Starting phenix.real_space_refine on Wed Feb 4 13:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uus_64517/02_2026/9uus_64517.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3 5.49 5 S 60 5.16 5 C 6894 2.51 5 N 1840 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10835 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "A" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4117 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 4 Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4462 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 21, 'TRANS': 528} Chain breaks: 2 Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 552 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' ZN': 1, 'ACO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1557 SG CYS A 303 39.878 50.996 55.295 1.00 32.04 S ATOM 6117 SG CYS B 269 78.091 47.183 34.214 1.00 45.99 S ATOM 6301 SG CYS B 294 76.792 48.743 37.796 1.00 44.76 S ATOM 6513 SG CYS B 320 61.944 53.294 27.911 1.00 41.65 S ATOM 6535 SG CYS B 323 63.843 52.341 25.084 1.00 39.57 S ATOM 6991 SG CYS B 379 63.683 52.977 15.810 1.00 54.75 S ATOM 7174 SG CYS B 402 65.995 51.789 18.588 1.00 42.70 S ATOM 6221 SG CYS B 283 63.422 39.245 38.259 1.00 45.74 S ATOM 6239 SG CYS B 286 62.902 40.159 34.551 1.00 49.99 S ATOM 6409 SG CYS B 307 62.325 43.309 37.534 1.00 44.34 S ATOM 6437 SG CYS B 310 60.044 40.846 36.317 1.00 48.41 S Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10835 At special positions: 0 Unit cell: (100.287, 101.252, 126.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 60 16.00 P 3 15.00 O 2033 8.00 N 1840 7.00 C 6894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 391.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 303 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 319 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 294 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 269 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 291 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" ND1 HIS B 340 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 320 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 323 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" ND1 HIS B 399 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 379 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 402 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 283 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 286 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 310 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 307 " Number of angles added : 6 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 49.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 142 removed outlier: 3.631A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.512A pdb=" N TRP A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.518A pdb=" N GLY A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.807A pdb=" N LEU A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.848A pdb=" N THR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 484 removed outlier: 3.996A pdb=" N ARG A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 4.103A pdb=" N LEU A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 4.463A pdb=" N PHE A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 removed outlier: 4.099A pdb=" N ILE A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.057A pdb=" N LEU A 569 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 removed outlier: 4.074A pdb=" N TYR A 670 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.879A pdb=" N ILE B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 removed outlier: 4.495A pdb=" N GLN B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.775A pdb=" N LYS B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.564A pdb=" N VAL B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.853A pdb=" N HIS B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 228 Processing helix chain 'B' and resid 234 through 253 removed outlier: 4.066A pdb=" N LEU B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 341 through 347 removed outlier: 3.518A pdb=" N LEU B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.904A pdb=" N ASN B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.676A pdb=" N HIS B 438 " --> pdb=" O CYS B 435 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 439 " --> pdb=" O HIS B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 439' Processing helix chain 'B' and resid 446 through 465 removed outlier: 3.976A pdb=" N THR B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.753A pdb=" N ALA B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 533 removed outlier: 3.982A pdb=" N ILE B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 602 removed outlier: 3.539A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 22 through 42 removed outlier: 4.128A pdb=" N CYS C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 99 removed outlier: 3.784A pdb=" N ALA C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'E' and resid 178 through 187 removed outlier: 3.737A pdb=" N THR E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.760A pdb=" N ASN E 204 " --> pdb=" O MET E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 228 through 244 Processing helix chain 'D' and resid 12 through 53 removed outlier: 4.255A pdb=" N SER D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.857A pdb=" N VAL D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 removed outlier: 7.084A pdb=" N TYR A 379 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR A 403 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 381 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 397 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AA9, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 411 removed outlier: 3.688A pdb=" N GLU B 432 " --> pdb=" O SER B 411 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 1774 1.30 - 1.44: 3054 1.44 - 1.58: 6147 1.58 - 1.72: 11 1.72 - 1.87: 86 Bond restraints: 11072 Sorted by residual: bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.529 1.281 0.248 1.34e-02 5.57e+03 3.41e+02 bond pdb=" C2B ACO A 902 " pdb=" C3B ACO A 902 " ideal model delta sigma weight residual 1.527 1.321 0.206 1.20e-02 6.94e+03 2.94e+02 bond pdb=" C9P ACO A 902 " pdb=" N8P ACO A 902 " ideal model delta sigma weight residual 1.333 1.505 -0.172 1.30e-02 5.92e+03 1.75e+02 bond pdb=" C1B ACO A 902 " pdb=" O4B ACO A 902 " ideal model delta sigma weight residual 1.416 1.587 -0.171 1.40e-02 5.10e+03 1.49e+02 bond pdb=" C5P ACO A 902 " pdb=" N4P ACO A 902 " ideal model delta sigma weight residual 1.331 1.472 -0.141 1.20e-02 6.94e+03 1.38e+02 ... (remaining 11067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 14895 5.07 - 10.15: 32 10.15 - 15.22: 5 15.22 - 20.29: 0 20.29 - 25.37: 2 Bond angle restraints: 14934 Sorted by residual: angle pdb=" C1B ACO A 902 " pdb=" N9A ACO A 902 " pdb=" C4A ACO A 902 " ideal model delta sigma weight residual 126.88 151.36 -24.48 1.80e+00 3.09e-01 1.85e+02 angle pdb=" C1B ACO A 902 " pdb=" N9A ACO A 902 " pdb=" C8A ACO A 902 " ideal model delta sigma weight residual 126.78 101.41 25.37 1.94e+00 2.65e-01 1.71e+02 angle pdb=" P1A ACO A 902 " pdb=" O3A ACO A 902 " pdb=" P2A ACO A 902 " ideal model delta sigma weight residual 136.83 123.87 12.96 1.00e+00 1.00e+00 1.68e+02 angle pdb=" N1A ACO A 902 " pdb=" C2A ACO A 902 " pdb=" N3A ACO A 902 " ideal model delta sigma weight residual 128.69 120.05 8.64 1.00e+00 1.00e+00 7.46e+01 angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" CB LYS A 367 " ideal model delta sigma weight residual 110.69 97.69 13.00 1.61e+00 3.86e-01 6.52e+01 ... (remaining 14929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5710 17.95 - 35.90: 750 35.90 - 53.85: 189 53.85 - 71.80: 48 71.80 - 89.75: 13 Dihedral angle restraints: 6710 sinusoidal: 2829 harmonic: 3881 Sorted by residual: dihedral pdb=" CA GLU B 359 " pdb=" C GLU B 359 " pdb=" N PRO B 360 " pdb=" CA PRO B 360 " ideal model delta harmonic sigma weight residual -180.00 -133.86 -46.14 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" C LYS A 367 " pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" CB LYS A 367 " ideal model delta harmonic sigma weight residual -122.60 -101.77 -20.83 0 2.50e+00 1.60e-01 6.94e+01 dihedral pdb=" N LYS A 367 " pdb=" C LYS A 367 " pdb=" CA LYS A 367 " pdb=" CB LYS A 367 " ideal model delta harmonic sigma weight residual 122.80 102.03 20.77 0 2.50e+00 1.60e-01 6.90e+01 ... (remaining 6707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 1602 0.172 - 0.345: 3 0.345 - 0.517: 0 0.517 - 0.689: 0 0.689 - 0.862: 2 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA LYS A 367 " pdb=" N LYS A 367 " pdb=" C LYS A 367 " pdb=" CB LYS A 367 " both_signs ideal model delta sigma weight residual False 2.51 3.37 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CA SER A 366 " pdb=" N SER A 366 " pdb=" C SER A 366 " pdb=" CB SER A 366 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C2B ACO A 902 " pdb=" C1B ACO A 902 " pdb=" C3B ACO A 902 " pdb=" O2B ACO A 902 " both_signs ideal model delta sigma weight residual False -2.72 -2.49 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1604 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 359 " 0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO B 360 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 367 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C LYS A 367 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 367 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 368 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 374 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 375 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.030 5.00e-02 4.00e+02 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 216 2.66 - 3.22: 10127 3.22 - 3.78: 15338 3.78 - 4.34: 20823 4.34 - 4.90: 35055 Nonbonded interactions: 81559 Sorted by model distance: nonbonded pdb=" OE2 GLU D 40 " pdb=" OG SER D 96 " model vdw 2.103 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" OD1 ASN D 68 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP B 191 " pdb=" OH TYR B 525 " model vdw 2.145 3.040 nonbonded pdb=" O6A ACO A 902 " pdb=" OAP ACO A 902 " model vdw 2.165 3.040 nonbonded pdb=" O VAL E 239 " pdb=" OG1 THR E 243 " model vdw 2.168 3.040 ... (remaining 81554 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4850 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 : 0.013 0.671 11087 Z= 0.626 Angle : 0.880 25.365 14940 Z= 0.498 Chirality : 0.052 0.862 1607 Planarity : 0.005 0.092 1897 Dihedral : 17.677 89.751 4190 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 7.24 % Allowed : 20.49 % Favored : 72.26 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.20), residues: 1287 helix: -1.37 (0.18), residues: 592 sheet: -2.16 (0.64), residues: 60 loop : -3.40 (0.20), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.017 0.002 TYR B 525 PHE 0.024 0.002 PHE A 404 TRP 0.017 0.002 TRP B 223 HIS 0.007 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00807 (11072) covalent geometry : angle 0.83034 (14934) hydrogen bonds : bond 0.10897 ( 440) hydrogen bonds : angle 4.92823 ( 1263) metal coordination : bond 0.28723 ( 15) metal coordination : angle 14.56988 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 0.372 Fit side-chains REVERT: A 144 LYS cc_start: 0.3109 (OUTLIER) cc_final: 0.1652 (ttpt) REVERT: A 538 ASN cc_start: 0.4475 (OUTLIER) cc_final: 0.3901 (m110) REVERT: A 586 MET cc_start: 0.3531 (ttt) cc_final: 0.2957 (ttp) REVERT: B 26 ASN cc_start: 0.4382 (OUTLIER) cc_final: 0.4133 (p0) REVERT: B 85 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6568 (pttt) REVERT: B 123 ILE cc_start: 0.2451 (OUTLIER) cc_final: 0.2159 (tp) REVERT: B 325 SER cc_start: 0.3572 (OUTLIER) cc_final: 0.3031 (p) REVERT: B 367 VAL cc_start: 0.4012 (OUTLIER) cc_final: 0.3710 (t) REVERT: B 393 ASN cc_start: 0.4660 (OUTLIER) cc_final: 0.4228 (p0) REVERT: B 423 ASN cc_start: 0.4401 (OUTLIER) cc_final: 0.3745 (t0) outliers start: 88 outliers final: 18 residues processed: 281 average time/residue: 0.1110 time to fit residues: 43.3684 Evaluate side-chains 146 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 98 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 GLN A 143 ASN A 156 GLN A 432 GLN A 496 GLN A 500 ASN A 538 ASN A 672 ASN A 691 HIS B 26 ASN B 190 GLN B 209 HIS ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN C 65 ASN D 49 ASN D 52 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.203762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161450 restraints weight = 12086.680| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.86 r_work: 0.3746 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 11087 Z= 0.183 Angle : 0.729 18.577 14940 Z= 0.376 Chirality : 0.044 0.177 1607 Planarity : 0.006 0.090 1897 Dihedral : 9.272 67.662 1520 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.94 % Allowed : 22.63 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.22), residues: 1287 helix: 0.55 (0.21), residues: 553 sheet: -0.41 (0.95), residues: 34 loop : -2.56 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 14 TYR 0.029 0.002 TYR A 463 PHE 0.015 0.002 PHE B 282 TRP 0.027 0.002 TRP A 215 HIS 0.006 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00410 (11072) covalent geometry : angle 0.72546 (14934) hydrogen bonds : bond 0.04935 ( 440) hydrogen bonds : angle 4.30009 ( 1263) metal coordination : bond 0.02271 ( 15) metal coordination : angle 3.81711 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.3540 (OUTLIER) cc_final: 0.1285 (mtmt) REVERT: A 333 ILE cc_start: 0.8037 (tp) cc_final: 0.7736 (pt) REVERT: A 502 ILE cc_start: 0.6268 (mt) cc_final: 0.6019 (mt) REVERT: B 16 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4428 (ptmt) REVERT: B 598 ASP cc_start: 0.5955 (OUTLIER) cc_final: 0.5526 (t0) outliers start: 60 outliers final: 23 residues processed: 185 average time/residue: 0.0853 time to fit residues: 23.2736 Evaluate side-chains 121 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 490 ASN B 136 GLN B 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147049 restraints weight = 12284.681| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.64 r_work: 0.3484 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.8321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11087 Z= 0.182 Angle : 0.667 11.189 14940 Z= 0.347 Chirality : 0.044 0.354 1607 Planarity : 0.005 0.081 1897 Dihedral : 8.967 85.450 1496 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.53 % Allowed : 24.20 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1287 helix: 0.95 (0.22), residues: 556 sheet: -1.19 (0.68), residues: 60 loop : -2.34 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.014 0.002 TYR B 525 PHE 0.028 0.002 PHE A 206 TRP 0.011 0.001 TRP B 223 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00421 (11072) covalent geometry : angle 0.64923 (14934) hydrogen bonds : bond 0.05677 ( 440) hydrogen bonds : angle 4.17637 ( 1263) metal coordination : bond 0.00593 ( 15) metal coordination : angle 7.68934 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.432 Fit side-chains REVERT: A 144 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.1085 (ttmt) REVERT: A 281 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: A 698 ARG cc_start: 0.4206 (OUTLIER) cc_final: 0.3557 (ptp-170) REVERT: B 21 PHE cc_start: 0.5045 (OUTLIER) cc_final: 0.4658 (t80) REVERT: B 224 PHE cc_start: 0.7300 (t80) cc_final: 0.6641 (m-10) REVERT: C 35 MET cc_start: 0.7962 (ttp) cc_final: 0.7666 (ttp) REVERT: C 72 ILE cc_start: 0.6565 (tp) cc_final: 0.6297 (pt) REVERT: C 97 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7012 (tp30) REVERT: C 100 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6925 (ttpp) REVERT: E 200 MET cc_start: 0.7809 (ttp) cc_final: 0.7485 (ptm) REVERT: D 24 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: D 93 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5650 (ptp-170) outliers start: 55 outliers final: 23 residues processed: 182 average time/residue: 0.1123 time to fit residues: 28.4730 Evaluate side-chains 147 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 21 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 93 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN B 438 HIS C 65 ASN E 242 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.186398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143313 restraints weight = 12455.890| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.62 r_work: 0.3440 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.9299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11087 Z= 0.152 Angle : 0.598 10.302 14940 Z= 0.310 Chirality : 0.042 0.251 1607 Planarity : 0.005 0.079 1897 Dihedral : 8.619 88.270 1490 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.87 % Allowed : 26.01 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1287 helix: 1.12 (0.22), residues: 568 sheet: -0.99 (0.71), residues: 60 loop : -2.21 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.012 0.001 TYR B 525 PHE 0.019 0.001 PHE A 206 TRP 0.015 0.001 TRP B 223 HIS 0.004 0.001 HIS B 436 Details of bonding type rmsd covalent geometry : bond 0.00360 (11072) covalent geometry : angle 0.58694 (14934) hydrogen bonds : bond 0.05176 ( 440) hydrogen bonds : angle 3.95075 ( 1263) metal coordination : bond 0.00389 ( 15) metal coordination : angle 5.66886 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.432 Fit side-chains REVERT: A 210 ARG cc_start: 0.8547 (ttt180) cc_final: 0.8323 (mmm-85) REVERT: A 271 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: A 385 GLU cc_start: 0.8044 (pp20) cc_final: 0.7671 (pp20) REVERT: A 453 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5716 (mmtt) REVERT: A 463 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7267 (t80) REVERT: A 524 TYR cc_start: 0.6835 (m-80) cc_final: 0.6581 (m-80) REVERT: B 224 PHE cc_start: 0.7154 (t80) cc_final: 0.6627 (m-10) REVERT: B 248 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6367 (t0) REVERT: B 422 SER cc_start: 0.8532 (t) cc_final: 0.8190 (p) REVERT: C 15 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: C 72 ILE cc_start: 0.6771 (tp) cc_final: 0.6563 (pt) REVERT: C 77 GLN cc_start: 0.6826 (mt0) cc_final: 0.6455 (mt0) REVERT: C 83 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6554 (mt-10) REVERT: C 97 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7103 (tp30) REVERT: C 100 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7132 (ttpp) REVERT: D 24 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7469 (pt0) outliers start: 47 outliers final: 29 residues processed: 169 average time/residue: 0.1236 time to fit residues: 28.8913 Evaluate side-chains 152 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain D residue 24 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 136 GLN E 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.181468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138150 restraints weight = 12495.975| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.61 r_work: 0.3381 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 1.0052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11087 Z= 0.170 Angle : 0.624 9.868 14940 Z= 0.323 Chirality : 0.043 0.240 1607 Planarity : 0.005 0.079 1897 Dihedral : 8.777 89.905 1490 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.77 % Allowed : 25.68 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1287 helix: 1.06 (0.22), residues: 568 sheet: -0.81 (0.73), residues: 60 loop : -2.16 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 119 TYR 0.014 0.002 TYR B 525 PHE 0.023 0.002 PHE A 400 TRP 0.013 0.001 TRP B 223 HIS 0.006 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00414 (11072) covalent geometry : angle 0.60857 (14934) hydrogen bonds : bond 0.05839 ( 440) hydrogen bonds : angle 4.09495 ( 1263) metal coordination : bond 0.00457 ( 15) metal coordination : angle 6.88720 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.428 Fit side-chains REVERT: A 203 MET cc_start: 0.6510 (mmm) cc_final: 0.6240 (mpp) REVERT: A 210 ARG cc_start: 0.8580 (ttt180) cc_final: 0.8296 (mmm-85) REVERT: A 271 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 374 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7752 (mp0) REVERT: A 385 GLU cc_start: 0.8049 (pp20) cc_final: 0.7750 (pp20) REVERT: A 453 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5586 (mmtt) REVERT: A 463 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7111 (t80) REVERT: B 21 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.3920 (t80) REVERT: B 224 PHE cc_start: 0.7291 (t80) cc_final: 0.6846 (m-10) REVERT: B 245 ASP cc_start: 0.6670 (m-30) cc_final: 0.6358 (m-30) REVERT: B 270 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 422 SER cc_start: 0.8569 (t) cc_final: 0.8125 (p) REVERT: B 598 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5269 (t0) REVERT: C 15 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: C 42 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6474 (ptmm) REVERT: C 83 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6528 (mt-10) REVERT: C 97 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7056 (tp30) REVERT: C 100 LYS cc_start: 0.7506 (ttpt) cc_final: 0.7111 (ttpp) REVERT: D 24 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: D 35 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7699 (mm-30) REVERT: D 65 TYR cc_start: 0.3696 (OUTLIER) cc_final: 0.3439 (p90) REVERT: D 93 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7629 (ptp-170) outliers start: 58 outliers final: 31 residues processed: 178 average time/residue: 0.1055 time to fit residues: 27.0239 Evaluate side-chains 160 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 21 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 93 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN E 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146620 restraints weight = 12375.961| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.65 r_work: 0.3427 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11087 Z= 0.106 Angle : 0.516 8.062 14940 Z= 0.272 Chirality : 0.039 0.165 1607 Planarity : 0.004 0.071 1897 Dihedral : 8.206 88.483 1489 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.05 % Allowed : 26.83 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1287 helix: 1.51 (0.22), residues: 570 sheet: 0.14 (0.82), residues: 50 loop : -1.98 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 119 TYR 0.010 0.001 TYR B 202 PHE 0.034 0.001 PHE A 206 TRP 0.019 0.001 TRP B 223 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00237 (11072) covalent geometry : angle 0.50865 (14934) hydrogen bonds : bond 0.04444 ( 440) hydrogen bonds : angle 3.71034 ( 1263) metal coordination : bond 0.00202 ( 15) metal coordination : angle 4.27725 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.516 Fit side-chains REVERT: A 128 PHE cc_start: 0.7221 (m-80) cc_final: 0.6971 (m-80) REVERT: A 203 MET cc_start: 0.6399 (mmm) cc_final: 0.6155 (mpp) REVERT: A 374 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7575 (mp0) REVERT: A 385 GLU cc_start: 0.8153 (pp20) cc_final: 0.7826 (pp20) REVERT: A 453 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.4680 (mtpt) REVERT: A 463 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6751 (t80) REVERT: A 585 MET cc_start: 0.2618 (ptt) cc_final: 0.2223 (ptp) REVERT: A 698 ARG cc_start: 0.5462 (OUTLIER) cc_final: 0.4686 (ttm-80) REVERT: B 220 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 224 PHE cc_start: 0.7291 (t80) cc_final: 0.6748 (m-10) REVERT: B 598 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.5337 (t0) REVERT: C 15 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7199 (m-80) REVERT: C 50 MET cc_start: 0.6328 (mtt) cc_final: 0.5780 (mmm) REVERT: C 77 GLN cc_start: 0.6769 (mt0) cc_final: 0.6455 (mt0) REVERT: C 97 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7191 (tp30) REVERT: C 100 LYS cc_start: 0.7506 (ttpt) cc_final: 0.7073 (ttpp) REVERT: D 24 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: D 35 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7601 (mm-30) outliers start: 37 outliers final: 20 residues processed: 163 average time/residue: 0.1107 time to fit residues: 25.4773 Evaluate side-chains 146 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain D residue 24 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142057 restraints weight = 12312.671| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.72 r_work: 0.3415 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 1.0380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.662 11087 Z= 0.539 Angle : 0.530 8.695 14940 Z= 0.278 Chirality : 0.040 0.161 1607 Planarity : 0.004 0.069 1897 Dihedral : 8.178 88.017 1489 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.46 % Allowed : 26.91 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1287 helix: 1.64 (0.22), residues: 570 sheet: 0.20 (0.83), residues: 50 loop : -1.87 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 119 TYR 0.010 0.001 TYR B 525 PHE 0.032 0.001 PHE A 206 TRP 0.016 0.001 TRP B 223 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00274 (11072) covalent geometry : angle 0.52094 (14934) hydrogen bonds : bond 0.04678 ( 440) hydrogen bonds : angle 3.70393 ( 1263) metal coordination : bond 0.42902 ( 15) metal coordination : angle 4.97929 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7586 (mp0) REVERT: A 385 GLU cc_start: 0.8154 (pp20) cc_final: 0.7773 (pp20) REVERT: A 453 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.4421 (mtpt) REVERT: A 463 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 518 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 21 PHE cc_start: 0.4916 (OUTLIER) cc_final: 0.4483 (t80) REVERT: B 207 MET cc_start: 0.7973 (tpt) cc_final: 0.6962 (tpt) REVERT: B 220 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 224 PHE cc_start: 0.7258 (t80) cc_final: 0.6754 (m-10) REVERT: B 598 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5428 (t0) REVERT: C 15 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: C 42 LYS cc_start: 0.6783 (ttpt) cc_final: 0.6274 (ptmm) REVERT: C 77 GLN cc_start: 0.6730 (mt0) cc_final: 0.6402 (mt0) REVERT: C 83 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6536 (mt-10) REVERT: C 100 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7209 (ttpp) REVERT: D 24 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7645 (pt0) outliers start: 42 outliers final: 27 residues processed: 164 average time/residue: 0.1037 time to fit residues: 24.4224 Evaluate side-chains 155 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 21 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain D residue 24 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 500 ASN B 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.181762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139015 restraints weight = 12122.567| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.51 r_work: 0.3359 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 1.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11087 Z= 0.172 Angle : 0.612 9.869 14940 Z= 0.318 Chirality : 0.043 0.188 1607 Planarity : 0.004 0.072 1897 Dihedral : 8.535 85.866 1489 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.62 % Allowed : 27.24 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.23), residues: 1287 helix: 1.48 (0.22), residues: 563 sheet: -0.44 (0.76), residues: 60 loop : -1.89 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 119 TYR 0.014 0.001 TYR B 525 PHE 0.031 0.002 PHE A 206 TRP 0.010 0.001 TRP B 223 HIS 0.005 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00415 (11072) covalent geometry : angle 0.59700 (14934) hydrogen bonds : bond 0.05784 ( 440) hydrogen bonds : angle 3.97503 ( 1263) metal coordination : bond 0.01868 ( 15) metal coordination : angle 6.78417 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: A 281 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: A 296 GLN cc_start: 0.8338 (mm110) cc_final: 0.8064 (mm-40) REVERT: A 374 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7642 (mp0) REVERT: A 453 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.4363 (mtpt) REVERT: B 224 PHE cc_start: 0.7270 (t80) cc_final: 0.6866 (m-10) REVERT: B 314 LYS cc_start: 0.6449 (mmtm) cc_final: 0.5999 (tppt) REVERT: B 598 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5466 (t0) REVERT: C 15 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: C 42 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6511 (ptmm) REVERT: C 77 GLN cc_start: 0.6844 (mt0) cc_final: 0.6528 (mt0) REVERT: C 97 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7203 (tp30) REVERT: C 100 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7243 (ttpp) REVERT: D 24 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: D 93 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7285 (ptp-170) outliers start: 44 outliers final: 31 residues processed: 154 average time/residue: 0.1158 time to fit residues: 25.2416 Evaluate side-chains 151 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 104 optimal weight: 0.2980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143219 restraints weight = 12135.601| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.76 r_work: 0.3439 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 1.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11087 Z= 0.108 Angle : 0.520 7.914 14940 Z= 0.273 Chirality : 0.040 0.146 1607 Planarity : 0.004 0.067 1897 Dihedral : 8.140 88.354 1489 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.96 % Allowed : 28.23 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1287 helix: 1.71 (0.22), residues: 569 sheet: 0.33 (0.84), residues: 50 loop : -1.76 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 563 TYR 0.010 0.001 TYR B 525 PHE 0.030 0.001 PHE A 206 TRP 0.019 0.001 TRP B 223 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00240 (11072) covalent geometry : angle 0.51220 (14934) hydrogen bonds : bond 0.04455 ( 440) hydrogen bonds : angle 3.67198 ( 1263) metal coordination : bond 0.00506 ( 15) metal coordination : angle 4.36658 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.486 Fit side-chains REVERT: A 281 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: A 453 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.4425 (mtpt) REVERT: A 463 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6667 (t80) REVERT: A 698 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.4917 (ttm-80) REVERT: B 207 MET cc_start: 0.8031 (tpt) cc_final: 0.6926 (tpt) REVERT: B 220 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 224 PHE cc_start: 0.7323 (t80) cc_final: 0.6795 (m-10) REVERT: B 455 LYS cc_start: 0.7004 (tppt) cc_final: 0.6660 (tppt) REVERT: C 15 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: C 42 LYS cc_start: 0.6832 (ttpt) cc_final: 0.6333 (ptmm) REVERT: C 77 GLN cc_start: 0.6755 (mt0) cc_final: 0.6452 (mt0) REVERT: C 100 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7219 (ttpp) REVERT: D 24 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: D 93 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6667 (ptp-170) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.1136 time to fit residues: 24.4001 Evaluate side-chains 153 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 0.0040 chunk 94 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142497 restraints weight = 12132.023| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.71 r_work: 0.3394 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 1.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11087 Z= 0.119 Angle : 0.532 8.559 14940 Z= 0.280 Chirality : 0.040 0.152 1607 Planarity : 0.004 0.066 1897 Dihedral : 8.108 85.256 1489 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.05 % Allowed : 28.31 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1287 helix: 1.73 (0.22), residues: 569 sheet: 0.39 (0.85), residues: 50 loop : -1.69 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 563 TYR 0.010 0.001 TYR B 525 PHE 0.032 0.001 PHE A 206 TRP 0.016 0.001 TRP B 223 HIS 0.008 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00276 (11072) covalent geometry : angle 0.52323 (14934) hydrogen bonds : bond 0.04670 ( 440) hydrogen bonds : angle 3.69719 ( 1263) metal coordination : bond 0.00461 ( 15) metal coordination : angle 4.95515 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.456 Fit side-chains REVERT: A 271 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: A 281 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 453 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4348 (mtpt) REVERT: A 463 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 698 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4833 (ttm-80) REVERT: B 207 MET cc_start: 0.8047 (tpt) cc_final: 0.6990 (tpt) REVERT: B 220 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 224 PHE cc_start: 0.7311 (t80) cc_final: 0.6786 (m-10) REVERT: B 455 LYS cc_start: 0.7011 (tppt) cc_final: 0.6663 (tppt) REVERT: C 15 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: C 42 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6359 (ptmm) REVERT: C 77 GLN cc_start: 0.6759 (mt0) cc_final: 0.6443 (mt0) REVERT: C 83 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6540 (mt-10) REVERT: C 100 LYS cc_start: 0.7495 (ttpt) cc_final: 0.7175 (ttpp) REVERT: D 24 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: D 93 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6475 (ptp-170) outliers start: 37 outliers final: 27 residues processed: 143 average time/residue: 0.1136 time to fit residues: 23.0861 Evaluate side-chains 145 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 15 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain D residue 24 GLU Chi-restraints excluded: chain D residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145224 restraints weight = 12199.063| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.54 r_work: 0.3425 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 1.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11087 Z= 0.107 Angle : 0.510 7.939 14940 Z= 0.268 Chirality : 0.039 0.147 1607 Planarity : 0.004 0.063 1897 Dihedral : 7.965 85.648 1489 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.13 % Allowed : 28.23 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1287 helix: 1.82 (0.22), residues: 571 sheet: 0.47 (0.86), residues: 50 loop : -1.64 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 563 TYR 0.008 0.001 TYR B 525 PHE 0.031 0.001 PHE A 206 TRP 0.019 0.001 TRP B 223 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00243 (11072) covalent geometry : angle 0.50330 (14934) hydrogen bonds : bond 0.04270 ( 440) hydrogen bonds : angle 3.61422 ( 1263) metal coordination : bond 0.00396 ( 15) metal coordination : angle 4.25310 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.31 seconds wall clock time: 45 minutes 55.53 seconds (2755.53 seconds total)