Starting phenix.real_space_refine on Fri Jul 3 17:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.map" model { file = "/net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u60_63893/07_2026/9u60_63893.cif" } resolution = 2.9 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 1 6.56 5 S 69 5.16 5 C 9297 2.51 5 N 2571 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14725 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3076 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 21, 'TRANS': 377} Chain breaks: 2 Chain: "E" Number of atoms: 11648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1500, 11648 Classifications: {'peptide': 1500} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 75, 'TRANS': 1421} Chain breaks: 10 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NI': 1} Chain breaks: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.23 Number of scatterers: 14725 At special positions: 0 Unit cell: (165.3, 131.1, 112.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 1 28.00 S 69 16.00 O 2787 8.00 N 2571 7.00 C 9297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 567 " - pdb=" SG CYS E 820 " distance=2.03 Simple disulfide: pdb=" SG CYS E1394 " - pdb=" SG CYS E1566 " distance=2.03 Simple disulfide: pdb=" SG CYS E1471 " - pdb=" SG CYS E1535 " distance=2.05 Simple disulfide: pdb=" SG CYS E1583 " - pdb=" SG CYS E1588 " distance=2.05 Simple disulfide: pdb=" SG CYS E1595 " - pdb=" SG CYS E1673 " distance=2.03 Simple disulfide: pdb=" SG CYS E1618 " - pdb=" SG CYS E1742 " distance=2.04 Simple disulfide: pdb=" SG CYS E1718 " - pdb=" SG CYS E1727 " distance=2.02 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: 1.05 Conformation dependent library (CDL) restraints added in 754.1 milliseconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 31 sheets defined 20.3% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.824A pdb=" N ALA B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 4.040A pdb=" N HIS B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 287 removed outlier: 3.946A pdb=" N PHE B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.579A pdb=" N SER B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 314 " --> pdb=" O ASP B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.598A pdb=" N VAL B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.770A pdb=" N ASP B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 332' Processing helix chain 'B' and resid 338 through 358 removed outlier: 3.560A pdb=" N ALA B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.672A pdb=" N ILE B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.719A pdb=" N LEU B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.543A pdb=" N LEU B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 removed outlier: 3.703A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 115 through 120 removed outlier: 4.124A pdb=" N ASP E 119 " --> pdb=" O PRO E 115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 120 " --> pdb=" O TRP E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 120' Processing helix chain 'E' and resid 315 through 326 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.768A pdb=" N LEU E 333 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 538 removed outlier: 3.842A pdb=" N ALA E 538 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.571A pdb=" N ALA E 611 " --> pdb=" O LEU E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 629 Processing helix chain 'E' and resid 630 through 632 No H-bonds generated for 'chain 'E' and resid 630 through 632' Processing helix chain 'E' and resid 642 through 651 Processing helix chain 'E' and resid 762 through 766 Processing helix chain 'E' and resid 768 through 772 removed outlier: 3.531A pdb=" N ASP E 771 " --> pdb=" O ASP E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1001 Processing helix chain 'E' and resid 1014 through 1029 Proline residue: E1020 - end of helix removed outlier: 3.556A pdb=" N ALA E1023 " --> pdb=" O ALA E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1056 removed outlier: 4.386A pdb=" N LYS E1042 " --> pdb=" O PRO E1038 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP E1043 " --> pdb=" O PRO E1039 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E1056 " --> pdb=" O GLY E1052 " (cutoff:3.500A) Processing helix chain 'E' and resid 1072 through 1083 Processing helix chain 'E' and resid 1099 through 1110 removed outlier: 3.960A pdb=" N ASN E1105 " --> pdb=" O GLN E1101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E1106 " --> pdb=" O GLU E1102 " (cutoff:3.500A) Processing helix chain 'E' and resid 1137 through 1152 removed outlier: 3.623A pdb=" N THR E1142 " --> pdb=" O THR E1138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E1147 " --> pdb=" O ALA E1143 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E1148 " --> pdb=" O PHE E1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 1161 through 1183 Processing helix chain 'E' and resid 1189 through 1200 removed outlier: 4.349A pdb=" N LEU E1200 " --> pdb=" O THR E1196 " (cutoff:3.500A) Processing helix chain 'E' and resid 1209 through 1218 Processing helix chain 'E' and resid 1260 through 1272 removed outlier: 3.534A pdb=" N LEU E1272 " --> pdb=" O ALA E1268 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1289 Processing helix chain 'E' and resid 1410 through 1414 Processing helix chain 'E' and resid 1501 through 1507 removed outlier: 3.782A pdb=" N THR E1505 " --> pdb=" O LEU E1501 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU E1507 " --> pdb=" O LYS E1503 " (cutoff:3.500A) Processing helix chain 'E' and resid 1611 through 1619 Processing helix chain 'E' and resid 1723 through 1740 removed outlier: 3.708A pdb=" N GLN E1740 " --> pdb=" O GLU E1736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.560A pdb=" N SER B 31 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS B 84 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.548A pdb=" N THR B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 48 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 64 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA8, first strand: chain 'B' and resid 182 through 184 Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 306 removed outlier: 6.560A pdb=" N ILE B 295 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 253 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA B 294 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 255 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE B 296 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU B 257 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE B 298 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 259 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 369 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR B 409 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 371 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 411 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 373 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 413 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 375 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 437 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 410 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 439 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY B 412 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 87 removed outlier: 7.924A pdb=" N SER E 38 " --> pdb=" O PRO E 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN E 44 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 30 through 32 Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 145 removed outlier: 3.863A pdb=" N ASP E 200 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 149 through 150 removed outlier: 6.673A pdb=" N ILE E 174 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU E 190 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL E 176 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS E 188 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 178 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG E 187 " --> pdb=" O GLU E1355 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N GLU E1357 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 16.123A pdb=" N LYS E 189 " --> pdb=" O GLU E1357 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASP E 973 " --> pdb=" O ASN E1385 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN E1385 " --> pdb=" O ASP E 973 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN E 975 " --> pdb=" O THR E1383 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR E1383 " --> pdb=" O ASN E 975 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 241 through 247 removed outlier: 4.007A pdb=" N MET E 262 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 251 through 253 Processing sheet with id=AB7, first strand: chain 'E' and resid 293 through 304 removed outlier: 10.640A pdb=" N ARG E 297 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU E 286 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU E 299 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE E 284 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL E 340 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 367 through 370 removed outlier: 3.720A pdb=" N ALA E 388 " --> pdb=" O VAL E 431 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 417 through 424 removed outlier: 6.248A pdb=" N GLU E 417 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL E 409 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN E 419 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA E 407 " --> pdb=" O GLN E 419 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER E 406 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER E 447 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR E 408 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN E 445 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER E 410 " --> pdb=" O GLU E 443 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 443 " --> pdb=" O SER E 410 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 472 through 476 Processing sheet with id=AC2, first strand: chain 'E' and resid 514 through 522 removed outlier: 5.356A pdb=" N ILE E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER E 511 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS E 504 " --> pdb=" O TYR E 548 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR E 548 " --> pdb=" O HIS E 504 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 571 through 575 Processing sheet with id=AC4, first strand: chain 'E' and resid 781 through 798 removed outlier: 7.547A pdb=" N ASN E 781 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP E 605 " --> pdb=" O ASN E 781 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU E 783 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA E 603 " --> pdb=" O LEU E 783 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 785 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 791 " --> pdb=" O SER E 595 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER E 595 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLN E 793 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR E 593 " --> pdb=" O GLN E 793 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU E 795 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU E 591 " --> pdb=" O LEU E 795 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 797 " --> pdb=" O LEU E 589 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU E 589 " --> pdb=" O LEU E 797 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 834 through 837 Processing sheet with id=AC6, first strand: chain 'E' and resid 849 through 851 Processing sheet with id=AC7, first strand: chain 'E' and resid 885 through 889 Processing sheet with id=AC8, first strand: chain 'E' and resid 958 through 960 Processing sheet with id=AC9, first strand: chain 'E' and resid 1344 through 1345 Processing sheet with id=AD1, first strand: chain 'E' and resid 1397 through 1405 removed outlier: 3.623A pdb=" N VAL E1470 " --> pdb=" O VAL E1536 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL E1536 " --> pdb=" O VAL E1470 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE E1472 " --> pdb=" O GLU E1534 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E1534 " --> pdb=" O ILE E1472 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 1512 through 1514 removed outlier: 6.586A pdb=" N TYR E1525 " --> pdb=" O SER E1513 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER E1553 " --> pdb=" O THR E1489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1581 through 1584 removed outlier: 4.086A pdb=" N SER E1584 " --> pdb=" O VAL E1587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL E1587 " --> pdb=" O SER E1584 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1598 through 1599 removed outlier: 4.610A pdb=" N GLU E1711 " --> pdb=" O ARG E1599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E1685 " --> pdb=" O PHE E1627 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR E1625 " --> pdb=" O GLY E1687 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLY E1626 " --> pdb=" O VAL E1650 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL E1650 " --> pdb=" O GLY E1626 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN E1628 " --> pdb=" O THR E1648 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU E1644 " --> pdb=" O LEU E1632 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU E1634 " --> pdb=" O LEU E1642 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU E1642 " --> pdb=" O GLU E1634 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR E1701 " --> pdb=" O ASN E1666 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1494 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: 3.29 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2470 1.32 - 1.45: 4099 1.45 - 1.59: 8359 1.59 - 1.72: 0 1.72 - 1.86: 106 Bond restraints: 15034 Sorted by residual: bond pdb=" C GLN E 42 " pdb=" O GLN E 42 " ideal model delta sigma weight residual 1.234 1.183 0.050 1.22e-02 6.72e+03 1.71e+01 bond pdb=" CA GLU B 360 " pdb=" CB GLU B 360 " ideal model delta sigma weight residual 1.525 1.574 -0.049 1.47e-02 4.63e+03 1.12e+01 bond pdb=" CA SER E1714 " pdb=" C SER E1714 " ideal model delta sigma weight residual 1.520 1.479 0.041 1.39e-02 5.18e+03 8.79e+00 bond pdb=" N GLU E1418 " pdb=" CA GLU E1418 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta sigma weight residual 1.467 1.437 0.030 1.09e-02 8.42e+03 7.66e+00 ... (remaining 15029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 20107 3.39 - 6.77: 218 6.77 - 10.16: 46 10.16 - 13.55: 10 13.55 - 16.94: 5 Bond angle restraints: 20386 Sorted by residual: angle pdb=" N ARG E1716 " pdb=" CA ARG E1716 " pdb=" C ARG E1716 " ideal model delta sigma weight residual 113.16 98.10 15.06 1.24e+00 6.50e-01 1.48e+02 angle pdb=" N CYS E1742 " pdb=" CA CYS E1742 " pdb=" C CYS E1742 " ideal model delta sigma weight residual 113.50 123.55 -10.05 1.23e+00 6.61e-01 6.68e+01 angle pdb=" C HIS E 953 " pdb=" N ARG E 954 " pdb=" CA ARG E 954 " ideal model delta sigma weight residual 121.54 135.46 -13.92 1.91e+00 2.74e-01 5.31e+01 angle pdb=" C SER B 179 " pdb=" CA SER B 179 " pdb=" CB SER B 179 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" C LEU E1217 " pdb=" N MET E1218 " pdb=" CA MET E1218 " ideal model delta sigma weight residual 122.56 113.72 8.84 1.72e+00 3.38e-01 2.64e+01 ... (remaining 20381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7673 17.86 - 35.71: 1018 35.71 - 53.57: 314 53.57 - 71.43: 60 71.43 - 89.29: 17 Dihedral angle restraints: 9082 sinusoidal: 3633 harmonic: 5449 Sorted by residual: dihedral pdb=" CA SER B 58 " pdb=" C SER B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual 180.00 132.20 47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 64 " pdb=" CB CYS B 64 " ideal model delta sinusoidal sigma weight residual 93.00 172.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA LEU E 259 " pdb=" C LEU E 259 " pdb=" N ASP E 260 " pdb=" CA ASP E 260 " ideal model delta harmonic sigma weight residual -180.00 -146.39 -33.61 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2100 0.102 - 0.204: 178 0.204 - 0.305: 3 0.305 - 0.407: 2 0.407 - 0.509: 2 Chirality restraints: 2285 Sorted by residual: chirality pdb=" CA GLN E1743 " pdb=" N GLN E1743 " pdb=" C GLN E1743 " pdb=" CB GLN E1743 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" CA ASP E 45 " pdb=" N ASP E 45 " pdb=" C ASP E 45 " pdb=" CB ASP E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB ILE B 289 " pdb=" CA ILE B 289 " pdb=" CG1 ILE B 289 " pdb=" CG2 ILE B 289 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2282 not shown) Planarity restraints: 2653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 58 " -0.077 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO B 59 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E1712 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET E1712 " -0.059 2.00e-02 2.50e+03 pdb=" O MET E1712 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO E1713 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 217 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO B 218 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.048 5.00e-02 4.00e+02 ... (remaining 2650 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 100 2.62 - 3.19: 10559 3.19 - 3.76: 20818 3.76 - 4.33: 28575 4.33 - 4.90: 49374 Nonbonded interactions: 109426 Sorted by model distance: nonbonded pdb=" OG SER B 264 " pdb="NI NI B 801 " model vdw 2.048 2.920 nonbonded pdb=" OG1 THR B 337 " pdb="NI NI B 801 " model vdw 2.066 2.920 nonbonded pdb=" N ARG E1716 " pdb=" N LEU E1717 " model vdw 2.284 2.560 nonbonded pdb=" O ASN E1105 " pdb=" OG SER E1109 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP E 146 " pdb=" OH TYR E 150 " model vdw 2.287 3.040 ... (remaining 109421 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.004 0.066 15048 Z= 0.220 Angle : 0.969 16.937 20414 Z= 0.504 Chirality : 0.054 0.509 2285 Planarity : 0.008 0.119 2653 Dihedral : 18.053 89.287 5536 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.78 % Allowed : 30.42 % Favored : 65.80 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.06 % 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: -1.32 (0.18), residues: 1871 helix: -1.94 (0.23), residues: 324 sheet: 0.89 (0.21), residues: 638 loop : -1.82 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 954 TYR 0.025 0.002 TYR B 210 PHE 0.050 0.002 PHE E 921 TRP 0.023 0.002 TRP E1230 HIS 0.015 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (15034) covalent geometry : angle 0.96818 / 0.50 (20386) SS BOND : bond 0.00674 / 0.44 ( 14) SS BOND : angle 1.66038 / 0.99 ( 28) hydrogen bonds : bond 0.21733 / 14.80 ( 532) hydrogen bonds : angle 7.61443 / 5.26 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 SER cc_start: 0.9031 (m) cc_final: 0.8745 (p) REVERT: B 359 MET cc_start: 0.7073 (mtt) cc_final: 0.6426 (tmm) REVERT: E 92 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7504 (pttp) REVERT: E 164 ASP cc_start: 0.8443 (p0) cc_final: 0.8122 (p0) REVERT: E 1029 ASP cc_start: 0.6163 (m-30) cc_final: 0.5955 (m-30) REVERT: E 1261 TRP cc_start: 0.5306 (p90) cc_final: 0.4538 (p90) REVERT: E 1359 GLN cc_start: 0.8179 (mt0) cc_final: 0.7653 (mm-40) outliers start: 61 outliers final: 46 residues processed: 231 average time/residue: 0.4861 time to fit residues: 126.4994 Evaluate side-chains 222 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 841 MET Chi-restraints excluded: chain E residue 849 LEU Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 957 THR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1200 LEU Chi-restraints excluded: chain E residue 1334 THR Chi-restraints excluded: chain E residue 1472 ILE Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1505 THR Chi-restraints excluded: chain E residue 1574 SER Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1684 LEU Chi-restraints excluded: chain E residue 1705 SER Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 149 optimal weight: 8.9990 overall best weight: 0.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 ASN E 64 ASN E 419 GLN E 590 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1628 GLN E1723 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111204 restraints weight = 18665.293| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.39 r_work: 0.3195 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15048 Z= 0.119 Angle : 0.638 12.427 20414 Z= 0.315 Chirality : 0.044 0.178 2285 Planarity : 0.006 0.083 2653 Dihedral : 7.122 63.078 2124 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.77 % Allowed : 28.13 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.06 % 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: -0.53 (0.19), residues: 1871 helix: -0.16 (0.28), residues: 325 sheet: 1.10 (0.21), residues: 648 loop : -1.59 (0.18), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1577 TYR 0.013 0.001 TYR B 100 PHE 0.017 0.001 PHE E 134 TRP 0.010 0.001 TRP E 784 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (15034) covalent geometry : angle 0.63723 / 0.31 (20386) SS BOND : bond 0.00254 / 0.17 ( 14) SS BOND : angle 1.10252 / 0.76 ( 28) hydrogen bonds : bond 0.04116 / 2.79 ( 532) hydrogen bonds : angle 5.21226 / 3.62 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 171 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6569 (tp) REVERT: B 180 ASN cc_start: 0.7762 (t0) cc_final: 0.7544 (m-40) REVERT: B 320 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.7007 (tp) REVERT: B 359 MET cc_start: 0.7165 (mtt) cc_final: 0.6219 (tmm) REVERT: B 366 GLU cc_start: 0.4075 (OUTLIER) cc_final: 0.3838 (tp30) REVERT: B 401 LYS cc_start: 0.7704 (tptm) cc_final: 0.7487 (mmtm) REVERT: B 433 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: E 19 GLN cc_start: 0.4501 (OUTLIER) cc_final: 0.4065 (tt0) REVERT: E 80 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7419 (mtp-110) REVERT: E 164 ASP cc_start: 0.7927 (p0) cc_final: 0.7658 (p0) REVERT: E 258 HIS cc_start: 0.8273 (t-170) cc_final: 0.7935 (t-170) REVERT: E 262 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.6986 (mpt) REVERT: E 318 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7238 (mt-10) REVERT: E 324 GLU cc_start: 0.7565 (tt0) cc_final: 0.6838 (mm-30) REVERT: E 535 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7465 (t-90) REVERT: E 665 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7918 (mmtp) REVERT: E 667 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6683 (tp) REVERT: E 844 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8036 (mtp180) REVERT: E 1005 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7750 (mpp80) REVERT: E 1034 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: E 1278 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.4955 (tptt) REVERT: E 1280 GLU cc_start: 0.7633 (mp0) cc_final: 0.7382 (mp0) REVERT: E 1352 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6211 (ttp-170) REVERT: E 1408 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: E 1590 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7527 (t) REVERT: E 1670 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8052 (mtm110) outliers start: 77 outliers final: 29 residues processed: 226 average time/residue: 0.5207 time to fit residues: 131.0220 Evaluate side-chains 212 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1288 TRP Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1664 MET Chi-restraints excluded: chain E residue 1670 ARG Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 20 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 590 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108854 restraints weight = 18900.374| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.35 r_work: 0.3160 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15048 Z= 0.154 Angle : 0.645 13.170 20414 Z= 0.317 Chirality : 0.045 0.182 2285 Planarity : 0.005 0.073 2653 Dihedral : 6.038 58.026 2076 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.01 % Allowed : 27.51 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.06 % 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: -0.33 (0.19), residues: 1871 helix: 0.47 (0.29), residues: 325 sheet: 1.13 (0.20), residues: 645 loop : -1.57 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 954 TYR 0.014 0.001 TYR B 100 PHE 0.018 0.001 PHE E 134 TRP 0.013 0.001 TRP E 784 HIS 0.006 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.15 (15034) covalent geometry : angle 0.64428 / 0.32 (20386) SS BOND : bond 0.00378 / 0.27 ( 14) SS BOND : angle 1.24729 / 0.85 ( 28) hydrogen bonds : bond 0.03834 / 2.62 ( 532) hydrogen bonds : angle 4.83573 / 3.36 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 174 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6632 (tp) REVERT: B 180 ASN cc_start: 0.7783 (t0) cc_final: 0.7528 (m-40) REVERT: B 320 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7088 (tp) REVERT: B 401 LYS cc_start: 0.7738 (tptm) cc_final: 0.7461 (mmtm) REVERT: B 405 TYR cc_start: 0.8522 (m-80) cc_final: 0.8207 (m-80) REVERT: B 433 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: E 19 GLN cc_start: 0.4638 (OUTLIER) cc_final: 0.4209 (tt0) REVERT: E 80 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7354 (mtp-110) REVERT: E 164 ASP cc_start: 0.8065 (p0) cc_final: 0.7774 (p0) REVERT: E 258 HIS cc_start: 0.8261 (t-170) cc_final: 0.7972 (t-170) REVERT: E 324 GLU cc_start: 0.7567 (tt0) cc_final: 0.6906 (mm-30) REVERT: E 490 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8359 (t0) REVERT: E 535 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7431 (t-90) REVERT: E 619 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (tt) REVERT: E 667 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6678 (tp) REVERT: E 844 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8057 (mtp180) REVERT: E 1034 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: E 1278 LYS cc_start: 0.6315 (OUTLIER) cc_final: 0.5227 (tmtt) REVERT: E 1352 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6217 (ttp-170) REVERT: E 1400 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: E 1408 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: E 1678 GLU cc_start: 0.8083 (pm20) cc_final: 0.7813 (pm20) outliers start: 97 outliers final: 44 residues processed: 242 average time/residue: 0.4903 time to fit residues: 132.4435 Evaluate side-chains 227 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 841 MET Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1334 THR Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1400 GLU Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 137 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 590 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109226 restraints weight = 18957.363| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.35 r_work: 0.3148 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15048 Z= 0.120 Angle : 0.616 12.863 20414 Z= 0.298 Chirality : 0.044 0.188 2285 Planarity : 0.005 0.064 2653 Dihedral : 5.588 50.748 2071 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.01 % Allowed : 28.00 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.17 (0.19), residues: 1871 helix: 0.75 (0.30), residues: 323 sheet: 1.12 (0.20), residues: 650 loop : -1.44 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1005 TYR 0.012 0.001 TYR B 100 PHE 0.015 0.001 PHE E 134 TRP 0.012 0.001 TRP E 784 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (15034) covalent geometry : angle 0.61508 / 0.30 (20386) SS BOND : bond 0.00333 / 0.22 ( 14) SS BOND : angle 1.22473 / 0.80 ( 28) hydrogen bonds : bond 0.03277 / 2.22 ( 532) hydrogen bonds : angle 4.57822 / 3.18 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 171 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7132 (tp) REVERT: B 320 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7379 (tp) REVERT: E 80 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7287 (mtp-110) REVERT: E 324 GLU cc_start: 0.7768 (tt0) cc_final: 0.7178 (mm-30) REVERT: E 459 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8096 (tpp-160) REVERT: E 490 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8553 (t0) REVERT: E 535 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: E 665 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7957 (pmtt) REVERT: E 667 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6905 (tp) REVERT: E 844 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.8338 (mtp180) REVERT: E 939 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8742 (tp) REVERT: E 1005 ARG cc_start: 0.8446 (mtm180) cc_final: 0.8056 (mpp80) REVERT: E 1034 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: E 1218 MET cc_start: 0.6567 (mpm) cc_final: 0.5936 (ptp) REVERT: E 1278 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5192 (tptt) REVERT: E 1352 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6494 (ttp-170) REVERT: E 1362 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7705 (pp) REVERT: E 1408 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7950 (mp0) outliers start: 97 outliers final: 45 residues processed: 237 average time/residue: 0.5292 time to fit residues: 139.1704 Evaluate side-chains 227 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1138 THR Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1334 THR Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1506 SER Chi-restraints excluded: chain E residue 1521 HIS Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1642 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 48 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 590 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107735 restraints weight = 18877.143| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.34 r_work: 0.3124 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15048 Z= 0.147 Angle : 0.641 12.803 20414 Z= 0.311 Chirality : 0.045 0.191 2285 Planarity : 0.005 0.062 2653 Dihedral : 5.625 48.582 2071 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.26 % Allowed : 28.31 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.14 (0.19), residues: 1871 helix: 0.97 (0.30), residues: 318 sheet: 0.99 (0.20), residues: 660 loop : -1.39 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1577 TYR 0.014 0.001 TYR B 100 PHE 0.017 0.001 PHE E 134 TRP 0.013 0.001 TRP E 784 HIS 0.010 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (15034) covalent geometry : angle 0.63906 / 0.31 (20386) SS BOND : bond 0.00353 / 0.23 ( 14) SS BOND : angle 1.33974 / 0.89 ( 28) hydrogen bonds : bond 0.03425 / 2.33 ( 532) hydrogen bonds : angle 4.54221 / 3.15 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 168 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7114 (tp) REVERT: B 320 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7388 (tp) REVERT: B 400 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.5506 (tp40) REVERT: E 19 GLN cc_start: 0.4636 (OUTLIER) cc_final: 0.4094 (tt0) REVERT: E 235 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8901 (mtmm) REVERT: E 261 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: E 262 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: E 324 GLU cc_start: 0.7854 (tt0) cc_final: 0.7263 (mm-30) REVERT: E 439 GLN cc_start: 0.7777 (mt0) cc_final: 0.7576 (tm-30) REVERT: E 459 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8211 (tpp-160) REVERT: E 490 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8561 (t0) REVERT: E 535 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.7679 (t-90) REVERT: E 619 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8595 (tt) REVERT: E 665 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7983 (pmtt) REVERT: E 667 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6876 (tp) REVERT: E 844 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8312 (mtp180) REVERT: E 1034 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.7273 (m-10) REVERT: E 1218 MET cc_start: 0.5972 (mpm) cc_final: 0.5555 (ptp) REVERT: E 1278 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5328 (tptt) REVERT: E 1280 GLU cc_start: 0.7860 (mp0) cc_final: 0.7496 (mp0) REVERT: E 1352 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6435 (ttp-170) REVERT: E 1362 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7762 (pp) REVERT: E 1408 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: E 1712 MET cc_start: 0.7515 (tpp) cc_final: 0.7185 (tpp) outliers start: 101 outliers final: 57 residues processed: 241 average time/residue: 0.5118 time to fit residues: 138.1185 Evaluate side-chains 238 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 164 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 518 MET Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1334 THR Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1506 SER Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1642 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1686 MET Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 144 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 258 HIS E 563 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105543 restraints weight = 18740.235| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.31 r_work: 0.3104 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15048 Z= 0.224 Angle : 0.726 13.399 20414 Z= 0.353 Chirality : 0.048 0.188 2285 Planarity : 0.005 0.066 2653 Dihedral : 6.013 49.793 2071 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 7.25 % Allowed : 27.45 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.35 (0.19), residues: 1871 helix: 0.78 (0.31), residues: 325 sheet: 0.82 (0.20), residues: 663 loop : -1.50 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1005 TYR 0.017 0.002 TYR B 100 PHE 0.020 0.002 PHE E 74 TRP 0.017 0.002 TRP E 784 HIS 0.009 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.22 (15034) covalent geometry : angle 0.72364 / 0.35 (20386) SS BOND : bond 0.00453 / 0.28 ( 14) SS BOND : angle 1.67780 / 1.11 ( 28) hydrogen bonds : bond 0.04032 / 2.75 ( 532) hydrogen bonds : angle 4.72990 / 3.29 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 167 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6718 (tp) REVERT: B 320 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7321 (tp) REVERT: B 366 GLU cc_start: 0.4551 (tp30) cc_final: 0.3597 (pt0) REVERT: B 400 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5215 (tp-100) REVERT: B 401 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7831 (tptm) REVERT: E 19 GLN cc_start: 0.4722 (OUTLIER) cc_final: 0.4131 (tt0) REVERT: E 235 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8784 (mtmm) REVERT: E 261 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: E 324 GLU cc_start: 0.7674 (tt0) cc_final: 0.7000 (mm-30) REVERT: E 439 GLN cc_start: 0.7802 (mt0) cc_final: 0.7357 (tm-30) REVERT: E 481 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7063 (ttm170) REVERT: E 490 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8366 (t0) REVERT: E 535 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7492 (t-90) REVERT: E 619 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8414 (tt) REVERT: E 665 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7812 (pmtt) REVERT: E 667 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6755 (tp) REVERT: E 844 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.7894 (mtp180) REVERT: E 1005 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7923 (mpp80) REVERT: E 1034 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: E 1278 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.5557 (tptt) REVERT: E 1280 GLU cc_start: 0.7905 (mp0) cc_final: 0.7456 (mp0) REVERT: E 1352 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6366 (ttp-170) REVERT: E 1408 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: E 1676 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7390 (tpp-160) REVERT: E 1712 MET cc_start: 0.7352 (tpp) cc_final: 0.7006 (tpp) outliers start: 117 outliers final: 56 residues processed: 257 average time/residue: 0.5463 time to fit residues: 156.4304 Evaluate side-chains 236 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 165 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 948 LEU Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1334 THR Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1506 SER Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1521 HIS Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1619 TYR Chi-restraints excluded: chain E residue 1642 LEU Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 124 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 137 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 258 HIS E 334 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107376 restraints weight = 18618.295| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.37 r_work: 0.3136 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15048 Z= 0.139 Angle : 0.649 13.796 20414 Z= 0.315 Chirality : 0.045 0.193 2285 Planarity : 0.005 0.065 2653 Dihedral : 5.686 48.470 2070 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.45 % Allowed : 29.37 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.17 (0.19), residues: 1871 helix: 1.01 (0.31), residues: 319 sheet: 0.91 (0.20), residues: 658 loop : -1.38 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 80 TYR 0.013 0.001 TYR B 100 PHE 0.016 0.001 PHE E 241 TRP 0.013 0.001 TRP E 784 HIS 0.012 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (15034) covalent geometry : angle 0.64729 / 0.31 (20386) SS BOND : bond 0.00426 / 0.28 ( 14) SS BOND : angle 1.44350 / 0.94 ( 28) hydrogen bonds : bond 0.03373 / 2.28 ( 532) hydrogen bonds : angle 4.54642 / 3.16 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 169 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6690 (tp) REVERT: B 289 ILE cc_start: 0.8677 (mp) cc_final: 0.8276 (mt) REVERT: B 320 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7148 (tp) REVERT: B 366 GLU cc_start: 0.4488 (tp30) cc_final: 0.3673 (pt0) REVERT: B 401 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7849 (tptm) REVERT: B 433 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8749 (mp0) REVERT: E 80 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7261 (mtp-110) REVERT: E 235 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8741 (mtmm) REVERT: E 261 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: E 324 GLU cc_start: 0.7656 (tt0) cc_final: 0.6964 (mm-30) REVERT: E 439 GLN cc_start: 0.7801 (mt0) cc_final: 0.7376 (tm-30) REVERT: E 490 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8309 (t0) REVERT: E 535 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7498 (t-90) REVERT: E 619 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8346 (tt) REVERT: E 665 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7817 (pmtt) REVERT: E 667 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6756 (tp) REVERT: E 844 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.7934 (mtp180) REVERT: E 919 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7265 (m-10) REVERT: E 1005 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7826 (mpp80) REVERT: E 1034 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: E 1218 MET cc_start: 0.5826 (mpm) cc_final: 0.5306 (ptm) REVERT: E 1278 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5510 (tptt) REVERT: E 1280 GLU cc_start: 0.7785 (mp0) cc_final: 0.7370 (mp0) REVERT: E 1352 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6320 (ttp-170) REVERT: E 1408 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: E 1712 MET cc_start: 0.7302 (tpp) cc_final: 0.7023 (tpp) outliers start: 88 outliers final: 52 residues processed: 235 average time/residue: 0.5483 time to fit residues: 143.8213 Evaluate side-chains 232 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 665 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 813 LEU Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 919 PHE Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1034 TRP Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1492 SER Chi-restraints excluded: chain E residue 1506 SER Chi-restraints excluded: chain E residue 1521 HIS Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1732 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 GLN E 64 ASN E 258 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109231 restraints weight = 18715.733| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.38 r_work: 0.3166 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15048 Z= 0.111 Angle : 0.617 13.347 20414 Z= 0.299 Chirality : 0.044 0.203 2285 Planarity : 0.005 0.062 2653 Dihedral : 5.345 46.906 2068 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.89 % Allowed : 30.11 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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 (0.19), residues: 1871 helix: 1.20 (0.31), residues: 317 sheet: 0.98 (0.20), residues: 668 loop : -1.28 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E1577 TYR 0.011 0.001 TYR B 100 PHE 0.024 0.001 PHE E 921 TRP 0.011 0.001 TRP E 784 HIS 0.013 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 (15034) covalent geometry : angle 0.61571 / 0.30 (20386) SS BOND : bond 0.00349 / 0.24 ( 14) SS BOND : angle 1.23939 / 0.78 ( 28) hydrogen bonds : bond 0.02992 / 2.02 ( 532) hydrogen bonds : angle 4.37330 / 3.03 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 173 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 ILE cc_start: 0.8690 (mp) cc_final: 0.8270 (mt) REVERT: B 320 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7125 (tp) REVERT: B 433 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: E 80 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7268 (mtp-110) REVERT: E 324 GLU cc_start: 0.7626 (tt0) cc_final: 0.6962 (mm-30) REVERT: E 439 GLN cc_start: 0.7800 (mt0) cc_final: 0.7401 (tm-30) REVERT: E 490 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8310 (t0) REVERT: E 535 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7459 (t-90) REVERT: E 617 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6201 (mtmm) REVERT: E 619 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8390 (tt) REVERT: E 665 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7805 (pmtt) REVERT: E 667 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6754 (tp) REVERT: E 844 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.7962 (mtp180) REVERT: E 1005 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7820 (mpp80) REVERT: E 1218 MET cc_start: 0.5790 (mpm) cc_final: 0.5210 (ptm) REVERT: E 1278 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.5583 (tptp) REVERT: E 1280 GLU cc_start: 0.7764 (mp0) cc_final: 0.7402 (mp0) REVERT: E 1352 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6378 (ttp-170) REVERT: E 1408 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: E 1676 ARG cc_start: 0.7402 (tpp80) cc_final: 0.7156 (tpp-160) outliers start: 79 outliers final: 39 residues processed: 233 average time/residue: 0.5100 time to fit residues: 133.2752 Evaluate side-chains 214 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 528 SER Chi-restraints excluded: chain E residue 535 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 617 LYS Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 665 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 897 VAL Chi-restraints excluded: chain E residue 939 ILE Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1278 LYS Chi-restraints excluded: chain E residue 1352 ARG Chi-restraints excluded: chain E residue 1379 LYS Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1506 SER Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1672 SER Chi-restraints excluded: chain E residue 1704 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 119 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 57 optimal weight: 0.0970 chunk 162 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 HIS E 64 ASN E 258 HIS E 334 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1662 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112120 restraints weight = 18811.754| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.34 r_work: 0.3205 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15048 Z= 0.095 Angle : 0.594 13.021 20414 Z= 0.286 Chirality : 0.043 0.191 2285 Planarity : 0.004 0.059 2653 Dihedral : 4.829 44.366 2063 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.28 % Allowed : 31.97 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: 0.21 (0.20), residues: 1871 helix: 1.35 (0.31), residues: 319 sheet: 0.97 (0.20), residues: 673 loop : -1.02 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1577 TYR 0.009 0.001 TYR E 158 PHE 0.013 0.001 PHE B 298 TRP 0.008 0.001 TRP E 782 HIS 0.013 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.09 (15034) covalent geometry : angle 0.59312 / 0.29 (20386) SS BOND : bond 0.00354 / 0.25 ( 14) SS BOND : angle 1.00515 / 0.62 ( 28) hydrogen bonds : bond 0.02655 / 1.78 ( 532) hydrogen bonds : angle 4.19864 / 2.90 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 ILE cc_start: 0.8715 (mp) cc_final: 0.8234 (mt) REVERT: B 320 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7238 (tp) REVERT: E 324 GLU cc_start: 0.7757 (tt0) cc_final: 0.7162 (mm-30) REVERT: E 328 MET cc_start: 0.8278 (ttm) cc_final: 0.7835 (ttt) REVERT: E 439 GLN cc_start: 0.7873 (mt0) cc_final: 0.7665 (tm-30) REVERT: E 445 GLN cc_start: 0.7581 (tt0) cc_final: 0.7017 (tm-30) REVERT: E 619 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8598 (tt) REVERT: E 665 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7993 (pmtt) REVERT: E 667 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6862 (tp) REVERT: E 844 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8254 (mtp180) REVERT: E 1005 ARG cc_start: 0.8385 (mtm180) cc_final: 0.8013 (mpp80) REVERT: E 1218 MET cc_start: 0.5698 (mpm) cc_final: 0.5200 (ptm) REVERT: E 1261 TRP cc_start: 0.5561 (p90) cc_final: 0.4773 (p90) REVERT: E 1280 GLU cc_start: 0.7850 (mp0) cc_final: 0.7505 (mp0) REVERT: E 1408 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7840 (mp0) outliers start: 53 outliers final: 31 residues processed: 209 average time/residue: 0.5492 time to fit residues: 128.0605 Evaluate side-chains 198 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 957 THR Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1133 VAL Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1260 LEU Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1379 LYS Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 32 optimal weight: 0.0050 chunk 84 optimal weight: 0.0570 chunk 180 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 151 optimal weight: 0.0040 chunk 7 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 258 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112424 restraints weight = 18723.981| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.34 r_work: 0.3209 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15048 Z= 0.096 Angle : 0.593 12.812 20414 Z= 0.288 Chirality : 0.043 0.182 2285 Planarity : 0.004 0.059 2653 Dihedral : 4.645 43.238 2059 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.91 % Allowed : 32.34 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: 0.28 (0.20), residues: 1871 helix: 1.37 (0.31), residues: 320 sheet: 1.02 (0.20), residues: 679 loop : -0.97 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1577 TYR 0.009 0.001 TYR B 100 PHE 0.030 0.001 PHE E 921 TRP 0.009 0.001 TRP E 784 HIS 0.014 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (15034) covalent geometry : angle 0.59266 / 0.29 (20386) SS BOND : bond 0.00276 / 0.18 ( 14) SS BOND : angle 1.02100 / 0.66 ( 28) hydrogen bonds : bond 0.02644 / 1.77 ( 532) hydrogen bonds : angle 4.14005 / 2.86 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8347 (m) REVERT: B 289 ILE cc_start: 0.8704 (mp) cc_final: 0.8199 (mt) REVERT: B 320 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7348 (tp) REVERT: B 419 ASP cc_start: 0.8322 (m-30) cc_final: 0.8002 (m-30) REVERT: E 235 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8841 (mtmm) REVERT: E 324 GLU cc_start: 0.7782 (tt0) cc_final: 0.7208 (mm-30) REVERT: E 328 MET cc_start: 0.8317 (ttm) cc_final: 0.7895 (ttt) REVERT: E 445 GLN cc_start: 0.7571 (tt0) cc_final: 0.7071 (tm-30) REVERT: E 619 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8635 (tt) REVERT: E 665 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8026 (pmtt) REVERT: E 667 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6922 (tp) REVERT: E 844 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8303 (mtp180) REVERT: E 1005 ARG cc_start: 0.8394 (mtm180) cc_final: 0.8013 (mpp80) REVERT: E 1215 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6673 (t0) REVERT: E 1218 MET cc_start: 0.5696 (mpm) cc_final: 0.5210 (ptm) REVERT: E 1280 GLU cc_start: 0.7933 (mp0) cc_final: 0.7617 (mp0) REVERT: E 1408 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7830 (mp0) outliers start: 47 outliers final: 32 residues processed: 199 average time/residue: 0.5517 time to fit residues: 122.3610 Evaluate side-chains 203 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 945 VAL Chi-restraints excluded: chain E residue 954 ARG Chi-restraints excluded: chain E residue 957 THR Chi-restraints excluded: chain E residue 1040 GLU Chi-restraints excluded: chain E residue 1083 LEU Chi-restraints excluded: chain E residue 1085 VAL Chi-restraints excluded: chain E residue 1133 VAL Chi-restraints excluded: chain E residue 1215 ASN Chi-restraints excluded: chain E residue 1260 LEU Chi-restraints excluded: chain E residue 1271 HIS Chi-restraints excluded: chain E residue 1379 LYS Chi-restraints excluded: chain E residue 1408 GLU Chi-restraints excluded: chain E residue 1478 VAL Chi-restraints excluded: chain E residue 1535 CYS Chi-restraints excluded: chain E residue 1583 CYS Chi-restraints excluded: chain E residue 1590 CYS Chi-restraints excluded: chain E residue 1704 ASP Chi-restraints excluded: chain E residue 1734 LEU Chi-restraints excluded: chain E residue 1744 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 155 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN E 258 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105665 restraints weight = 18766.894| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.32 r_work: 0.3109 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15048 Z= 0.236 Angle : 0.746 14.699 20414 Z= 0.362 Chirality : 0.048 0.177 2285 Planarity : 0.005 0.066 2653 Dihedral : 5.385 47.746 2059 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.72 % Allowed : 31.85 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.03 (0.19), residues: 1871 helix: 1.08 (0.31), residues: 324 sheet: 0.97 (0.20), residues: 665 loop : -1.26 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 80 TYR 0.017 0.002 TYR B 100 PHE 0.020 0.002 PHE E 241 TRP 0.018 0.002 TRP E 784 HIS 0.012 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.24 (15034) covalent geometry : angle 0.74431 / 0.36 (20386) SS BOND : bond 0.00458 / 0.29 ( 14) SS BOND : angle 1.67188 / 1.14 ( 28) hydrogen bonds : bond 0.03920 / 2.67 ( 532) hydrogen bonds : angle 4.55574 / 3.15 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.12 seconds wall clock time: 101 minutes 10.11 seconds (6070.11 seconds total)