Starting phenix.real_space_refine on Tue Jan 21 23:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1j_18818/01_2025/8r1j_18818.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.969 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 239 5.16 5 C 21410 2.51 5 N 5877 2.21 5 O 6375 1.98 5 H 33874 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67775 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11256 Classifications: {'peptide': 699} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 668} Chain breaks: 4 Chain: "B" Number of atoms: 10982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 10982 Classifications: {'peptide': 689} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 657} Chain breaks: 6 Chain: "C" Number of atoms: 11937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 11937 Classifications: {'peptide': 743} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 714} Chain breaks: 1 Chain: "D" Number of atoms: 11373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11373 Classifications: {'peptide': 707} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 675} Chain breaks: 1 Chain: "E" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 9585 Classifications: {'peptide': 607} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 579} Chain breaks: 3 Chain: "F" Number of atoms: 10071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 10071 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 605} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2571 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Time building chain proxies: 22.58, per 1000 atoms: 0.33 Number of scatterers: 67775 At special positions: 0 Unit cell: (114.328, 150.367, 201.317, 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 239 16.00 O 6375 8.00 N 5877 7.00 C 21410 6.00 H 33874 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.35 Conformation dependent library (CDL) restraints added in 4.1 seconds 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7984 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 47 sheets defined 46.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.664A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.780A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 184 removed outlier: 4.014A pdb=" N ILE A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.634A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.562A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.720A pdb=" N CYS A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.552A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.614A pdb=" N ILE A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 580 through 604 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.856A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.726A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 removed outlier: 3.564A pdb=" N HIS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.561A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.666A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 250 through 266 removed outlier: 3.754A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 3.627A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.507A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.569A pdb=" N ASN B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.765A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.212A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.701A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.649A pdb=" N MET B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.832A pdb=" N THR B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.874A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 Processing helix chain 'B' and resid 701 through 704 Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.843A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 removed outlier: 4.226A pdb=" N ILE C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.249A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.623A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.351A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 167 removed outlier: 3.533A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.757A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.571A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 254 through 272 Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 389 through 404 removed outlier: 3.934A pdb=" N SER C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 removed outlier: 4.252A pdb=" N ILE C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 442 through 450 Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.517A pdb=" N LEU C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 576 removed outlier: 6.427A pdb=" N GLU C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 576' Processing helix chain 'C' and resid 577 through 584 removed outlier: 3.790A pdb=" N LEU C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 701 through 705 Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 744 through 755 removed outlier: 3.879A pdb=" N GLN C 748 " --> pdb=" O LEU C 744 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 754 " --> pdb=" O ALA C 750 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 755 " --> pdb=" O THR C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 9 removed outlier: 3.719A pdb=" N PHE D 9 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.596A pdb=" N VAL D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 50 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 164 through 185 Processing helix chain 'D' and resid 186 through 191 removed outlier: 5.686A pdb=" N ASP D 189 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.641A pdb=" N GLY D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 312 removed outlier: 3.774A pdb=" N ILE D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 removed outlier: 3.630A pdb=" N ALA D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 370 Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 433 through 452 removed outlier: 4.641A pdb=" N HIS D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 476 removed outlier: 3.570A pdb=" N ALA D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.547A pdb=" N LEU D 532 " --> pdb=" O ASP D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 580 removed outlier: 3.643A pdb=" N GLU D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 604 removed outlier: 4.146A pdb=" N LEU D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 599 " --> pdb=" O MET D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.653A pdb=" N PHE D 612 " --> pdb=" O THR D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 650 removed outlier: 3.928A pdb=" N ARG D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 641 " --> pdb=" O CYS D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 675 removed outlier: 3.547A pdb=" N ARG D 663 " --> pdb=" O SER D 659 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 694 removed outlier: 3.736A pdb=" N LEU D 686 " --> pdb=" O ASP D 682 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 715 Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 35 through 49 removed outlier: 3.567A pdb=" N THR E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 115 Processing helix chain 'E' and resid 118 through 124 removed outlier: 3.677A pdb=" N GLN E 124 " --> pdb=" O LYS E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 156 through 161 Processing helix chain 'E' and resid 162 through 176 Processing helix chain 'E' and resid 214 through 222 Processing helix chain 'E' and resid 245 through 264 removed outlier: 3.706A pdb=" N ARG E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY E 250 " --> pdb=" O MET E 246 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE E 251 " --> pdb=" O GLN E 247 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 removed outlier: 3.647A pdb=" N ALA E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 removed outlier: 3.714A pdb=" N TYR E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 338 through 346 removed outlier: 3.569A pdb=" N ILE E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 346 " --> pdb=" O ILE E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 375 removed outlier: 4.207A pdb=" N ALA E 374 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 412 through 426 removed outlier: 3.817A pdb=" N THR E 417 " --> pdb=" O ASN E 413 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 418 " --> pdb=" O MET E 414 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 470 Processing helix chain 'E' and resid 518 through 537 removed outlier: 3.757A pdb=" N MET E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 559 Processing helix chain 'E' and resid 572 through 582 Processing helix chain 'E' and resid 585 through 589 removed outlier: 3.508A pdb=" N LEU E 589 " --> pdb=" O LYS E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 594 removed outlier: 3.771A pdb=" N GLY E 594 " --> pdb=" O VAL E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.510A pdb=" N LEU E 604 " --> pdb=" O ILE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'F' and resid 42 through 53 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.573A pdb=" N MET F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 removed outlier: 3.593A pdb=" N THR F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 115 through 127 Processing helix chain 'F' and resid 199 through 216 removed outlier: 3.861A pdb=" N ARG F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 216 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.527A pdb=" N GLN F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 271 Processing helix chain 'F' and resid 275 through 287 Processing helix chain 'F' and resid 294 through 301 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 390 through 406 removed outlier: 3.657A pdb=" N GLN F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 413 Processing helix chain 'F' and resid 429 through 441 Processing helix chain 'F' and resid 442 through 450 removed outlier: 4.032A pdb=" N GLY F 450 " --> pdb=" O PHE F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 556 removed outlier: 3.621A pdb=" N VAL F 545 " --> pdb=" O GLY F 541 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 546 " --> pdb=" O PRO F 542 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL F 547 " --> pdb=" O GLU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 567 Processing helix chain 'F' and resid 567 through 573 removed outlier: 3.542A pdb=" N LEU F 571 " --> pdb=" O ASP F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 577 through 584 removed outlier: 3.785A pdb=" N LEU F 583 " --> pdb=" O PRO F 579 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 584 " --> pdb=" O PHE F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 606 removed outlier: 3.763A pdb=" N SER F 593 " --> pdb=" O ARG F 589 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 606 " --> pdb=" O GLN F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 619 Processing helix chain 'F' and resid 620 through 623 removed outlier: 3.794A pdb=" N ALA F 623 " --> pdb=" O PRO F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 701 through 705 Processing helix chain 'F' and resid 712 through 716 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.558A pdb=" N HIS G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 80 through 87 removed outlier: 4.008A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Proline residue: G 108 - end of helix Processing helix chain 'G' and resid 123 through 128 removed outlier: 3.686A pdb=" N ASN G 127 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 128 " --> pdb=" O VAL G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.132A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG A 559 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.735A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.614A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 2 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.514A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.593A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 134 removed outlier: 5.992A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB7, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AB8, first strand: chain 'C' and resid 323 through 325 removed outlier: 3.834A pdb=" N PHE C 323 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 372 " --> pdb=" O MET C 365 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AC1, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC2, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AC3, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC4, first strand: chain 'C' and resid 657 through 658 removed outlier: 6.653A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 694 through 698 removed outlier: 5.341A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 698 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.391A pdb=" N GLU D 119 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE D 148 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY D 121 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AC8, first strand: chain 'D' and resid 292 through 293 removed outlier: 7.271A pdb=" N TYR D 501 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 557 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU D 549 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG D 559 " --> pdb=" O ASN D 547 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN D 547 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET D 561 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N CYS D 541 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE D 322 " --> pdb=" O CYS D 541 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU D 543 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE D 545 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 292 through 293 removed outlier: 5.508A pdb=" N THR D 498 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N CYS D 489 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU D 500 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER D 487 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 502 " --> pdb=" O MET D 485 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN D 481 " --> pdb=" O LYS D 506 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE D 480 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.111A pdb=" N GLU D 377 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN E 367 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 619 through 620 Processing sheet with id=AD3, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AD4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AD5, first strand: chain 'E' and resid 178 through 182 Processing sheet with id=AD6, first strand: chain 'E' and resid 243 through 244 removed outlier: 3.511A pdb=" N ASN E 225 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 224 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 439 through 442 removed outlier: 3.594A pdb=" N ILE E 450 " --> pdb=" O ASP E 439 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 447 " --> pdb=" O GLY E 304 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 489 through 492 removed outlier: 3.541A pdb=" N PHE E 492 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.718A pdb=" N MET F 90 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 129 through 135 removed outlier: 5.155A pdb=" N MET F 243 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL F 133 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU F 241 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 292 through 293 Processing sheet with id=AE3, first strand: chain 'F' and resid 319 through 320 removed outlier: 4.009A pdb=" N ILE F 319 " --> pdb=" O VAL F 494 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 323 through 325 removed outlier: 3.870A pdb=" N PHE F 323 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU F 362 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 383 " --> pdb=" O ARG F 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 342 through 344 Processing sheet with id=AE6, first strand: chain 'F' and resid 451 through 453 Processing sheet with id=AE7, first strand: chain 'F' and resid 497 through 498 Processing sheet with id=AE8, first strand: chain 'F' and resid 635 through 640 Processing sheet with id=AE9, first strand: chain 'F' and resid 657 through 659 removed outlier: 6.543A pdb=" N LEU F 665 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 694 through 698 removed outlier: 6.841A pdb=" N LEU F 733 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 730 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 22 through 23 removed outlier: 7.200A pdb=" N LEU G 47 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU G 69 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU G 93 " --> pdb=" O ASP G 119 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4050 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: 24.94 Time building geometry restraints manager: 16.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33814 1.03 - 1.23: 80 1.23 - 1.42: 14109 1.42 - 1.62: 19995 1.62 - 1.81: 416 Bond restraints: 68414 Sorted by residual: bond pdb=" CA ALA A 215 " pdb=" CB ALA A 215 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.41e-02 5.03e+03 1.64e+01 bond pdb=" C THR A 210 " pdb=" O THR A 210 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" CA ALA B 63 " pdb=" CB ALA B 63 " ideal model delta sigma weight residual 1.529 1.493 0.036 1.37e-02 5.33e+03 7.03e+00 bond pdb=" N LYS B 57 " pdb=" H LYS B 57 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" N ASN B 58 " pdb=" H ASN B 58 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 68409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.00: 123659 8.00 - 15.99: 1 15.99 - 23.99: 6 23.99 - 31.99: 13 31.99 - 39.99: 14 Bond angle restraints: 123693 Sorted by residual: angle pdb=" C PRO F 453 " pdb=" CA PRO F 453 " pdb=" HA PRO F 453 " ideal model delta sigma weight residual 109.00 69.01 39.99 3.00e+00 1.11e-01 1.78e+02 angle pdb=" C ILE B 682 " pdb=" CA ILE B 682 " pdb=" HA ILE B 682 " ideal model delta sigma weight residual 109.00 73.71 35.29 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C VAL A 253 " pdb=" CA VAL A 253 " pdb=" HA VAL A 253 " ideal model delta sigma weight residual 109.00 74.01 34.99 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N PRO F 453 " pdb=" CA PRO F 453 " pdb=" HA PRO F 453 " ideal model delta sigma weight residual 110.00 75.01 34.99 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ILE B 682 " pdb=" CA ILE B 682 " pdb=" HA ILE B 682 " ideal model delta sigma weight residual 110.00 75.05 34.95 3.00e+00 1.11e-01 1.36e+02 ... (remaining 123688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 28844 17.97 - 35.94: 2435 35.94 - 53.91: 562 53.91 - 71.88: 164 71.88 - 89.85: 28 Dihedral angle restraints: 32033 sinusoidal: 17791 harmonic: 14242 Sorted by residual: dihedral pdb=" CA ILE E 450 " pdb=" C ILE E 450 " pdb=" N VAL E 451 " pdb=" CA VAL E 451 " ideal model delta harmonic sigma weight residual 180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LYS B 736 " pdb=" C LYS B 736 " pdb=" N LYS B 737 " pdb=" CA LYS B 737 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C ILE B 682 " pdb=" N ILE B 682 " pdb=" CA ILE B 682 " pdb=" CB ILE B 682 " ideal model delta harmonic sigma weight residual -122.00 -132.65 10.65 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 32030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4880 0.086 - 0.171: 276 0.171 - 0.257: 1 0.257 - 0.343: 2 0.343 - 0.428: 3 Chirality restraints: 5162 Sorted by residual: chirality pdb=" CA SER D 296 " pdb=" N SER D 296 " pdb=" C SER D 296 " pdb=" CB SER D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PRO F 453 " pdb=" N PRO F 453 " pdb=" C PRO F 453 " pdb=" CB PRO F 453 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA ILE B 682 " pdb=" N ILE B 682 " pdb=" C ILE B 682 " pdb=" CB ILE B 682 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5159 not shown) Planarity restraints: 10010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 58 " 0.241 2.00e-02 2.50e+03 2.91e-01 1.27e+03 pdb=" CG ASN B 58 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 58 " -0.230 2.00e-02 2.50e+03 pdb=" ND2 ASN B 58 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 58 " -0.442 2.00e-02 2.50e+03 pdb="HD22 ASN B 58 " 0.448 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 212 " 0.306 9.50e-02 1.11e+02 1.77e-01 4.81e+02 pdb=" NE ARG A 212 " 0.142 2.00e-02 2.50e+03 pdb=" CZ ARG A 212 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 212 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 212 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG A 212 " -0.300 2.00e-02 2.50e+03 pdb="HH12 ARG A 212 " 0.259 2.00e-02 2.50e+03 pdb="HH21 ARG A 212 " -0.088 2.00e-02 2.50e+03 pdb="HH22 ARG A 212 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 217 " -0.031 2.00e-02 2.50e+03 3.18e-02 1.52e+01 pdb=" CD GLN A 217 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 217 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 GLN A 217 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 217 " 0.046 2.00e-02 2.50e+03 pdb="HE22 GLN A 217 " -0.047 2.00e-02 2.50e+03 ... (remaining 10007 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1958 2.13 - 2.75: 127727 2.75 - 3.37: 194517 3.37 - 3.98: 248413 3.98 - 4.60: 393929 Nonbonded interactions: 966544 Sorted by model distance: nonbonded pdb=" OD1 ASP D 55 " pdb=" H GLU D 59 " model vdw 1.516 2.450 nonbonded pdb=" H GLY E 26 " pdb=" OE1 GLU E 508 " model vdw 1.556 2.450 nonbonded pdb=" H GLY A 679 " pdb=" O ILE B 484 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASN D 647 " pdb=" HE1 TRP D 699 " model vdw 1.585 2.450 nonbonded pdb="HH21 ARG A 583 " pdb=" O PHE B 512 " model vdw 1.597 2.450 ... (remaining 966539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 141 or (resid 142 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 143 through 192 or \ (resid 202 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 o \ r name HG3)) or resid 203 through 716)) selection = (chain 'D' and (resid 1 through 63 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid \ 71 through 212 or (resid 213 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H \ or name HA )) or resid 214 through 295 or resid 299 through 392 or (resid 396 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame OD2 or name HA or name HB2 or name HB3)) or resid 397 through 550 or (resid \ 551 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE or name CZ or name NH1 or name NH2 or name HA )) or resid 557 through \ 716)) } ncs_group { reference = (chain 'B' and (resid 1 through 183 or (resid 184 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2)) or (resid 208 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ )) or (resid 209 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name NZ or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 210 through 63 \ 2 or (resid 655 and (name N or name CA or name C or name O or name CB or name CG \ or name SD or name CE or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HE1 or name HE2 or name HE3)) or resid 656 through 665)) selection = (chain 'E' and (resid 1 through 31 or (resid 35 and (name N or name CA or name C \ or name O or name HA2 or name HA3)) or resid 36 through 225 or (resid 226 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or re \ sid 244 through 502 or resid 510 through 576 or (resid 577 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 o \ r name H or name HA )) or resid 578 through 665)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.860 Extract box with map and model: 1.850 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 107.430 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 0.076 34540 Z= 0.209 Angle : 0.538 8.759 46573 Z= 0.303 Chirality : 0.041 0.428 5162 Planarity : 0.004 0.077 5992 Dihedral : 14.463 89.849 13195 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4187 helix: 0.27 (0.13), residues: 1826 sheet: -1.76 (0.25), residues: 444 loop : -1.73 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 88 HIS 0.005 0.001 HIS D 146 PHE 0.011 0.001 PHE C 323 TYR 0.017 0.001 TYR F 205 ARG 0.015 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 513 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 THR cc_start: 0.9182 (m) cc_final: 0.8966 (m) REVERT: B 735 ILE cc_start: 0.8442 (mm) cc_final: 0.8186 (tp) REVERT: D 77 GLU cc_start: 0.8213 (tp30) cc_final: 0.7913 (tp30) REVERT: D 374 MET cc_start: 0.8575 (mtp) cc_final: 0.7980 (mtp) REVERT: E 169 ASP cc_start: 0.6837 (m-30) cc_final: 0.6511 (m-30) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 1.0029 time to fit residues: 806.8887 Evaluate side-chains 443 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 199 optimal weight: 0.0870 chunk 244 optimal weight: 0.5980 chunk 380 optimal weight: 6.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104218 restraints weight = 139464.640| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.55 r_work: 0.3261 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34540 Z= 0.324 Angle : 0.564 8.748 46573 Z= 0.304 Chirality : 0.042 0.414 5162 Planarity : 0.005 0.061 5992 Dihedral : 4.263 22.136 4595 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 0.45 % Allowed : 4.81 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4187 helix: 0.34 (0.13), residues: 1842 sheet: -1.66 (0.25), residues: 441 loop : -1.81 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS B 605 PHE 0.013 0.001 PHE D 520 TYR 0.015 0.001 TYR E 555 ARG 0.007 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 475 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 458 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 691 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 128 THR cc_start: 0.9324 (t) cc_final: 0.9123 (m) REVERT: B 132 THR cc_start: 0.9276 (m) cc_final: 0.9051 (m) REVERT: C 356 VAL cc_start: 0.7169 (t) cc_final: 0.6927 (p) REVERT: D 77 GLU cc_start: 0.8258 (tp30) cc_final: 0.8023 (tp30) REVERT: D 160 ASP cc_start: 0.7692 (t0) cc_final: 0.7460 (t0) REVERT: D 305 TYR cc_start: 0.8103 (t80) cc_final: 0.7560 (t80) REVERT: D 327 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: D 374 MET cc_start: 0.8963 (mtp) cc_final: 0.8322 (mtp) REVERT: D 478 ASP cc_start: 0.7965 (t0) cc_final: 0.7628 (t0) REVERT: D 599 GLU cc_start: 0.8423 (tp30) cc_final: 0.8179 (tp30) REVERT: D 674 ASP cc_start: 0.8603 (t0) cc_final: 0.8257 (t0) REVERT: E 169 ASP cc_start: 0.7791 (m-30) cc_final: 0.7483 (m-30) REVERT: E 171 MET cc_start: 0.8700 (mmm) cc_final: 0.8420 (mmm) REVERT: F 715 ASN cc_start: 0.8543 (m-40) cc_final: 0.8116 (p0) outliers start: 17 outliers final: 13 residues processed: 468 average time/residue: 0.9835 time to fit residues: 713.0259 Evaluate side-chains 445 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 431 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 319 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 405 optimal weight: 5.9990 chunk 318 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 418 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106038 restraints weight = 139084.331| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.66 r_work: 0.3278 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34540 Z= 0.213 Angle : 0.514 8.862 46573 Z= 0.274 Chirality : 0.040 0.421 5162 Planarity : 0.004 0.053 5992 Dihedral : 4.157 23.199 4595 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.74 % Favored : 93.10 % Rotamer: Outliers : 0.43 % Allowed : 6.33 % Favored : 93.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4187 helix: 0.52 (0.13), residues: 1853 sheet: -1.59 (0.25), residues: 456 loop : -1.76 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS D 128 PHE 0.014 0.001 PHE F 438 TYR 0.015 0.001 TYR A 305 ARG 0.006 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 456 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 691 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 128 THR cc_start: 0.9334 (t) cc_final: 0.9131 (m) REVERT: B 132 THR cc_start: 0.9264 (m) cc_final: 0.9031 (m) REVERT: B 348 MET cc_start: 0.8298 (mmm) cc_final: 0.7819 (mtp) REVERT: C 120 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8120 (mt-10) REVERT: C 356 VAL cc_start: 0.7138 (t) cc_final: 0.6888 (p) REVERT: D 35 PHE cc_start: 0.8001 (t80) cc_final: 0.7399 (t80) REVERT: D 77 GLU cc_start: 0.8243 (tp30) cc_final: 0.8000 (tp30) REVERT: D 160 ASP cc_start: 0.7706 (t0) cc_final: 0.7438 (t0) REVERT: D 305 TYR cc_start: 0.8123 (t80) cc_final: 0.7563 (t80) REVERT: D 478 ASP cc_start: 0.7929 (t0) cc_final: 0.7548 (t0) REVERT: D 674 ASP cc_start: 0.8706 (t0) cc_final: 0.8223 (t0) REVERT: E 24 TYR cc_start: 0.8825 (m-80) cc_final: 0.8600 (m-80) REVERT: E 169 ASP cc_start: 0.7807 (m-30) cc_final: 0.7499 (m-30) outliers start: 16 outliers final: 10 residues processed: 465 average time/residue: 1.0063 time to fit residues: 732.9026 Evaluate side-chains 436 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 426 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 332 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 321 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 143 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 305 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107431 restraints weight = 138306.513| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.70 r_work: 0.3303 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 34540 Z= 0.149 Angle : 0.485 8.939 46573 Z= 0.256 Chirality : 0.040 0.423 5162 Planarity : 0.004 0.053 5992 Dihedral : 3.990 23.931 4595 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.50 % Rotamer: Outliers : 0.40 % Allowed : 6.84 % Favored : 92.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4187 helix: 0.82 (0.13), residues: 1847 sheet: -1.48 (0.25), residues: 471 loop : -1.68 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 438 HIS 0.004 0.000 HIS D 128 PHE 0.016 0.001 PHE D 4 TYR 0.018 0.001 TYR A 305 ARG 0.007 0.000 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 469 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 691 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 128 THR cc_start: 0.9309 (t) cc_final: 0.9107 (m) REVERT: B 132 THR cc_start: 0.9261 (m) cc_final: 0.9030 (m) REVERT: B 348 MET cc_start: 0.8163 (mmm) cc_final: 0.7862 (mtp) REVERT: B 735 ILE cc_start: 0.8477 (mm) cc_final: 0.8066 (tp) REVERT: C 120 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8130 (mt-10) REVERT: C 356 VAL cc_start: 0.7099 (t) cc_final: 0.6867 (p) REVERT: D 35 PHE cc_start: 0.7951 (t80) cc_final: 0.7444 (t80) REVERT: D 77 GLU cc_start: 0.8231 (tp30) cc_final: 0.7887 (tp30) REVERT: D 82 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: D 160 ASP cc_start: 0.7675 (t0) cc_final: 0.7384 (t0) REVERT: D 305 TYR cc_start: 0.8154 (t80) cc_final: 0.7655 (t80) REVERT: D 478 ASP cc_start: 0.7929 (t0) cc_final: 0.7515 (t0) REVERT: D 674 ASP cc_start: 0.8746 (t0) cc_final: 0.8177 (t0) REVERT: E 169 ASP cc_start: 0.7802 (m-30) cc_final: 0.7495 (m-30) REVERT: F 208 GLU cc_start: 0.8353 (tp30) cc_final: 0.8129 (tp30) REVERT: F 536 MET cc_start: 0.8675 (ttm) cc_final: 0.8338 (mmm) outliers start: 15 outliers final: 10 residues processed: 476 average time/residue: 0.9984 time to fit residues: 747.1351 Evaluate side-chains 450 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 440 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 308 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 373 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104607 restraints weight = 139388.492| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.59 r_work: 0.3273 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34540 Z= 0.278 Angle : 0.515 8.795 46573 Z= 0.274 Chirality : 0.041 0.428 5162 Planarity : 0.004 0.073 5992 Dihedral : 4.076 23.797 4595 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.33 % Favored : 92.50 % Rotamer: Outliers : 0.56 % Allowed : 7.61 % Favored : 91.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4187 helix: 0.78 (0.13), residues: 1842 sheet: -1.50 (0.26), residues: 452 loop : -1.73 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS B 605 PHE 0.012 0.001 PHE D 520 TYR 0.015 0.001 TYR A 305 ARG 0.008 0.000 ARG B 670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 451 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.9056 (mtt) cc_final: 0.8493 (mtt) REVERT: A 524 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8442 (mt-10) REVERT: B 128 THR cc_start: 0.9346 (t) cc_final: 0.9119 (m) REVERT: B 132 THR cc_start: 0.9279 (m) cc_final: 0.9040 (m) REVERT: B 348 MET cc_start: 0.8230 (mmm) cc_final: 0.7878 (mtp) REVERT: B 735 ILE cc_start: 0.8528 (mm) cc_final: 0.8191 (tp) REVERT: C 82 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6172 (t0) REVERT: C 120 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8108 (mt-10) REVERT: C 356 VAL cc_start: 0.7120 (t) cc_final: 0.6879 (p) REVERT: D 3 ASP cc_start: 0.7393 (t0) cc_final: 0.7117 (t0) REVERT: D 35 PHE cc_start: 0.7975 (t80) cc_final: 0.7434 (t80) REVERT: D 77 GLU cc_start: 0.8223 (tp30) cc_final: 0.7970 (tp30) REVERT: D 86 MET cc_start: 0.8530 (ttp) cc_final: 0.8325 (ttp) REVERT: D 160 ASP cc_start: 0.7706 (t0) cc_final: 0.7415 (t0) REVERT: D 305 TYR cc_start: 0.8173 (t80) cc_final: 0.7659 (t80) REVERT: D 478 ASP cc_start: 0.7970 (t0) cc_final: 0.7573 (t0) REVERT: D 674 ASP cc_start: 0.8819 (t0) cc_final: 0.8284 (t0) REVERT: E 169 ASP cc_start: 0.7821 (m-30) cc_final: 0.7524 (m-30) REVERT: F 208 GLU cc_start: 0.8424 (tp30) cc_final: 0.8138 (tp30) REVERT: F 536 MET cc_start: 0.8713 (ttm) cc_final: 0.8435 (mmm) outliers start: 21 outliers final: 15 residues processed: 459 average time/residue: 0.9804 time to fit residues: 702.1296 Evaluate side-chains 452 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 436 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 362 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 244 optimal weight: 0.0870 chunk 132 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.137062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095577 restraints weight = 139284.632| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.56 r_work: 0.3066 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34540 Z= 0.269 Angle : 0.515 8.839 46573 Z= 0.274 Chirality : 0.041 0.426 5162 Planarity : 0.004 0.093 5992 Dihedral : 4.096 24.093 4595 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.28 % Favored : 92.55 % Rotamer: Outliers : 0.77 % Allowed : 8.03 % Favored : 91.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4187 helix: 0.79 (0.13), residues: 1839 sheet: -1.50 (0.25), residues: 455 loop : -1.74 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS B 605 PHE 0.013 0.001 PHE D 520 TYR 0.018 0.001 TYR A 305 ARG 0.010 0.000 ARG B 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 447 time to evaluate : 4.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8492 (mt-10) REVERT: B 128 THR cc_start: 0.9329 (t) cc_final: 0.9060 (m) REVERT: B 132 THR cc_start: 0.9286 (m) cc_final: 0.9051 (m) REVERT: B 264 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7563 (mp0) REVERT: B 348 MET cc_start: 0.8146 (mmm) cc_final: 0.7868 (mtp) REVERT: C 120 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8097 (mt-10) REVERT: D 3 ASP cc_start: 0.7429 (t0) cc_final: 0.7149 (t0) REVERT: D 35 PHE cc_start: 0.7958 (t80) cc_final: 0.7416 (t80) REVERT: D 77 GLU cc_start: 0.8196 (tp30) cc_final: 0.7924 (tp30) REVERT: D 160 ASP cc_start: 0.7713 (t0) cc_final: 0.7396 (t0) REVERT: D 305 TYR cc_start: 0.8126 (t80) cc_final: 0.7540 (t80) REVERT: D 374 MET cc_start: 0.8949 (mtp) cc_final: 0.8196 (mtp) REVERT: D 478 ASP cc_start: 0.8056 (t0) cc_final: 0.7638 (t0) REVERT: D 661 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 674 ASP cc_start: 0.8922 (t0) cc_final: 0.8383 (t0) REVERT: E 169 ASP cc_start: 0.8018 (m-30) cc_final: 0.7669 (m-30) REVERT: F 208 GLU cc_start: 0.8451 (tp30) cc_final: 0.8126 (tp30) REVERT: F 394 ILE cc_start: 0.8160 (mt) cc_final: 0.7720 (pt) REVERT: F 536 MET cc_start: 0.8743 (ttm) cc_final: 0.8497 (mmm) outliers start: 29 outliers final: 23 residues processed: 463 average time/residue: 1.0057 time to fit residues: 731.5117 Evaluate side-chains 457 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 434 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 169 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 358 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 65 GLN C 82 ASN D 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095975 restraints weight = 139325.132| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.55 r_work: 0.3070 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34540 Z= 0.244 Angle : 0.509 8.862 46573 Z= 0.270 Chirality : 0.041 0.426 5162 Planarity : 0.004 0.095 5992 Dihedral : 4.087 24.216 4595 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 0.74 % Allowed : 8.54 % Favored : 90.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4187 helix: 0.84 (0.13), residues: 1836 sheet: -1.44 (0.25), residues: 456 loop : -1.73 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.004 0.001 HIS B 605 PHE 0.012 0.001 PHE B 740 TYR 0.016 0.001 TYR A 305 ARG 0.012 0.000 ARG B 670 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 448 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6347 (ttt-90) REVERT: B 128 THR cc_start: 0.9335 (t) cc_final: 0.9053 (m) REVERT: B 132 THR cc_start: 0.9310 (m) cc_final: 0.9065 (m) REVERT: B 264 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7572 (mp0) REVERT: B 348 MET cc_start: 0.8149 (mmm) cc_final: 0.7876 (mtp) REVERT: C 82 ASN cc_start: 0.6672 (OUTLIER) cc_final: 0.6032 (t0) REVERT: C 120 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8089 (mt-10) REVERT: D 3 ASP cc_start: 0.7415 (t0) cc_final: 0.7124 (t0) REVERT: D 35 PHE cc_start: 0.7978 (t80) cc_final: 0.7478 (t80) REVERT: D 77 GLU cc_start: 0.8198 (tp30) cc_final: 0.7895 (tp30) REVERT: D 82 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: D 160 ASP cc_start: 0.7712 (t0) cc_final: 0.7395 (t0) REVERT: D 305 TYR cc_start: 0.8127 (t80) cc_final: 0.7541 (t80) REVERT: D 478 ASP cc_start: 0.8049 (t0) cc_final: 0.7626 (t0) REVERT: D 661 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 674 ASP cc_start: 0.8923 (t0) cc_final: 0.8354 (t0) REVERT: E 169 ASP cc_start: 0.7998 (m-30) cc_final: 0.7664 (m-30) REVERT: F 208 GLU cc_start: 0.8465 (tp30) cc_final: 0.8132 (tp30) REVERT: F 394 ILE cc_start: 0.8170 (mt) cc_final: 0.7728 (pt) REVERT: F 536 MET cc_start: 0.8740 (ttm) cc_final: 0.8217 (mmm) outliers start: 28 outliers final: 23 residues processed: 462 average time/residue: 0.9931 time to fit residues: 716.4702 Evaluate side-chains 464 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 440 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 734 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 301 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 404 optimal weight: 8.9990 chunk 294 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 417 optimal weight: 0.6980 chunk 330 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096580 restraints weight = 139056.747| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.57 r_work: 0.3072 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34540 Z= 0.232 Angle : 0.510 8.865 46573 Z= 0.270 Chirality : 0.040 0.425 5162 Planarity : 0.004 0.084 5992 Dihedral : 4.076 24.282 4595 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.83 % Rotamer: Outliers : 0.77 % Allowed : 8.86 % Favored : 90.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4187 helix: 0.88 (0.13), residues: 1835 sheet: -1.43 (0.25), residues: 457 loop : -1.72 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 605 PHE 0.012 0.001 PHE B 740 TYR 0.012 0.001 TYR D 131 ARG 0.008 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 447 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7062 (tpt170) cc_final: 0.6336 (ttt-90) REVERT: A 256 ARG cc_start: 0.8753 (tpt90) cc_final: 0.8488 (tpt90) REVERT: A 309 LYS cc_start: 0.8445 (mttm) cc_final: 0.8173 (mtmt) REVERT: B 132 THR cc_start: 0.9310 (m) cc_final: 0.9058 (m) REVERT: B 264 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7567 (mp0) REVERT: B 348 MET cc_start: 0.8137 (mmm) cc_final: 0.7873 (mtp) REVERT: C 82 ASN cc_start: 0.6563 (OUTLIER) cc_final: 0.5978 (t0) REVERT: C 120 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8094 (mt-10) REVERT: D 3 ASP cc_start: 0.7451 (t0) cc_final: 0.7155 (t0) REVERT: D 35 PHE cc_start: 0.7973 (t80) cc_final: 0.7481 (t80) REVERT: D 77 GLU cc_start: 0.8193 (tp30) cc_final: 0.7878 (tp30) REVERT: D 82 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7519 (mmm-85) REVERT: D 160 ASP cc_start: 0.7725 (t0) cc_final: 0.7402 (t0) REVERT: D 305 TYR cc_start: 0.8120 (t80) cc_final: 0.7534 (t80) REVERT: D 374 MET cc_start: 0.9006 (mtp) cc_final: 0.8298 (mtp) REVERT: D 478 ASP cc_start: 0.8040 (t0) cc_final: 0.7614 (t0) REVERT: D 661 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 674 ASP cc_start: 0.8919 (t0) cc_final: 0.8347 (t0) REVERT: E 169 ASP cc_start: 0.8009 (m-30) cc_final: 0.7672 (m-30) REVERT: F 208 GLU cc_start: 0.8465 (tp30) cc_final: 0.8125 (tp30) REVERT: F 329 THR cc_start: 0.7762 (m) cc_final: 0.7523 (p) outliers start: 29 outliers final: 23 residues processed: 462 average time/residue: 1.0160 time to fit residues: 731.1103 Evaluate side-chains 463 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 439 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 363 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 413 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 390 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN C 82 ASN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105203 restraints weight = 139000.041| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.63 r_work: 0.3279 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34540 Z= 0.222 Angle : 0.506 8.844 46573 Z= 0.267 Chirality : 0.040 0.425 5162 Planarity : 0.004 0.073 5992 Dihedral : 4.052 24.429 4595 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.97 % Favored : 92.86 % Rotamer: Outliers : 0.77 % Allowed : 8.88 % Favored : 90.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4187 helix: 0.90 (0.13), residues: 1842 sheet: -1.43 (0.25), residues: 457 loop : -1.71 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS B 605 PHE 0.031 0.001 PHE B 730 TYR 0.019 0.001 TYR D 131 ARG 0.008 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 447 time to evaluate : 4.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6472 (ttt-90) REVERT: A 256 ARG cc_start: 0.8738 (tpt90) cc_final: 0.8481 (tpt90) REVERT: A 309 LYS cc_start: 0.8470 (mttm) cc_final: 0.8220 (mtmt) REVERT: B 30 TYR cc_start: 0.8467 (p90) cc_final: 0.8254 (p90) REVERT: B 132 THR cc_start: 0.9309 (m) cc_final: 0.9034 (m) REVERT: B 264 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7601 (mp0) REVERT: B 348 MET cc_start: 0.8261 (mmm) cc_final: 0.7942 (mtp) REVERT: B 670 ARG cc_start: 0.7432 (tpt90) cc_final: 0.6750 (tpm170) REVERT: C 82 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6027 (t0) REVERT: C 120 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8088 (mt-10) REVERT: D 3 ASP cc_start: 0.7341 (t0) cc_final: 0.7046 (t0) REVERT: D 35 PHE cc_start: 0.8005 (t80) cc_final: 0.7468 (t80) REVERT: D 77 GLU cc_start: 0.8212 (tp30) cc_final: 0.7930 (tp30) REVERT: D 160 ASP cc_start: 0.7734 (t0) cc_final: 0.7433 (t0) REVERT: D 305 TYR cc_start: 0.8135 (t80) cc_final: 0.7621 (t80) REVERT: D 374 MET cc_start: 0.9008 (mtp) cc_final: 0.8360 (mtp) REVERT: D 478 ASP cc_start: 0.7961 (t0) cc_final: 0.7550 (t0) REVERT: D 674 ASP cc_start: 0.8825 (t0) cc_final: 0.8252 (t0) REVERT: E 169 ASP cc_start: 0.7805 (m-30) cc_final: 0.7523 (m-30) REVERT: F 208 GLU cc_start: 0.8433 (tp30) cc_final: 0.8111 (tp30) REVERT: F 214 LYS cc_start: 0.8438 (mttm) cc_final: 0.8076 (mttm) REVERT: F 329 THR cc_start: 0.7925 (m) cc_final: 0.7723 (p) REVERT: G 25 ASP cc_start: 0.8243 (p0) cc_final: 0.8006 (p0) outliers start: 29 outliers final: 24 residues processed: 461 average time/residue: 1.0054 time to fit residues: 720.2076 Evaluate side-chains 460 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 435 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain E residue 321 MET Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 734 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 71 optimal weight: 0.0070 chunk 346 optimal weight: 3.9990 chunk 376 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN C 82 ASN D 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106140 restraints weight = 138836.371| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.58 r_work: 0.3287 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34540 Z= 0.206 Angle : 0.504 8.863 46573 Z= 0.266 Chirality : 0.040 0.425 5162 Planarity : 0.004 0.068 5992 Dihedral : 4.036 24.541 4595 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 0.69 % Allowed : 9.02 % Favored : 90.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4187 helix: 0.94 (0.13), residues: 1846 sheet: -1.45 (0.25), residues: 465 loop : -1.69 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.004 0.001 HIS C 432 PHE 0.013 0.001 PHE B 740 TYR 0.017 0.001 TYR E 431 ARG 0.012 0.000 ARG G 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8374 Ramachandran restraints generated. 4187 Oldfield, 0 Emsley, 4187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 682 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue TYR 531 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 445 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.7150 (tpt170) cc_final: 0.6473 (ttt-90) REVERT: A 256 ARG cc_start: 0.8729 (tpt90) cc_final: 0.8456 (tpt90) REVERT: A 309 LYS cc_start: 0.8457 (mttm) cc_final: 0.8219 (mtmt) REVERT: B 30 TYR cc_start: 0.8419 (p90) cc_final: 0.8152 (p90) REVERT: B 132 THR cc_start: 0.9305 (m) cc_final: 0.9030 (m) REVERT: B 264 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7598 (mp0) REVERT: B 348 MET cc_start: 0.8273 (mmm) cc_final: 0.7957 (mtp) REVERT: B 670 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6851 (tpm170) REVERT: C 82 ASN cc_start: 0.6543 (OUTLIER) cc_final: 0.6250 (t0) REVERT: C 120 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8081 (mt-10) REVERT: D 3 ASP cc_start: 0.7292 (t0) cc_final: 0.6992 (t0) REVERT: D 35 PHE cc_start: 0.8021 (t80) cc_final: 0.7490 (t80) REVERT: D 77 GLU cc_start: 0.8215 (tp30) cc_final: 0.7905 (tp30) REVERT: D 160 ASP cc_start: 0.7725 (t0) cc_final: 0.7399 (t0) REVERT: D 305 TYR cc_start: 0.8145 (t80) cc_final: 0.7635 (t80) REVERT: D 374 MET cc_start: 0.8919 (mtp) cc_final: 0.8284 (mtp) REVERT: D 478 ASP cc_start: 0.7949 (t0) cc_final: 0.7539 (t0) REVERT: D 674 ASP cc_start: 0.8821 (t0) cc_final: 0.8247 (t0) REVERT: E 169 ASP cc_start: 0.7798 (m-30) cc_final: 0.7524 (m-30) REVERT: F 208 GLU cc_start: 0.8464 (tp30) cc_final: 0.8111 (tp30) REVERT: F 214 LYS cc_start: 0.8430 (mttm) cc_final: 0.8010 (mttm) REVERT: G 25 ASP cc_start: 0.8238 (p0) cc_final: 0.7998 (p0) outliers start: 26 outliers final: 23 residues processed: 457 average time/residue: 1.0070 time to fit residues: 717.8593 Evaluate side-chains 462 residues out of total 3761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 438 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 206 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN C 82 ASN D 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106759 restraints weight = 138535.435| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.67 r_work: 0.3292 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34540 Z= 0.195 Angle : 0.502 8.865 46573 Z= 0.264 Chirality : 0.040 0.424 5162 Planarity : 0.004 0.063 5992 Dihedral : 4.018 24.646 4595 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 0.69 % Allowed : 9.15 % Favored : 90.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4187 helix: 0.98 (0.13), residues: 1846 sheet: -1.40 (0.25), residues: 463 loop : -1.69 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 88 HIS 0.004 0.001 HIS C 432 PHE 0.014 0.001 PHE D 4 TYR 0.019 0.001 TYR D 131 ARG 0.012 0.000 ARG G 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31520.03 seconds wall clock time: 538 minutes 48.32 seconds (32328.32 seconds total)