Starting phenix.real_space_refine on Fri Aug 7 05:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.map" model { file = "/net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9whk_65968/08_2026/9whk_65968.cif" } resolution = 3.22 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= 0.011 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 P 16 5.49 5 S 58 5.16 5 C 12092 2.51 5 N 3170 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "B" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain breaks: 1 Chain: "D" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "E" Number of atoms: 6973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6973 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 828} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain breaks: 1 Time building chain proxies: 3.37, per 1000 atoms: 0.18 Number of scatterers: 18888 At special positions: 0 Unit cell: (102.52, 136.072, 151.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 16 15.00 O 3552 8.00 N 3170 7.00 C 12092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 273 " distance=2.03 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: 1.22 Conformation dependent library (CDL) restraints added in 588.4 milliseconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4388 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 13 sheets defined 57.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.631A pdb=" N ASN A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.841A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.660A pdb=" N ALA A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 345 removed outlier: 4.423A pdb=" N GLU A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 401 Processing helix chain 'A' and resid 402 through 405 removed outlier: 4.509A pdb=" N ARG A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.529A pdb=" N GLU A 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.973A pdb=" N SER A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 488 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 15 through 36 Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 62 through 77 Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.978A pdb=" N LEU B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.640A pdb=" N ILE B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.575A pdb=" N ILE B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.564A pdb=" N LEU B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 283 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.651A pdb=" N LEU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.554A pdb=" N TYR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 399 through 413 Processing helix chain 'B' and resid 417 through 424 removed outlier: 3.551A pdb=" N MET B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'B' and resid 458 through 461 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.758A pdb=" N LEU B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 588 through 591 Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 603 through 618 Processing helix chain 'B' and resid 621 through 628 removed outlier: 3.990A pdb=" N ILE B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.928A pdb=" N THR B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 699 removed outlier: 3.569A pdb=" N ASN B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.769A pdb=" N ASP B 712 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 Processing helix chain 'B' and resid 753 through 770 removed outlier: 3.914A pdb=" N TYR B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 785 removed outlier: 3.746A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.819A pdb=" N SER B 811 " --> pdb=" O ILE B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 822 through 825 removed outlier: 4.037A pdb=" N TYR B 825 " --> pdb=" O GLU B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 843 through 850 Processing helix chain 'D' and resid 282 through 297 Proline residue: D 293 - end of helix Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 309 through 326 Processing helix chain 'D' and resid 330 through 343 Processing helix chain 'D' and resid 385 through 401 removed outlier: 4.319A pdb=" N SER D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 421 through 433 Processing helix chain 'D' and resid 468 through 488 removed outlier: 3.670A pdb=" N LEU D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 495 Processing helix chain 'D' and resid 511 through 524 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 15 through 34 Processing helix chain 'E' and resid 43 through 59 removed outlier: 3.832A pdb=" N ASP E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.856A pdb=" N LEU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 124 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.731A pdb=" N THR E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.762A pdb=" N LYS E 145 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 184 through 199 Processing helix chain 'E' and resid 199 through 207 removed outlier: 3.637A pdb=" N PHE E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 241 Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.654A pdb=" N LEU E 259 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 355 through 367 removed outlier: 3.513A pdb=" N HIS E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 391 Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 417 through 424 removed outlier: 3.690A pdb=" N MET E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 448 removed outlier: 3.863A pdb=" N ILE E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 500 Processing helix chain 'E' and resid 525 through 530 removed outlier: 4.083A pdb=" N ILE E 528 " --> pdb=" O ASN E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 546 Processing helix chain 'E' and resid 546 through 559 removed outlier: 3.901A pdb=" N ASP E 559 " --> pdb=" O ARG E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 585 removed outlier: 3.826A pdb=" N GLU E 572 " --> pdb=" O ASN E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 601 Processing helix chain 'E' and resid 604 through 616 removed outlier: 3.772A pdb=" N SER E 608 " --> pdb=" O GLU E 604 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 612 " --> pdb=" O SER E 608 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS E 613 " --> pdb=" O LEU E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 628 removed outlier: 4.008A pdb=" N ILE E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 645 Processing helix chain 'E' and resid 647 through 651 removed outlier: 3.741A pdb=" N LYS E 651 " --> pdb=" O VAL E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 672 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 683 through 699 Processing helix chain 'E' and resid 702 through 714 Processing helix chain 'E' and resid 732 through 750 Processing helix chain 'E' and resid 753 through 771 Processing helix chain 'E' and resid 778 through 785 removed outlier: 3.692A pdb=" N PHE E 782 " --> pdb=" O ASN E 778 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 785 " --> pdb=" O THR E 781 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 799 Processing helix chain 'E' and resid 801 through 811 Processing helix chain 'E' and resid 811 through 817 removed outlier: 4.166A pdb=" N TYR E 817 " --> pdb=" O GLU E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 838 Processing helix chain 'E' and resid 843 through 852 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 removed outlier: 6.488A pdb=" N TYR A 270 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 447 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 505 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 449 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 507 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 451 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE A 509 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 453 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 362 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 211 removed outlier: 6.777A pdb=" N LYS B 209 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 230 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 211 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N SER B 291 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 253 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 149 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER B 292 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 151 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 313 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 152 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.590A pdb=" N ILE B 471 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 516 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 473 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 334 through 338 removed outlier: 4.101A pdb=" N ILE B 334 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 716 through 717 Processing sheet with id=AA7, first strand: chain 'B' and resid 818 through 821 removed outlier: 7.153A pdb=" N LYS B 819 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 821 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 826 " --> pdb=" O ASN B 821 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 269 through 271 removed outlier: 6.477A pdb=" N TYR D 270 " --> pdb=" O PHE D 506 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 362 " --> pdb=" O SER D 378 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 363 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 410 " --> pdb=" O SER D 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 149 through 153 removed outlier: 6.605A pdb=" N ASP E 249 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL E 289 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 251 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER E 291 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL E 253 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN E 177 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 250 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE E 178 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU E 231 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE E 180 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 321 through 325 removed outlier: 6.422A pdb=" N ILE E 471 " --> pdb=" O PHE E 514 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA E 428 " --> pdb=" O PHE E 455 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 334 through 337 removed outlier: 4.255A pdb=" N ILE E 334 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 716 through 717 removed outlier: 3.524A pdb=" N ILE E 726 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 818 through 821 removed outlier: 3.750A pdb=" N SER E 829 " --> pdb=" O LYS E 819 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASN E 821 " --> pdb=" O ILE E 827 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE E 827 " --> pdb=" O ASN E 821 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2688 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: 2.86 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6057 1.34 - 1.46: 4642 1.46 - 1.58: 8503 1.58 - 1.70: 28 1.70 - 1.82: 84 Bond restraints: 19314 Sorted by residual: bond pdb=" C3' DA C 14 " pdb=" C2' DA C 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA F 12 " pdb=" C2' DA F 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.57e+00 bond pdb=" C3' DA F 6 " pdb=" C2' DA F 6 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.54e+00 bond pdb=" C2' DA F 6 " pdb=" C1' DA F 6 " ideal model delta sigma weight residual 1.518 1.535 -0.017 1.00e-02 1.00e+04 3.05e+00 bond pdb=" C2' DA F 12 " pdb=" C1' DA F 12 " ideal model delta sigma weight residual 1.518 1.535 -0.017 1.00e-02 1.00e+04 2.74e+00 ... (remaining 19309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 25914 2.60 - 5.19: 185 5.19 - 7.79: 26 7.79 - 10.39: 8 10.39 - 12.98: 5 Bond angle restraints: 26138 Sorted by residual: angle pdb=" C ASP A 423 " pdb=" CA ASP A 423 " pdb=" CB ASP A 423 " ideal model delta sigma weight residual 110.42 118.14 -7.72 1.99e+00 2.53e-01 1.50e+01 angle pdb=" CA LEU B 102 " pdb=" CB LEU B 102 " pdb=" CG LEU B 102 " ideal model delta sigma weight residual 116.30 129.28 -12.98 3.50e+00 8.16e-02 1.38e+01 angle pdb=" CB MET B 424 " pdb=" CG MET B 424 " pdb=" SD MET B 424 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N ILE A 325 " pdb=" CA ILE A 325 " pdb=" C ILE A 325 " ideal model delta sigma weight residual 111.91 108.66 3.25 8.90e-01 1.26e+00 1.33e+01 angle pdb=" CA LEU B 385 " pdb=" CB LEU B 385 " pdb=" CG LEU B 385 " ideal model delta sigma weight residual 116.30 128.29 -11.99 3.50e+00 8.16e-02 1.17e+01 ... (remaining 26133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 9680 17.18 - 34.37: 1413 34.37 - 51.55: 429 51.55 - 68.73: 116 68.73 - 85.92: 38 Dihedral angle restraints: 11676 sinusoidal: 4908 harmonic: 6768 Sorted by residual: dihedral pdb=" CB CYS D 251 " pdb=" SG CYS D 251 " pdb=" SG CYS D 273 " pdb=" CB CYS D 273 " ideal model delta sinusoidal sigma weight residual -86.00 -167.05 81.05 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CA MET B 286 " pdb=" C MET B 286 " pdb=" N LYS B 287 " pdb=" CA LYS B 287 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TYR E 351 " pdb=" C TYR E 351 " pdb=" N THR E 352 " pdb=" CA THR E 352 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 11673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2028 0.039 - 0.078: 659 0.078 - 0.118: 192 0.118 - 0.157: 21 0.157 - 0.196: 4 Chirality restraints: 2904 Sorted by residual: chirality pdb=" CG LEU D 340 " pdb=" CB LEU D 340 " pdb=" CD1 LEU D 340 " pdb=" CD2 LEU D 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CB THR B 141 " pdb=" CA THR B 141 " pdb=" OG1 THR B 141 " pdb=" CG2 THR B 141 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA ILE E 513 " pdb=" N ILE E 513 " pdb=" C ILE E 513 " pdb=" CB ILE E 513 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2901 not shown) Planarity restraints: 3280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 63 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C GLN E 63 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN E 63 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 64 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 457 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO E 458 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 458 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 458 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 457 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 458 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.028 5.00e-02 4.00e+02 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 8321 2.93 - 3.42: 20978 3.42 - 3.92: 32601 3.92 - 4.41: 37903 4.41 - 4.90: 60419 Nonbonded interactions: 160222 Sorted by model distance: nonbonded pdb=" O GLY B 834 " pdb=" ND2 ASN B 837 " model vdw 2.439 3.120 nonbonded pdb=" N GLN E 833 " pdb=" OE1 GLN E 833 " model vdw 2.528 3.120 nonbonded pdb=" O ASN E 59 " pdb=" OD1 ASN E 59 " model vdw 2.537 3.040 nonbonded pdb=" O THR D 414 " pdb=" OG1 THR D 414 " model vdw 2.538 3.040 nonbonded pdb=" O LYS E 379 " pdb=" OD1 ASP E 382 " model vdw 2.546 3.040 ... (remaining 160217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 9.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.003 0.064 19316 Z= 0.157 Angle : 0.622 12.982 26142 Z= 0.324 Chirality : 0.041 0.196 2904 Planarity : 0.004 0.056 3280 Dihedral : 18.552 85.918 7282 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.56 % Allowed : 30.84 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2262 helix: 1.15 (0.15), residues: 1196 sheet: -1.23 (0.33), residues: 253 loop : -1.82 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 271 TYR 0.029 0.001 TYR E 505 PHE 0.015 0.001 PHE E 18 TRP 0.022 0.001 TRP E 697 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (19314) covalent geometry : angle 0.62193 / 0.32 (26138) SS BOND : bond 0.00155 / 0.08 ( 2) SS BOND : angle 1.62783 / 1.03 ( 4) hydrogen bonds : bond 0.13521 / 8.90 ( 916) hydrogen bonds : angle 6.50873 / 4.61 ( 2688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.636 Fit side-chains REVERT: A 248 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.5095 (m-10) REVERT: A 286 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7302 (mt-10) REVERT: A 303 MET cc_start: 0.7326 (mmm) cc_final: 0.6971 (mmm) REVERT: A 308 ARG cc_start: 0.8359 (tpp80) cc_final: 0.8119 (tpt-90) REVERT: A 487 TYR cc_start: 0.8509 (t80) cc_final: 0.8252 (t80) REVERT: B 282 ASN cc_start: 0.8114 (m-40) cc_final: 0.7451 (t0) REVERT: B 466 MET cc_start: 0.6010 (tpt) cc_final: 0.5404 (tpt) REVERT: B 486 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8581 (mmtm) REVERT: B 509 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9034 (mp) REVERT: B 769 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8013 (tt) REVERT: B 796 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7041 (mt0) REVERT: D 255 MET cc_start: 0.6960 (ppp) cc_final: 0.6444 (ptt) REVERT: D 382 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8075 (pp) REVERT: D 403 GLU cc_start: 0.7341 (pm20) cc_final: 0.7091 (pm20) REVERT: D 425 CYS cc_start: 0.8638 (m) cc_final: 0.8173 (p) REVERT: D 483 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8738 (pp30) REVERT: E 35 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: E 418 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: E 424 MET cc_start: 0.8359 (tpp) cc_final: 0.7845 (mpp) REVERT: E 466 MET cc_start: 0.4848 (tpt) cc_final: 0.4368 (ttm) REVERT: E 505 TYR cc_start: 0.6559 (t80) cc_final: 0.6295 (t80) REVERT: E 508 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 531 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: E 589 LEU cc_start: 0.8068 (mt) cc_final: 0.7670 (pp) REVERT: E 850 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8746 (tptt) REVERT: E 853 LEU cc_start: 0.7800 (tp) cc_final: 0.7512 (tp) outliers start: 53 outliers final: 37 residues processed: 237 average time/residue: 0.1105 time to fit residues: 42.9627 Evaluate side-chains 232 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 339 ASN B 414 HIS ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.106486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.088011 restraints weight = 52504.475| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.75 r_work: 0.3555 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19316 Z= 0.285 Angle : 0.656 10.085 26142 Z= 0.347 Chirality : 0.044 0.200 2904 Planarity : 0.004 0.059 3280 Dihedral : 11.017 84.659 2782 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.91 % Favored : 91.95 % Rotamer: Outliers : 6.61 % Allowed : 27.65 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2262 helix: 0.87 (0.15), residues: 1219 sheet: -1.11 (0.35), residues: 225 loop : -2.09 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 271 TYR 0.017 0.002 TYR E 70 PHE 0.029 0.002 PHE E 18 TRP 0.025 0.002 TRP E 697 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 (19314) covalent geometry : angle 0.65612 / 0.35 (26138) SS BOND : bond 0.00392 / 0.20 ( 2) SS BOND : angle 1.31503 / 0.80 ( 4) hydrogen bonds : bond 0.04720 / 3.08 ( 916) hydrogen bonds : angle 5.35768 / 3.74 ( 2688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 191 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.5192 (m-10) REVERT: A 263 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8248 (tptp) REVERT: A 286 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7311 (mt-10) REVERT: A 303 MET cc_start: 0.7057 (mmm) cc_final: 0.6664 (mmm) REVERT: A 307 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 411 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6619 (tt) REVERT: A 487 TYR cc_start: 0.8414 (t80) cc_final: 0.8213 (t80) REVERT: B 224 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5446 (mm) REVERT: B 255 GLU cc_start: 0.8607 (mp0) cc_final: 0.8107 (mt-10) REVERT: B 282 ASN cc_start: 0.8112 (m-40) cc_final: 0.7442 (t0) REVERT: B 418 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 466 MET cc_start: 0.6289 (tpt) cc_final: 0.5632 (tpt) REVERT: B 486 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8603 (mmtm) REVERT: B 748 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: B 769 ILE cc_start: 0.8383 (tt) cc_final: 0.8044 (tt) REVERT: B 798 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7452 (tt) REVERT: D 320 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6875 (mtt90) REVERT: D 403 GLU cc_start: 0.7390 (pm20) cc_final: 0.7126 (pm20) REVERT: D 469 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6707 (t80) REVERT: D 483 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8698 (pp30) REVERT: E 418 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: E 424 MET cc_start: 0.8407 (tpp) cc_final: 0.7892 (mpp) REVERT: E 466 MET cc_start: 0.5034 (tpt) cc_final: 0.4632 (ttm) REVERT: E 505 TYR cc_start: 0.7013 (t80) cc_final: 0.6659 (t80) REVERT: E 531 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: E 589 LEU cc_start: 0.8039 (mt) cc_final: 0.7624 (pp) REVERT: E 850 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8781 (tptt) outliers start: 137 outliers final: 81 residues processed: 301 average time/residue: 0.1146 time to fit residues: 56.1660 Evaluate side-chains 275 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 182 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 367 HIS Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 638 LYS Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 87 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 219 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 150 optimal weight: 0.2980 chunk 194 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 339 ASN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.109942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.091135 restraints weight = 51551.625| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.86 r_work: 0.3601 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19316 Z= 0.125 Angle : 0.563 11.093 26142 Z= 0.290 Chirality : 0.042 0.244 2904 Planarity : 0.004 0.053 3280 Dihedral : 10.385 84.994 2750 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 5.12 % Allowed : 28.52 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2262 helix: 1.18 (0.15), residues: 1215 sheet: -1.27 (0.33), residues: 256 loop : -1.91 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.012 0.001 TYR A 443 PHE 0.015 0.001 PHE E 18 TRP 0.022 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19314) covalent geometry : angle 0.56250 / 0.29 (26138) SS BOND : bond 0.00044 / 0.02 ( 2) SS BOND : angle 1.66442 / 1.04 ( 4) hydrogen bonds : bond 0.03875 / 2.56 ( 916) hydrogen bonds : angle 5.02255 / 3.51 ( 2688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 195 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.5107 (m-10) REVERT: A 263 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8242 (tptp) REVERT: A 286 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7275 (mt-10) REVERT: A 411 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6274 (tt) REVERT: A 443 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: B 255 GLU cc_start: 0.8478 (mp0) cc_final: 0.7934 (mp0) REVERT: B 282 ASN cc_start: 0.8026 (m-40) cc_final: 0.7407 (t0) REVERT: B 466 MET cc_start: 0.5991 (tpt) cc_final: 0.5381 (tpt) REVERT: B 486 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8490 (mmtm) REVERT: B 618 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9154 (mt) REVERT: B 748 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: B 769 ILE cc_start: 0.8310 (tt) cc_final: 0.7955 (tt) REVERT: D 320 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6915 (mtt90) REVERT: D 403 GLU cc_start: 0.7336 (pm20) cc_final: 0.7068 (pm20) REVERT: D 425 CYS cc_start: 0.8665 (m) cc_final: 0.8334 (p) REVERT: D 469 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6871 (t80) REVERT: E 418 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: E 424 MET cc_start: 0.8295 (tpp) cc_final: 0.7768 (mpp) REVERT: E 466 MET cc_start: 0.4961 (tpt) cc_final: 0.4519 (ttm) REVERT: E 531 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: E 589 LEU cc_start: 0.8058 (mt) cc_final: 0.7651 (pp) REVERT: E 850 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8776 (tptt) outliers start: 106 outliers final: 57 residues processed: 283 average time/residue: 0.1035 time to fit residues: 47.5975 Evaluate side-chains 253 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 710 ASN Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 127 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.090944 restraints weight = 51415.087| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.85 r_work: 0.3631 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19316 Z= 0.132 Angle : 0.557 11.039 26142 Z= 0.286 Chirality : 0.041 0.319 2904 Planarity : 0.004 0.055 3280 Dihedral : 10.250 85.028 2732 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.88 % Rotamer: Outliers : 5.98 % Allowed : 27.99 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2262 helix: 1.24 (0.15), residues: 1215 sheet: -1.34 (0.33), residues: 260 loop : -1.89 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.017 0.001 TYR B 565 PHE 0.017 0.001 PHE E 18 TRP 0.018 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19314) covalent geometry : angle 0.55666 / 0.29 (26138) SS BOND : bond 0.00034 / 0.02 ( 2) SS BOND : angle 1.54400 / 0.97 ( 4) hydrogen bonds : bond 0.03640 / 2.40 ( 916) hydrogen bonds : angle 4.85730 / 3.39 ( 2688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 204 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.5130 (m-10) REVERT: A 266 ILE cc_start: 0.7879 (mp) cc_final: 0.7654 (mt) REVERT: A 286 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7304 (mt-10) REVERT: A 303 MET cc_start: 0.6830 (mmm) cc_final: 0.6507 (mmm) REVERT: A 307 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 411 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6292 (tt) REVERT: A 443 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: B 37 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: B 255 GLU cc_start: 0.8455 (mp0) cc_final: 0.7900 (mp0) REVERT: B 282 ASN cc_start: 0.8027 (m-40) cc_final: 0.7372 (t0) REVERT: B 418 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: B 466 MET cc_start: 0.6025 (tpt) cc_final: 0.5375 (tpt) REVERT: B 486 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8485 (mmtm) REVERT: B 493 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 618 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9163 (mt) REVERT: B 748 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 769 ILE cc_start: 0.8291 (tt) cc_final: 0.7921 (tt) REVERT: B 796 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: B 798 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7398 (tt) REVERT: D 320 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6856 (mtt90) REVERT: D 403 GLU cc_start: 0.7335 (pm20) cc_final: 0.7061 (pm20) REVERT: D 469 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6866 (t80) REVERT: E 225 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7962 (pp) REVERT: E 418 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: E 424 MET cc_start: 0.8282 (tpp) cc_final: 0.7773 (mpp) REVERT: E 466 MET cc_start: 0.4999 (tpt) cc_final: 0.4554 (ttm) REVERT: E 531 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: E 589 LEU cc_start: 0.8029 (mt) cc_final: 0.7602 (pp) REVERT: E 850 LYS cc_start: 0.9076 (ttmm) cc_final: 0.8756 (tptt) outliers start: 124 outliers final: 75 residues processed: 302 average time/residue: 0.1075 time to fit residues: 53.4372 Evaluate side-chains 277 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 710 ASN Chi-restraints excluded: chain E residue 711 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 56 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.111124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.092509 restraints weight = 50233.127| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.81 r_work: 0.3664 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19316 Z= 0.110 Angle : 0.562 10.891 26142 Z= 0.283 Chirality : 0.041 0.286 2904 Planarity : 0.003 0.053 3280 Dihedral : 10.185 85.326 2730 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 5.02 % Allowed : 28.86 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2262 helix: 1.34 (0.15), residues: 1211 sheet: -1.33 (0.33), residues: 259 loop : -1.85 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.012 0.001 TYR D 270 PHE 0.017 0.001 PHE A 367 TRP 0.017 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (19314) covalent geometry : angle 0.56193 / 0.28 (26138) SS BOND : bond 0.00080 / 0.04 ( 2) SS BOND : angle 1.62506 / 1.02 ( 4) hydrogen bonds : bond 0.03422 / 2.27 ( 916) hydrogen bonds : angle 4.80712 / 3.35 ( 2688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 198 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.4971 (m-10) REVERT: A 266 ILE cc_start: 0.7932 (mp) cc_final: 0.7697 (mt) REVERT: A 286 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 303 MET cc_start: 0.6879 (mmm) cc_final: 0.6519 (mmm) REVERT: A 307 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 411 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6219 (tt) REVERT: A 443 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: B 37 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: B 255 GLU cc_start: 0.8407 (mp0) cc_final: 0.7939 (mp0) REVERT: B 282 ASN cc_start: 0.7976 (m-40) cc_final: 0.7343 (t0) REVERT: B 418 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: B 466 MET cc_start: 0.5908 (tpt) cc_final: 0.5314 (tpt) REVERT: B 486 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8481 (mmtm) REVERT: B 493 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8198 (mm) REVERT: B 618 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9146 (mt) REVERT: B 748 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: B 769 ILE cc_start: 0.8312 (tt) cc_final: 0.7917 (tt) REVERT: B 796 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: B 798 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7413 (tt) REVERT: D 343 TYR cc_start: 0.7155 (t80) cc_final: 0.6872 (t80) REVERT: D 403 GLU cc_start: 0.7354 (pm20) cc_final: 0.7073 (pm20) REVERT: D 425 CYS cc_start: 0.8614 (m) cc_final: 0.8182 (p) REVERT: D 456 LYS cc_start: 0.7032 (mtpt) cc_final: 0.6628 (mttt) REVERT: D 469 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6895 (t80) REVERT: E 225 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7887 (pp) REVERT: E 276 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7343 (mp) REVERT: E 391 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6741 (ttm170) REVERT: E 424 MET cc_start: 0.8259 (tpp) cc_final: 0.7738 (mpp) REVERT: E 466 MET cc_start: 0.5024 (tpt) cc_final: 0.4617 (ttm) REVERT: E 589 LEU cc_start: 0.8055 (mt) cc_final: 0.7632 (pp) REVERT: E 850 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8755 (tptt) outliers start: 104 outliers final: 64 residues processed: 280 average time/residue: 0.1028 time to fit residues: 47.0708 Evaluate side-chains 271 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 192 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 20 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN E 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.108740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.090217 restraints weight = 50955.712| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.81 r_work: 0.3618 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19316 Z= 0.172 Angle : 0.583 11.065 26142 Z= 0.298 Chirality : 0.042 0.352 2904 Planarity : 0.004 0.057 3280 Dihedral : 10.111 84.565 2721 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 6.18 % Allowed : 28.04 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2262 helix: 1.27 (0.15), residues: 1215 sheet: -1.31 (0.33), residues: 259 loop : -1.87 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 802 TYR 0.018 0.001 TYR B 565 PHE 0.021 0.002 PHE E 18 TRP 0.017 0.002 TRP E 697 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (19314) covalent geometry : angle 0.58301 / 0.30 (26138) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 1.38354 / 0.86 ( 4) hydrogen bonds : bond 0.03669 / 2.42 ( 916) hydrogen bonds : angle 4.79333 / 3.33 ( 2688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 189 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.5129 (m-10) REVERT: A 266 ILE cc_start: 0.7957 (mp) cc_final: 0.7714 (mt) REVERT: A 286 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7307 (mt-10) REVERT: A 303 MET cc_start: 0.6861 (mmm) cc_final: 0.6584 (mmm) REVERT: A 307 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: A 411 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6308 (tt) REVERT: A 523 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7547 (pp) REVERT: B 37 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: B 255 GLU cc_start: 0.8521 (mp0) cc_final: 0.7951 (mp0) REVERT: B 282 ASN cc_start: 0.8066 (m-40) cc_final: 0.7378 (t0) REVERT: B 418 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: B 466 MET cc_start: 0.6200 (tpt) cc_final: 0.5557 (tpt) REVERT: B 486 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8507 (mmtm) REVERT: B 618 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9173 (mt) REVERT: B 748 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: B 769 ILE cc_start: 0.8317 (tt) cc_final: 0.7926 (tt) REVERT: D 320 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6847 (mtt90) REVERT: D 343 TYR cc_start: 0.7315 (t80) cc_final: 0.6980 (t80) REVERT: D 403 GLU cc_start: 0.7342 (pm20) cc_final: 0.7043 (pm20) REVERT: D 425 CYS cc_start: 0.8631 (m) cc_final: 0.8239 (p) REVERT: D 456 LYS cc_start: 0.7040 (mtpt) cc_final: 0.6656 (mtpt) REVERT: E 225 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7997 (pp) REVERT: E 391 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6761 (ttm170) REVERT: E 418 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: E 424 MET cc_start: 0.8280 (tpp) cc_final: 0.7750 (mpp) REVERT: E 466 MET cc_start: 0.5053 (tpt) cc_final: 0.4570 (ttm) REVERT: E 531 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: E 589 LEU cc_start: 0.8051 (mt) cc_final: 0.7607 (pp) REVERT: E 850 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8769 (tptt) outliers start: 128 outliers final: 87 residues processed: 290 average time/residue: 0.1047 time to fit residues: 49.0908 Evaluate side-chains 289 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 189 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 710 ASN Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 44 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.109427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.090653 restraints weight = 51094.992| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.87 r_work: 0.3631 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19316 Z= 0.136 Angle : 0.581 11.155 26142 Z= 0.294 Chirality : 0.042 0.316 2904 Planarity : 0.004 0.053 3280 Dihedral : 10.098 84.512 2721 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % Rotamer: Outliers : 5.65 % Allowed : 29.01 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2262 helix: 1.30 (0.15), residues: 1215 sheet: -1.37 (0.32), residues: 261 loop : -1.84 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.013 0.001 TYR D 270 PHE 0.025 0.001 PHE E 305 TRP 0.019 0.001 TRP E 697 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19314) covalent geometry : angle 0.58065 / 0.29 (26138) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 1.49225 / 0.93 ( 4) hydrogen bonds : bond 0.03526 / 2.33 ( 916) hydrogen bonds : angle 4.76242 / 3.32 ( 2688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 200 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.5114 (m-10) REVERT: A 266 ILE cc_start: 0.7961 (mp) cc_final: 0.7727 (mt) REVERT: A 286 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7264 (mt-10) REVERT: A 303 MET cc_start: 0.6840 (mmm) cc_final: 0.6565 (mmm) REVERT: A 307 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 308 ARG cc_start: 0.7546 (tpt-90) cc_final: 0.7144 (tpt-90) REVERT: A 411 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6240 (tt) REVERT: A 443 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.6183 (m-80) REVERT: B 37 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: B 255 GLU cc_start: 0.8481 (mp0) cc_final: 0.7928 (mp0) REVERT: B 282 ASN cc_start: 0.8053 (m-40) cc_final: 0.7375 (t0) REVERT: B 418 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: B 466 MET cc_start: 0.5964 (tpt) cc_final: 0.5345 (tpt) REVERT: B 486 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8483 (mmtm) REVERT: B 493 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 618 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9167 (mt) REVERT: B 748 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 769 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 796 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: D 343 TYR cc_start: 0.7216 (t80) cc_final: 0.6912 (t80) REVERT: D 403 GLU cc_start: 0.7334 (pm20) cc_final: 0.7080 (pm20) REVERT: D 425 CYS cc_start: 0.8636 (m) cc_final: 0.8269 (p) REVERT: D 456 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6711 (mtpt) REVERT: E 225 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (pp) REVERT: E 391 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6884 (ttm170) REVERT: E 418 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: E 424 MET cc_start: 0.8246 (tpp) cc_final: 0.7739 (mpp) REVERT: E 466 MET cc_start: 0.5040 (tpt) cc_final: 0.4604 (ttm) REVERT: E 531 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: E 589 LEU cc_start: 0.8020 (mt) cc_final: 0.7585 (pp) REVERT: E 850 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8753 (tptt) outliers start: 117 outliers final: 83 residues processed: 291 average time/residue: 0.1054 time to fit residues: 49.8157 Evaluate side-chains 288 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 190 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 711 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 1 optimal weight: 0.0670 chunk 214 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 ASN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.110014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.091479 restraints weight = 50730.780| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.79 r_work: 0.3648 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19316 Z= 0.128 Angle : 0.585 11.222 26142 Z= 0.294 Chirality : 0.042 0.326 2904 Planarity : 0.004 0.056 3280 Dihedral : 10.061 84.569 2719 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.84 % Rotamer: Outliers : 5.60 % Allowed : 29.01 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2262 helix: 1.33 (0.15), residues: 1215 sheet: -1.37 (0.32), residues: 261 loop : -1.83 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.019 0.001 TYR D 463 PHE 0.019 0.001 PHE E 305 TRP 0.019 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19314) covalent geometry : angle 0.58480 / 0.29 (26138) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 1.50525 / 0.94 ( 4) hydrogen bonds : bond 0.03454 / 2.29 ( 916) hydrogen bonds : angle 4.72513 / 3.29 ( 2688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 196 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.5024 (m-10) REVERT: A 266 ILE cc_start: 0.7952 (mp) cc_final: 0.7722 (mt) REVERT: A 286 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7294 (mt-10) REVERT: A 303 MET cc_start: 0.6962 (mmm) cc_final: 0.6677 (mmm) REVERT: A 307 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 411 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6233 (tt) REVERT: A 443 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: B 37 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: B 255 GLU cc_start: 0.8479 (mp0) cc_final: 0.7952 (mp0) REVERT: B 282 ASN cc_start: 0.8015 (m-40) cc_final: 0.7368 (t0) REVERT: B 418 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: B 466 MET cc_start: 0.5979 (tpt) cc_final: 0.5366 (tpt) REVERT: B 486 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8494 (mmtm) REVERT: B 493 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8218 (mm) REVERT: B 618 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9180 (mt) REVERT: B 704 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6344 (t0) REVERT: B 748 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 769 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7910 (tt) REVERT: B 796 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: B 845 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: D 403 GLU cc_start: 0.7376 (pm20) cc_final: 0.7091 (pm20) REVERT: D 425 CYS cc_start: 0.8595 (m) cc_final: 0.8246 (p) REVERT: D 456 LYS cc_start: 0.7071 (mtpt) cc_final: 0.6686 (mtpt) REVERT: D 483 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8713 (pp30) REVERT: E 225 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7931 (pp) REVERT: E 391 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6874 (ttm170) REVERT: E 418 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: E 424 MET cc_start: 0.8241 (tpp) cc_final: 0.7748 (mpp) REVERT: E 466 MET cc_start: 0.5075 (tpt) cc_final: 0.4641 (ttm) REVERT: E 531 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: E 589 LEU cc_start: 0.8019 (mt) cc_final: 0.7586 (pp) REVERT: E 850 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8752 (tptt) outliers start: 116 outliers final: 86 residues processed: 286 average time/residue: 0.1113 time to fit residues: 51.9049 Evaluate side-chains 292 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 189 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 ASN Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 711 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 192 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.110335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.091672 restraints weight = 50433.844| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.77 r_work: 0.3650 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19316 Z= 0.128 Angle : 0.588 11.143 26142 Z= 0.293 Chirality : 0.042 0.364 2904 Planarity : 0.003 0.055 3280 Dihedral : 10.040 84.590 2719 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 5.41 % Allowed : 29.34 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2262 helix: 1.32 (0.15), residues: 1215 sheet: -1.34 (0.33), residues: 249 loop : -1.80 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.011 0.001 TYR E 70 PHE 0.017 0.001 PHE E 18 TRP 0.018 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19314) covalent geometry : angle 0.58732 / 0.29 (26138) SS BOND : bond 0.00049 / 0.02 ( 2) SS BOND : angle 1.48587 / 0.92 ( 4) hydrogen bonds : bond 0.03426 / 2.27 ( 916) hydrogen bonds : angle 4.70658 / 3.29 ( 2688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 198 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.5070 (m-10) REVERT: A 266 ILE cc_start: 0.7967 (mp) cc_final: 0.7736 (mt) REVERT: A 286 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7299 (mt-10) REVERT: A 303 MET cc_start: 0.6956 (mmm) cc_final: 0.6658 (mmm) REVERT: A 307 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 411 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6230 (tt) REVERT: A 443 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: B 37 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: B 255 GLU cc_start: 0.8487 (mp0) cc_final: 0.7967 (mp0) REVERT: B 282 ASN cc_start: 0.8005 (m-40) cc_final: 0.7369 (t0) REVERT: B 345 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 418 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 466 MET cc_start: 0.5967 (tpt) cc_final: 0.5342 (tpt) REVERT: B 486 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8624 (mmtm) REVERT: B 493 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 618 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9174 (mt) REVERT: B 748 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 769 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7783 (tt) REVERT: B 796 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: B 845 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: D 255 MET cc_start: 0.6975 (ppp) cc_final: 0.6456 (ptt) REVERT: D 403 GLU cc_start: 0.7381 (pm20) cc_final: 0.7093 (pm20) REVERT: D 425 CYS cc_start: 0.8559 (m) cc_final: 0.8223 (p) REVERT: D 456 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6733 (mtpt) REVERT: E 225 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7914 (pp) REVERT: E 391 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6896 (ttm170) REVERT: E 418 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: E 424 MET cc_start: 0.8221 (tpp) cc_final: 0.7731 (mpp) REVERT: E 466 MET cc_start: 0.5207 (tpt) cc_final: 0.4776 (ttm) REVERT: E 589 LEU cc_start: 0.8004 (mt) cc_final: 0.7574 (pp) REVERT: E 850 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8760 (tptt) outliers start: 112 outliers final: 85 residues processed: 283 average time/residue: 0.1138 time to fit residues: 51.6635 Evaluate side-chains 292 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 191 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 710 ASN Chi-restraints excluded: chain E residue 711 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 162 optimal weight: 0.0980 chunk 62 optimal weight: 0.0870 chunk 154 optimal weight: 0.8980 chunk 180 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 173 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.110865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092254 restraints weight = 49714.491| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.80 r_work: 0.3664 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19316 Z= 0.116 Angle : 0.598 11.629 26142 Z= 0.297 Chirality : 0.042 0.355 2904 Planarity : 0.003 0.055 3280 Dihedral : 9.977 84.747 2717 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 4.68 % Allowed : 30.16 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2262 helix: 1.36 (0.15), residues: 1203 sheet: -1.15 (0.33), residues: 251 loop : -1.79 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.017 0.001 TYR D 463 PHE 0.014 0.001 PHE E 18 TRP 0.019 0.001 TRP E 697 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (19314) covalent geometry : angle 0.59796 / 0.30 (26138) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 1.56215 / 0.97 ( 4) hydrogen bonds : bond 0.03338 / 2.21 ( 916) hydrogen bonds : angle 4.69296 / 3.27 ( 2688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 196 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.5026 (m-10) REVERT: A 266 ILE cc_start: 0.7969 (mp) cc_final: 0.7740 (mt) REVERT: A 286 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7277 (mt-10) REVERT: A 303 MET cc_start: 0.6933 (mmm) cc_final: 0.6634 (mmm) REVERT: A 307 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 411 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6209 (tt) REVERT: A 443 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.6084 (m-80) REVERT: B 37 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: B 255 GLU cc_start: 0.8402 (mp0) cc_final: 0.7857 (mp0) REVERT: B 282 ASN cc_start: 0.7993 (m-40) cc_final: 0.7352 (t0) REVERT: B 345 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 418 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: B 466 MET cc_start: 0.5910 (tpt) cc_final: 0.5319 (tpt) REVERT: B 486 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8610 (mmtm) REVERT: B 493 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 618 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9167 (mt) REVERT: B 748 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 754 PHE cc_start: 0.7163 (t80) cc_final: 0.6673 (t80) REVERT: B 769 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7747 (tt) REVERT: B 796 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: B 845 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: D 255 MET cc_start: 0.6955 (ppp) cc_final: 0.6450 (ptt) REVERT: D 403 GLU cc_start: 0.7371 (pm20) cc_final: 0.7035 (pm20) REVERT: D 425 CYS cc_start: 0.8533 (m) cc_final: 0.8214 (p) REVERT: D 456 LYS cc_start: 0.7092 (mtpt) cc_final: 0.6691 (mtpt) REVERT: D 483 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8678 (pp30) REVERT: E 225 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7888 (pp) REVERT: E 391 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.6919 (ttm170) REVERT: E 418 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: E 424 MET cc_start: 0.8291 (tpp) cc_final: 0.7794 (mpp) REVERT: E 466 MET cc_start: 0.5010 (tpt) cc_final: 0.4606 (ttm) REVERT: E 531 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: E 589 LEU cc_start: 0.7987 (mt) cc_final: 0.7569 (pp) REVERT: E 850 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8766 (tptt) outliers start: 97 outliers final: 76 residues processed: 270 average time/residue: 0.1090 time to fit residues: 47.3580 Evaluate side-chains 284 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 191 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 521 ASN Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 796 GLN Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 337 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 391 ARG Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 531 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 586 LYS Chi-restraints excluded: chain E residue 587 ASN Chi-restraints excluded: chain E residue 599 TYR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 710 ASN Chi-restraints excluded: chain E residue 711 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 828 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN E 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.109625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091011 restraints weight = 50747.297| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.76 r_work: 0.3636 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19316 Z= 0.158 Angle : 0.608 11.483 26142 Z= 0.304 Chirality : 0.043 0.367 2904 Planarity : 0.004 0.057 3280 Dihedral : 9.988 84.377 2717 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.40 % Rotamer: Outliers : 5.16 % Allowed : 29.83 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2262 helix: 1.30 (0.15), residues: 1205 sheet: -1.08 (0.34), residues: 239 loop : -1.84 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.014 0.001 TYR D 270 PHE 0.020 0.001 PHE E 18 TRP 0.015 0.002 TRP E 697 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (19314) covalent geometry : angle 0.60757 / 0.30 (26138) SS BOND : bond 0.00118 / 0.06 ( 2) SS BOND : angle 1.38898 / 0.86 ( 4) hydrogen bonds : bond 0.03488 / 2.31 ( 916) hydrogen bonds : angle 4.71126 / 3.28 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.41 seconds wall clock time: 71 minutes 0.93 seconds (4260.93 seconds total)