Starting phenix.real_space_refine on Thu Mar 5 11:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.map" model { file = "/net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk4_22361/03_2026/7jk4_22361.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 80 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13572 2.51 5 N 3813 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21717 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 3 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4918 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 588} Chain breaks: 7 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.24 Number of scatterers: 21717 At special positions: 0 Unit cell: (117.82, 161.68, 124.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 80 15.00 Mg 4 11.99 O 4137 8.00 N 3813 7.00 C 13572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 954.7 milliseconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 13 sheets defined 64.7% alpha, 7.2% beta 33 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 410 through 424 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.601A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.661A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.525A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 5.136A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 124 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.636A pdb=" N PHE C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.850A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 removed outlier: 3.690A pdb=" N PHE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 382 through 416 Proline residue: C 390 - end of helix removed outlier: 4.666A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.801A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.631A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 removed outlier: 3.681A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 590 through 593 removed outlier: 3.792A pdb=" N LEU C 593 " --> pdb=" O ILE C 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 598 through 607 removed outlier: 4.247A pdb=" N VAL C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.535A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 620 " --> pdb=" O THR C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.544A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.742A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.573A pdb=" N GLY D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.569A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 removed outlier: 6.292A pdb=" N ASN D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.834A pdb=" N SER D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.532A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 4.255A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.119A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.638A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 261' Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.514A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.719A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 344 through 362 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.722A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.653A pdb=" N ALA D 403 " --> pdb=" O HIS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.583A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.820A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.837A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.600A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.753A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.727A pdb=" N VAL E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.107A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.299A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 275 through 287 Proline residue: E 282 - end of helix removed outlier: 3.584A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 342 through 348 removed outlier: 4.040A pdb=" N VAL E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.182A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.013A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.659A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.571A pdb=" N GLN E 454 " --> pdb=" O ASN E 451 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 456 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 545 through 549 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 588 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.536A pdb=" N THR A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 4.038A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 685 through 690 removed outlier: 3.748A pdb=" N CYS A 690 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.609A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.078A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.652A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.823A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.672A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.027A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.865A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 382 removed outlier: 3.534A pdb=" N GLN G 380 " --> pdb=" O GLU G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 413 through 419 Processing helix chain 'G' and resid 420 through 425 removed outlier: 3.632A pdb=" N ALA G 424 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 454 removed outlier: 3.616A pdb=" N ALA G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA G 454 " --> pdb=" O ARG G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 460 removed outlier: 3.863A pdb=" N VAL G 459 " --> pdb=" O VAL G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.671A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.703A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.741A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 574 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.796A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 4.034A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.767A pdb=" N ALA G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 655 removed outlier: 3.648A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 655 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 660 removed outlier: 3.600A pdb=" N CYS G 659 " --> pdb=" O ASP G 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.265A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 378 " --> pdb=" O TYR C 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.516A pdb=" N MET B 553 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.794A pdb=" N VAL C 239 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 262 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR C 98 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.624A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 658 through 660 Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 7.250A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'E' and resid 65 through 70 removed outlier: 6.104A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.414A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 851 through 853 removed outlier: 3.532A pdb=" N THR A 852 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.954A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.483A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1094 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5882 1.34 - 1.46: 4713 1.46 - 1.58: 11322 1.58 - 1.70: 152 1.70 - 1.82: 164 Bond restraints: 22233 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.76e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 30175 4.23 - 8.47: 151 8.47 - 12.70: 13 12.70 - 16.93: 5 16.93 - 21.16: 5 Bond angle restraints: 30349 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 118.71 21.16 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.02 18.85 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.65 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.92 16.95 1.00e+00 1.00e+00 2.87e+02 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11568 17.93 - 35.87: 1277 35.87 - 53.80: 494 53.80 - 71.74: 113 71.74 - 89.67: 26 Dihedral angle restraints: 13478 sinusoidal: 6058 harmonic: 7420 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA SER G 349 " pdb=" C SER G 349 " pdb=" N GLY G 350 " pdb=" CA GLY G 350 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2828 0.063 - 0.126: 575 0.126 - 0.188: 95 0.188 - 0.251: 4 0.251 - 0.314: 1 Chirality restraints: 3503 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE C 356 " pdb=" CA ILE C 356 " pdb=" CG1 ILE C 356 " pdb=" CG2 ILE C 356 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3500 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 873 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 150 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" CG ASN E 150 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 150 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 281 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO E 282 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.032 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 304 2.66 - 3.22: 18660 3.22 - 3.78: 34636 3.78 - 4.34: 46710 4.34 - 4.90: 76308 Nonbonded interactions: 176618 Sorted by model distance: nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.102 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.115 2.170 nonbonded pdb=" O2B ATP G 901 " pdb="MG MG G 902 " model vdw 2.129 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.139 2.170 nonbonded pdb=" O3G ATP G 901 " pdb="MG MG G 902 " model vdw 2.162 2.170 ... (remaining 176613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.006 0.097 22233 Z= 0.315 Angle : 0.952 21.164 30349 Z= 0.589 Chirality : 0.052 0.314 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.944 89.669 8634 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.32 % Allowed : 5.00 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.14), residues: 2481 helix: -2.59 (0.08), residues: 1477 sheet: -2.74 (0.28), residues: 233 loop : 0.52 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 480 TYR 0.027 0.002 TYR E 258 PHE 0.026 0.003 PHE C 215 TRP 0.015 0.002 TRP C 57 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00599 (22233) covalent geometry : angle 0.95170 (30349) hydrogen bonds : bond 0.13614 ( 1167) hydrogen bonds : angle 6.16052 ( 3338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 260 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: B 333 MET cc_start: 0.8758 (mmm) cc_final: 0.8495 (mmm) REVERT: B 575 ARG cc_start: 0.8983 (mtt-85) cc_final: 0.8783 (mtt-85) REVERT: B 588 LYS cc_start: 0.9428 (mmtm) cc_final: 0.9225 (mmmt) REVERT: C 387 LYS cc_start: 0.9712 (tttt) cc_final: 0.9208 (ptpt) REVERT: C 443 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 637 LEU cc_start: 0.8010 (tt) cc_final: 0.7783 (tt) REVERT: C 654 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8220 (tm-30) REVERT: D 116 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8890 (mmtp) REVERT: D 185 ASP cc_start: 0.8333 (p0) cc_final: 0.7880 (p0) REVERT: D 347 GLU cc_start: 0.8382 (mp0) cc_final: 0.8107 (mp0) REVERT: E 169 LYS cc_start: 0.8814 (mttm) cc_final: 0.8457 (mtpt) REVERT: E 198 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8524 (tm-30) REVERT: E 337 HIS cc_start: 0.8195 (t-90) cc_final: 0.7884 (t-90) REVERT: E 426 MET cc_start: 0.8720 (mtp) cc_final: 0.8513 (mtm) REVERT: F 226 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9326 (mt-10) REVERT: A 577 ASN cc_start: 0.8919 (t0) cc_final: 0.8652 (m-40) REVERT: A 903 LYS cc_start: 0.9269 (mttm) cc_final: 0.8969 (mtpp) REVERT: A 915 TYR cc_start: 0.9110 (t80) cc_final: 0.8770 (t80) outliers start: 7 outliers final: 2 residues processed: 267 average time/residue: 0.1919 time to fit residues: 74.6051 Evaluate side-chains 155 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS B 498 ASN B 577 GLN B 609 GLN C 113 GLN C 194 ASN C 250 HIS C 391 GLN E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN E 433 GLN A 622 ASN A 749 GLN A 828 ASN A 838 GLN G 386 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.079504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059048 restraints weight = 57261.890| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.05 r_work: 0.2752 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22233 Z= 0.134 Angle : 0.564 7.489 30349 Z= 0.304 Chirality : 0.039 0.226 3503 Planarity : 0.004 0.063 3607 Dihedral : 17.564 80.558 3664 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.95 % Allowed : 8.87 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2481 helix: -0.05 (0.12), residues: 1489 sheet: -2.29 (0.29), residues: 229 loop : 0.32 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 277 TYR 0.019 0.001 TYR A 579 PHE 0.013 0.001 PHE C 196 TRP 0.014 0.001 TRP E 276 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00292 (22233) covalent geometry : angle 0.56413 (30349) hydrogen bonds : bond 0.03977 ( 1167) hydrogen bonds : angle 4.28435 ( 3338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 279 GLU cc_start: 0.8050 (tp30) cc_final: 0.7774 (tp30) REVERT: B 588 LYS cc_start: 0.9447 (mmtm) cc_final: 0.9236 (mmmt) REVERT: C 387 LYS cc_start: 0.9718 (tttt) cc_final: 0.9165 (ptpt) REVERT: C 443 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8395 (mm-30) REVERT: C 504 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7983 (pp20) REVERT: C 654 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8522 (tm-30) REVERT: D 116 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8995 (mmtm) REVERT: D 185 ASP cc_start: 0.8747 (p0) cc_final: 0.7527 (p0) REVERT: D 188 GLU cc_start: 0.8648 (pt0) cc_final: 0.8024 (pt0) REVERT: D 347 GLU cc_start: 0.8803 (mp0) cc_final: 0.8509 (mp0) REVERT: D 426 MET cc_start: 0.9103 (mmm) cc_final: 0.8503 (mmm) REVERT: E 1 MET cc_start: 0.8036 (ppp) cc_final: 0.7648 (ptm) REVERT: E 82 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8534 (mt-10) REVERT: E 276 TRP cc_start: 0.8361 (t-100) cc_final: 0.8110 (t-100) REVERT: E 337 HIS cc_start: 0.8582 (t-90) cc_final: 0.8275 (t-90) REVERT: A 577 ASN cc_start: 0.9143 (t0) cc_final: 0.8850 (m-40) REVERT: A 851 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 903 LYS cc_start: 0.9414 (mttm) cc_final: 0.8778 (mmmt) REVERT: A 915 TYR cc_start: 0.9371 (t80) cc_final: 0.8980 (t80) REVERT: G 484 ASP cc_start: 0.9021 (t0) cc_final: 0.8745 (t0) REVERT: G 575 ARG cc_start: 0.7721 (mmp-170) cc_final: 0.7476 (mmp-170) REVERT: G 621 MET cc_start: 0.9189 (ttp) cc_final: 0.8911 (ttm) outliers start: 21 outliers final: 12 residues processed: 194 average time/residue: 0.1428 time to fit residues: 44.3056 Evaluate side-chains 169 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 168 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 228 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 239 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 641 HIS ** 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 = 0.3338 r_free = 0.3338 target = 0.077848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057424 restraints weight = 57632.742| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.02 r_work: 0.2718 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22233 Z= 0.164 Angle : 0.536 8.830 30349 Z= 0.286 Chirality : 0.039 0.174 3503 Planarity : 0.004 0.053 3607 Dihedral : 17.490 78.429 3663 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.67 % Allowed : 10.09 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2481 helix: 0.98 (0.13), residues: 1493 sheet: -1.94 (0.29), residues: 241 loop : 0.22 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 443 TYR 0.019 0.001 TYR E 258 PHE 0.011 0.001 PHE D 149 TRP 0.008 0.001 TRP C 191 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00374 (22233) covalent geometry : angle 0.53642 (30349) hydrogen bonds : bond 0.03778 ( 1167) hydrogen bonds : angle 3.91924 ( 3338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLU cc_start: 0.7969 (tp30) cc_final: 0.7679 (tp30) REVERT: B 585 LYS cc_start: 0.9261 (pttp) cc_final: 0.9044 (pttm) REVERT: C 443 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8477 (mm-30) REVERT: C 654 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8486 (tm-30) REVERT: D 95 ASP cc_start: 0.8574 (t0) cc_final: 0.8328 (t0) REVERT: D 116 LYS cc_start: 0.9260 (mmtt) cc_final: 0.9020 (mmtm) REVERT: D 185 ASP cc_start: 0.8779 (p0) cc_final: 0.7933 (p0) REVERT: D 188 GLU cc_start: 0.8670 (pt0) cc_final: 0.8020 (pt0) REVERT: D 347 GLU cc_start: 0.8809 (mp0) cc_final: 0.8539 (mp0) REVERT: D 426 MET cc_start: 0.9088 (mmm) cc_final: 0.8498 (mmm) REVERT: E 63 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.9104 (t0) REVERT: E 106 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8509 (tp30) REVERT: E 276 TRP cc_start: 0.8550 (t-100) cc_final: 0.8241 (t-100) REVERT: E 337 HIS cc_start: 0.8624 (t-90) cc_final: 0.8335 (t-90) REVERT: A 577 ASN cc_start: 0.9179 (t0) cc_final: 0.8820 (m-40) REVERT: A 851 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 903 LYS cc_start: 0.9444 (mttm) cc_final: 0.8906 (mmmt) REVERT: A 915 TYR cc_start: 0.9356 (t80) cc_final: 0.8983 (t80) REVERT: G 320 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8987 (pp) REVERT: G 484 ASP cc_start: 0.9002 (t0) cc_final: 0.8749 (t0) REVERT: G 621 MET cc_start: 0.9220 (ttp) cc_final: 0.8956 (ttt) outliers start: 37 outliers final: 17 residues processed: 196 average time/residue: 0.1575 time to fit residues: 48.4601 Evaluate side-chains 166 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 172 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 110 HIS ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056938 restraints weight = 57828.030| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.01 r_work: 0.2702 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22233 Z= 0.183 Angle : 0.531 9.162 30349 Z= 0.282 Chirality : 0.039 0.183 3503 Planarity : 0.004 0.050 3607 Dihedral : 17.444 79.750 3663 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.35 % Allowed : 11.44 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2481 helix: 1.42 (0.14), residues: 1496 sheet: -1.75 (0.30), residues: 241 loop : 0.14 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 443 TYR 0.023 0.001 TYR A 579 PHE 0.010 0.001 PHE D 149 TRP 0.008 0.001 TRP A 658 HIS 0.005 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00418 (22233) covalent geometry : angle 0.53136 (30349) hydrogen bonds : bond 0.03653 ( 1167) hydrogen bonds : angle 3.80851 ( 3338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLU cc_start: 0.7968 (tp30) cc_final: 0.7668 (tp30) REVERT: C 654 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8518 (tm-30) REVERT: D 95 ASP cc_start: 0.8557 (t0) cc_final: 0.8310 (t0) REVERT: D 116 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8986 (mmtm) REVERT: D 185 ASP cc_start: 0.8811 (p0) cc_final: 0.8108 (p0) REVERT: D 188 GLU cc_start: 0.8677 (pt0) cc_final: 0.8402 (pt0) REVERT: D 347 GLU cc_start: 0.8758 (mp0) cc_final: 0.8509 (mp0) REVERT: D 426 MET cc_start: 0.9086 (mmm) cc_final: 0.8530 (mmm) REVERT: E 106 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8521 (tp30) REVERT: E 276 TRP cc_start: 0.8592 (t-100) cc_final: 0.8306 (t-100) REVERT: E 337 HIS cc_start: 0.8642 (t-90) cc_final: 0.8368 (t-90) REVERT: A 851 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 903 LYS cc_start: 0.9464 (mttm) cc_final: 0.8943 (mmmt) REVERT: A 915 TYR cc_start: 0.9356 (t80) cc_final: 0.8996 (t80) REVERT: G 384 SER cc_start: 0.8821 (p) cc_final: 0.8549 (m) REVERT: G 484 ASP cc_start: 0.9004 (t0) cc_final: 0.8752 (t0) REVERT: G 563 MET cc_start: 0.8570 (tmm) cc_final: 0.8029 (tmm) REVERT: G 613 GLU cc_start: 0.9165 (tt0) cc_final: 0.8917 (tm-30) REVERT: G 621 MET cc_start: 0.9217 (ttp) cc_final: 0.8893 (ttm) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.1701 time to fit residues: 48.2788 Evaluate side-chains 170 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 21 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN E 150 ASN ** G 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057744 restraints weight = 57063.607| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.04 r_work: 0.2724 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22233 Z= 0.106 Angle : 0.490 7.231 30349 Z= 0.260 Chirality : 0.037 0.200 3503 Planarity : 0.003 0.046 3607 Dihedral : 17.286 76.578 3663 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 12.16 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2481 helix: 1.74 (0.14), residues: 1494 sheet: -1.43 (0.30), residues: 234 loop : 0.10 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 417 TYR 0.023 0.001 TYR A 579 PHE 0.012 0.001 PHE C 49 TRP 0.008 0.001 TRP A 658 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00228 (22233) covalent geometry : angle 0.48961 (30349) hydrogen bonds : bond 0.03175 ( 1167) hydrogen bonds : angle 3.63909 ( 3338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLU cc_start: 0.7995 (tp30) cc_final: 0.7661 (tp30) REVERT: B 540 TYR cc_start: 0.7996 (t80) cc_final: 0.7708 (t80) REVERT: C 654 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8495 (tm-30) REVERT: D 116 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8999 (mmtm) REVERT: D 185 ASP cc_start: 0.8798 (p0) cc_final: 0.7583 (p0) REVERT: D 188 GLU cc_start: 0.8651 (pt0) cc_final: 0.8162 (pt0) REVERT: D 347 GLU cc_start: 0.8733 (mp0) cc_final: 0.8439 (mp0) REVERT: D 426 MET cc_start: 0.9100 (mmm) cc_final: 0.8512 (mmm) REVERT: E 276 TRP cc_start: 0.8567 (t-100) cc_final: 0.8290 (t-100) REVERT: E 337 HIS cc_start: 0.8662 (t-90) cc_final: 0.8395 (t-90) REVERT: A 851 GLU cc_start: 0.8554 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 903 LYS cc_start: 0.9457 (mttm) cc_final: 0.8924 (mmmt) REVERT: A 915 TYR cc_start: 0.9335 (t80) cc_final: 0.8931 (t80) REVERT: G 320 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8921 (pp) REVERT: G 484 ASP cc_start: 0.8992 (t0) cc_final: 0.8742 (t0) REVERT: G 563 MET cc_start: 0.8598 (tmm) cc_final: 0.8060 (tmm) REVERT: G 613 GLU cc_start: 0.9128 (tt0) cc_final: 0.8877 (tm-30) REVERT: G 621 MET cc_start: 0.9184 (ttp) cc_final: 0.8854 (ttm) outliers start: 33 outliers final: 21 residues processed: 192 average time/residue: 0.1736 time to fit residues: 50.6511 Evaluate side-chains 177 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 66 optimal weight: 0.0040 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 82 optimal weight: 0.0000 chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059674 restraints weight = 57627.439| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.98 r_work: 0.2708 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22233 Z= 0.144 Angle : 0.511 11.697 30349 Z= 0.267 Chirality : 0.038 0.211 3503 Planarity : 0.003 0.044 3607 Dihedral : 17.210 79.157 3661 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.40 % Allowed : 12.88 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.17), residues: 2481 helix: 1.88 (0.14), residues: 1502 sheet: -1.30 (0.31), residues: 235 loop : 0.03 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 417 TYR 0.024 0.001 TYR A 579 PHE 0.011 0.001 PHE C 49 TRP 0.008 0.001 TRP A 658 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00328 (22233) covalent geometry : angle 0.51122 (30349) hydrogen bonds : bond 0.03271 ( 1167) hydrogen bonds : angle 3.61215 ( 3338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLU cc_start: 0.7992 (tp30) cc_final: 0.7699 (tp30) REVERT: B 540 TYR cc_start: 0.8046 (t80) cc_final: 0.7786 (t80) REVERT: C 453 PHE cc_start: 0.7378 (m-10) cc_final: 0.7110 (m-10) REVERT: C 654 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8450 (tm-30) REVERT: D 95 ASP cc_start: 0.8579 (t0) cc_final: 0.8358 (t0) REVERT: D 116 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8972 (mmtm) REVERT: D 185 ASP cc_start: 0.8809 (p0) cc_final: 0.8062 (p0) REVERT: D 188 GLU cc_start: 0.8639 (pt0) cc_final: 0.8287 (pt0) REVERT: D 347 GLU cc_start: 0.8741 (mp0) cc_final: 0.8434 (mp0) REVERT: D 426 MET cc_start: 0.9098 (mmm) cc_final: 0.8532 (mmm) REVERT: E 276 TRP cc_start: 0.8634 (t-100) cc_final: 0.8402 (t-100) REVERT: E 337 HIS cc_start: 0.8677 (t-90) cc_final: 0.8415 (t-90) REVERT: A 851 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 903 LYS cc_start: 0.9469 (mttm) cc_final: 0.8944 (mmmt) REVERT: A 914 HIS cc_start: 0.8842 (m-70) cc_final: 0.8638 (m-70) REVERT: A 915 TYR cc_start: 0.9338 (t80) cc_final: 0.8970 (t80) REVERT: G 320 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8912 (pp) REVERT: G 484 ASP cc_start: 0.8958 (t0) cc_final: 0.8720 (t0) REVERT: G 613 GLU cc_start: 0.9107 (tt0) cc_final: 0.8851 (tm-30) REVERT: G 621 MET cc_start: 0.9201 (ttp) cc_final: 0.8870 (ttm) outliers start: 31 outliers final: 19 residues processed: 186 average time/residue: 0.1627 time to fit residues: 46.4470 Evaluate side-chains 173 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 115 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057193 restraints weight = 57253.466| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.09 r_work: 0.2712 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22233 Z= 0.127 Angle : 0.500 11.546 30349 Z= 0.262 Chirality : 0.038 0.183 3503 Planarity : 0.003 0.044 3607 Dihedral : 17.115 81.080 3661 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 13.24 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2481 helix: 2.01 (0.14), residues: 1503 sheet: -1.32 (0.30), residues: 244 loop : 0.07 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 417 TYR 0.020 0.001 TYR A 579 PHE 0.011 0.001 PHE C 49 TRP 0.008 0.001 TRP A 658 HIS 0.005 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00287 (22233) covalent geometry : angle 0.50039 (30349) hydrogen bonds : bond 0.03138 ( 1167) hydrogen bonds : angle 3.54761 ( 3338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8668 (mm-30) REVERT: C 654 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8427 (tm-30) REVERT: D 95 ASP cc_start: 0.8562 (t0) cc_final: 0.8327 (t0) REVERT: D 116 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8997 (mmtm) REVERT: D 185 ASP cc_start: 0.8822 (p0) cc_final: 0.8267 (p0) REVERT: D 188 GLU cc_start: 0.8643 (pt0) cc_final: 0.8244 (pt0) REVERT: D 347 GLU cc_start: 0.8749 (mp0) cc_final: 0.8451 (mp0) REVERT: D 426 MET cc_start: 0.9095 (mmm) cc_final: 0.8595 (mmm) REVERT: E 337 HIS cc_start: 0.8671 (t-90) cc_final: 0.8412 (t-90) REVERT: A 851 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 903 LYS cc_start: 0.9465 (mttm) cc_final: 0.8958 (mmmt) REVERT: A 915 TYR cc_start: 0.9330 (t80) cc_final: 0.8925 (t80) REVERT: G 320 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8904 (pp) REVERT: G 484 ASP cc_start: 0.8952 (t0) cc_final: 0.8722 (t0) REVERT: G 563 MET cc_start: 0.8403 (tmm) cc_final: 0.7883 (tmm) REVERT: G 613 GLU cc_start: 0.9106 (tt0) cc_final: 0.8845 (tm-30) REVERT: G 621 MET cc_start: 0.9189 (ttp) cc_final: 0.8856 (ttm) outliers start: 35 outliers final: 24 residues processed: 182 average time/residue: 0.1631 time to fit residues: 46.1807 Evaluate side-chains 178 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 220 optimal weight: 7.9990 chunk 82 optimal weight: 0.0470 chunk 225 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 162 optimal weight: 0.0570 chunk 34 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058636 restraints weight = 56267.623| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.01 r_work: 0.2750 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22233 Z= 0.101 Angle : 0.491 13.357 30349 Z= 0.257 Chirality : 0.037 0.207 3503 Planarity : 0.003 0.043 3607 Dihedral : 16.961 80.968 3661 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 13.65 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.18), residues: 2481 helix: 2.13 (0.14), residues: 1497 sheet: -0.98 (0.32), residues: 229 loop : 0.02 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 417 TYR 0.026 0.001 TYR A 579 PHE 0.012 0.001 PHE C 49 TRP 0.015 0.001 TRP E 276 HIS 0.005 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00216 (22233) covalent geometry : angle 0.49134 (30349) hydrogen bonds : bond 0.02846 ( 1167) hydrogen bonds : angle 3.45064 ( 3338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8651 (mm-30) REVERT: C 654 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8407 (tm-30) REVERT: D 95 ASP cc_start: 0.8509 (t0) cc_final: 0.8274 (t0) REVERT: D 116 LYS cc_start: 0.9223 (mmtt) cc_final: 0.9004 (mmtm) REVERT: D 185 ASP cc_start: 0.8790 (p0) cc_final: 0.7912 (p0) REVERT: D 188 GLU cc_start: 0.8611 (pt0) cc_final: 0.8159 (pt0) REVERT: D 209 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8950 (pp) REVERT: D 347 GLU cc_start: 0.8719 (mp0) cc_final: 0.8434 (mp0) REVERT: D 426 MET cc_start: 0.9091 (mmm) cc_final: 0.8602 (mmm) REVERT: E 337 HIS cc_start: 0.8677 (t-90) cc_final: 0.8430 (t-90) REVERT: A 577 ASN cc_start: 0.9106 (t0) cc_final: 0.8838 (t0) REVERT: A 851 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 903 LYS cc_start: 0.9449 (mttm) cc_final: 0.8951 (mmmt) REVERT: A 915 TYR cc_start: 0.9308 (t80) cc_final: 0.8918 (t80) REVERT: G 320 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8865 (pp) REVERT: G 417 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8426 (ttp80) REVERT: G 484 ASP cc_start: 0.8907 (t0) cc_final: 0.8700 (t0) REVERT: G 563 MET cc_start: 0.8449 (tmm) cc_final: 0.8076 (tmm) REVERT: G 613 GLU cc_start: 0.9093 (tt0) cc_final: 0.8826 (tm-30) REVERT: G 621 MET cc_start: 0.9189 (ttp) cc_final: 0.8857 (ttm) outliers start: 32 outliers final: 20 residues processed: 183 average time/residue: 0.1702 time to fit residues: 48.0563 Evaluate side-chains 171 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059635 restraints weight = 57936.868| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.06 r_work: 0.2773 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22233 Z= 0.140 Angle : 0.516 13.165 30349 Z= 0.267 Chirality : 0.038 0.205 3503 Planarity : 0.003 0.044 3607 Dihedral : 16.943 86.984 3661 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.99 % Allowed : 14.59 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2481 helix: 2.17 (0.14), residues: 1505 sheet: -1.07 (0.31), residues: 243 loop : 0.07 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 417 TYR 0.029 0.001 TYR A 629 PHE 0.017 0.001 PHE A 867 TRP 0.011 0.001 TRP E 276 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00321 (22233) covalent geometry : angle 0.51610 (30349) hydrogen bonds : bond 0.03140 ( 1167) hydrogen bonds : angle 3.48134 ( 3338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 591 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8220 (tpp80) REVERT: C 145 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8688 (mm-30) REVERT: C 654 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8377 (tm-30) REVERT: D 95 ASP cc_start: 0.8530 (t0) cc_final: 0.8286 (t0) REVERT: D 347 GLU cc_start: 0.8668 (mp0) cc_final: 0.8396 (mp0) REVERT: D 426 MET cc_start: 0.9083 (mmm) cc_final: 0.8637 (mmm) REVERT: E 337 HIS cc_start: 0.8630 (t-90) cc_final: 0.8389 (t-90) REVERT: F 224 ASP cc_start: 0.8760 (t0) cc_final: 0.8517 (t0) REVERT: A 851 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 903 LYS cc_start: 0.9437 (mttm) cc_final: 0.8957 (mmmt) REVERT: A 915 TYR cc_start: 0.9277 (t80) cc_final: 0.8889 (t80) REVERT: G 320 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8948 (pp) REVERT: G 417 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8492 (ttp80) REVERT: G 484 ASP cc_start: 0.8895 (t0) cc_final: 0.8694 (t0) REVERT: G 563 MET cc_start: 0.8454 (tmm) cc_final: 0.8118 (tmm) REVERT: G 613 GLU cc_start: 0.9101 (tt0) cc_final: 0.8844 (tm-30) REVERT: G 621 MET cc_start: 0.9214 (ttp) cc_final: 0.8954 (ttt) outliers start: 22 outliers final: 18 residues processed: 174 average time/residue: 0.1640 time to fit residues: 44.7712 Evaluate side-chains 172 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 252 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.080497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059064 restraints weight = 58668.328| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.12 r_work: 0.2765 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22233 Z= 0.140 Angle : 0.517 13.718 30349 Z= 0.268 Chirality : 0.038 0.203 3503 Planarity : 0.003 0.044 3607 Dihedral : 16.934 87.953 3661 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 14.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2481 helix: 2.22 (0.14), residues: 1500 sheet: -1.02 (0.31), residues: 242 loop : 0.13 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 417 TYR 0.028 0.001 TYR A 629 PHE 0.010 0.001 PHE C 49 TRP 0.012 0.001 TRP E 276 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00321 (22233) covalent geometry : angle 0.51743 (30349) hydrogen bonds : bond 0.03132 ( 1167) hydrogen bonds : angle 3.48276 ( 3338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 591 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8220 (tpp80) REVERT: C 145 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8696 (mm-30) REVERT: C 654 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8377 (tm-30) REVERT: D 95 ASP cc_start: 0.8586 (t0) cc_final: 0.8336 (t0) REVERT: D 185 ASP cc_start: 0.8598 (p0) cc_final: 0.7427 (p0) REVERT: D 188 GLU cc_start: 0.8510 (pt0) cc_final: 0.8169 (pt0) REVERT: D 347 GLU cc_start: 0.8665 (mp0) cc_final: 0.8393 (mp0) REVERT: D 426 MET cc_start: 0.9086 (mmm) cc_final: 0.8577 (mmm) REVERT: E 337 HIS cc_start: 0.8647 (t-90) cc_final: 0.8409 (t-90) REVERT: A 851 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 903 LYS cc_start: 0.9442 (mttm) cc_final: 0.8981 (mmmt) REVERT: A 915 TYR cc_start: 0.9272 (t80) cc_final: 0.8874 (t80) REVERT: G 320 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8967 (pp) REVERT: G 417 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8535 (ttp80) REVERT: G 484 ASP cc_start: 0.8904 (t0) cc_final: 0.8685 (t0) REVERT: G 563 MET cc_start: 0.8473 (tmm) cc_final: 0.8144 (tmm) REVERT: G 613 GLU cc_start: 0.9105 (tt0) cc_final: 0.8847 (tm-30) REVERT: G 621 MET cc_start: 0.9215 (ttp) cc_final: 0.8960 (ttt) outliers start: 23 outliers final: 20 residues processed: 172 average time/residue: 0.1684 time to fit residues: 45.1753 Evaluate side-chains 174 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 158 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 228 optimal weight: 0.1980 chunk 238 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 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 = 0.3396 r_free = 0.3396 target = 0.080170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059160 restraints weight = 58574.978| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.09 r_work: 0.2767 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22233 Z= 0.140 Angle : 0.523 13.587 30349 Z= 0.270 Chirality : 0.038 0.200 3503 Planarity : 0.003 0.044 3607 Dihedral : 16.912 89.809 3661 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.04 % Allowed : 14.68 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2481 helix: 2.25 (0.14), residues: 1493 sheet: -0.99 (0.31), residues: 242 loop : 0.15 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 417 TYR 0.026 0.001 TYR A 629 PHE 0.018 0.001 PHE A 867 TRP 0.012 0.001 TRP E 276 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00321 (22233) covalent geometry : angle 0.52307 (30349) hydrogen bonds : bond 0.03143 ( 1167) hydrogen bonds : angle 3.48677 ( 3338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.21 seconds wall clock time: 73 minutes 16.23 seconds (4396.23 seconds total)