtmt) REVERT: A 283 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: A 284 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4937 (p90) REVERT: A 291 LEU cc_start: 0.7634 (mp) cc_final: 0.7348 (tp) REVERT: A 305 LYS cc_start: 0.7040 (pttp) cc_final: 0.6413 (mtmm) REVERT: A 309 LYS cc_start: 0.6432 (mtpt) cc_final: 0.5957 (mppt) REVERT: A 420 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6166 (m-30) REVERT: A 472 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6948 (tppt) REVERT: A 475 GLN cc_start: 0.7384 (mm110) cc_final: 0.7150 (mm110) REVERT: A 498 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7158 (t0) REVERT: A 617 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7659 (pp) REVERT: A 640 GLU cc_start: 0.8176 (tt0) cc_final: 0.7817 (mt-10) REVERT: A 671 ASN cc_start: 0.7923 (t0) cc_final: 0.7613 (t0) REVERT: A 732 LYS cc_start: 0.4994 (OUTLIER) cc_final: 0.4268 (mptp) REVERT: B 177 LYS cc_start: 0.7408 (ttmt) cc_final: 0.6858 (ttpp) REVERT: B 190 ARG cc_start: 0.5786 (ptm-80) cc_final: 0.4899 (mtp180) REVERT: B 192 LYS cc_start: 0.7221 (ptpt) cc_final: 0.5951 (tptt) REVERT: B 468 ASN cc_start: 0.8161 (p0) cc_final: 0.7676 (p0) REVERT: B 511 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 642 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8016 (mmmt) REVERT: B 661 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6398 (t0) REVERT: B 688 GLU cc_start: 0.7525 (mp0) cc_final: 0.7033 (mp0) REVERT: B 830 LYS cc_start: 0.7861 (pttt) cc_final: 0.7372 (pttm) outliers start: 41 outliers final: 24 residues processed: 164 average time/residue: 1.0762 time to fit residues: 193.5826 Evaluate side-chains 170 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 563 ASN A 590 HIS A 684 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.232056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.202222 restraints weight = 33925.321| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.97 r_work: 0.4318 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 10822 Z= 0.163 Angle : 0.634 17.503 14569 Z= 0.336 Chirality : 0.042 0.200 1523 Planarity : 0.004 0.036 1914 Dihedral : 6.052 35.780 1440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.11 % Allowed : 20.48 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.21), residues: 1313 helix: -0.74 (0.27), residues: 342 sheet: 0.44 (0.47), residues: 118 loop : -1.87 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.050 0.002 TYR A 284 PHE 0.013 0.001 PHE B 855 TRP 0.006 0.001 TRP A 286 HIS 0.016 0.002 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00378 (10821) covalent geometry : angle 0.63445 (14569) hydrogen bonds : bond 0.03624 ( 303) hydrogen bonds : angle 5.13363 ( 777) Misc. bond : bond 0.02836 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Residue TYR 245 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LEU 387 is missing expected H atoms. Skipping. Residue SER 759 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.587 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: A 174 LYS cc_start: 0.7838 (tptt) cc_final: 0.7543 (ttmm) REVERT: A 222 LYS cc_start: 0.7667 (mttt) cc_final: 0.7050 (mtpt) REVERT: A 268 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7284 (mtmt) REVERT: A 283 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6547 (tp30) REVERT: A 284 TYR cc_start: 0.5402 (OUTLIER) cc_final: 0.4855 (p90) REVERT: A 291 LEU cc_start: 0.7613 (mp) cc_final: 0.7362 (tp) REVERT: A 305 LYS cc_start: 0.6987 (pttp) cc_final: 0.6355 (mtmm) REVERT: A 309 LYS cc_start: 0.6408 (mtpt) cc_final: 0.5869 (mppt) REVERT: A 420 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: A 472 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6966 (tppt) REVERT: A 475 GLN cc_start: 0.7366 (mm110) cc_final: 0.7149 (mm110) REVERT: A 498 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7190 (t0) REVERT: A 617 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7620 (pp) REVERT: A 640 GLU cc_start: 0.8158 (tt0) cc_final: 0.7800 (mt-10) REVERT: A 671 ASN cc_start: 0.7961 (t0) cc_final: 0.7695 (t0) REVERT: A 732 LYS cc_start: 0.5055 (OUTLIER) cc_final: 0.4308 (mptp) REVERT: B 177 LYS cc_start: 0.7388 (ttmt) cc_final: 0.6828 (ttpp) REVERT: B 190 ARG cc_start: 0.5700 (ptm-80) cc_final: 0.4789 (mtp180) REVERT: B 192 LYS cc_start: 0.7167 (ptpt) cc_final: 0.5907 (tptt) REVERT: B 468 ASN cc_start: 0.8135 (p0) cc_final: 0.7625 (p0) REVERT: B 511 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 642 LYS cc_start: 0.8425 (mtpt) cc_final: 0.7990 (mmmt) REVERT: B 661 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6392 (t0) REVERT: B 688 GLU cc_start: 0.7487 (mp0) cc_final: 0.6961 (mp0) REVERT: B 830 LYS cc_start: 0.7731 (pttt) cc_final: 0.7223 (pttm) outliers start: 36 outliers final: 25 residues processed: 161 average time/residue: 1.1348 time to fit residues: 199.8312 Evaluate side-chains 168 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 401 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 ASP Chi-restraints excluded: chain B residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 260 ASN A 563 ASN A 684 ASN ** A 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.231298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.201203 restraints weight = 33767.692| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.97 r_work: 0.4326 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 10822 Z= 0.252 Angle : 0.925 59.200 14569 Z= 0.569 Chirality : 0.054 1.213 1523 Planarity : 0.006 0.208 1914 Dihedral : 6.081 35.741 1440 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.20 % Allowed : 20.66 % Favored : 76.15 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.21), residues: 1313 helix: -0.74 (0.27), residues: 342 sheet: 0.44 (0.47), residues: 118 loop : -1.86 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.050 0.002 TYR A 284 PHE 0.013 0.001 PHE B 855 TRP 0.006 0.001 TRP A 286 HIS 0.325 0.019 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00478 (10821) covalent geometry : angle 0.92516 (14569) hydrogen bonds : bond 0.03618 ( 303) hydrogen bonds : angle 5.13451 ( 777) Misc. bond : bond 0.02727 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.18 seconds wall clock time: 123 minutes 26.53 seconds (7406.53 seconds total)