Starting phenix.real_space_refine on Sun Sep 29 19:56:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/09_2024/7uiw_26555_trim.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 7 Type Number sf(0) Gaussians P 29 5.49 5 Mg 7 5.21 5 S 171 5.16 5 C 23703 2.51 5 N 6677 2.21 5 O 7189 1.98 5 H 38115 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 261 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75891 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9019 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain breaks: 2 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9141 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9154 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9143 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 8621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 8621 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 15, 'TRANS': 525} Chain breaks: 4 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2977 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "N" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 396 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.12, per 1000 atoms: 0.38 Number of scatterers: 75891 At special positions: 0 Unit cell: (150.51, 151.38, 169.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 171 16.00 P 29 15.00 Mg 7 11.99 O 7189 8.00 N 6677 7.00 C 23703 6.00 H 38115 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8866 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 45 sheets defined 56.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.532A pdb=" N ARG A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.877A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.500A pdb=" N ASP A 242 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 261 through 277 removed outlier: 3.510A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.989A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.584A pdb=" N ALA A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.619A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.522A pdb=" N ARG A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.000A pdb=" N GLY A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.858A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.536A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.527A pdb=" N ILE A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.729A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.633A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.911A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.600A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.267A pdb=" N PHE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.559A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 654 through 676 removed outlier: 3.558A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 Processing helix chain 'A' and resid 701 through 712 removed outlier: 4.019A pdb=" N ALA A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 724 through 727 Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 234 removed outlier: 3.729A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.546A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 302 through 314 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 350 through 370 removed outlier: 3.666A pdb=" N GLN B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.705A pdb=" N VAL B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 411 Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.600A pdb=" N THR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 463 through 480 Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.753A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.822A pdb=" N GLU B 523 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.933A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.988A pdb=" N PHE B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 636 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 654 through 676 removed outlier: 3.514A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 694 Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.736A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 723 through 727 removed outlier: 4.223A pdb=" N ASP B 727 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.823A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.511A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 278 removed outlier: 3.540A pdb=" N LEU C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 302 through 314 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.538A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 370 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'C' and resid 393 through 412 removed outlier: 3.586A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 463 through 480 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.699A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 529 through 535 removed outlier: 4.185A pdb=" N LEU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 570 through 584 removed outlier: 3.934A pdb=" N PHE C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN C 575 " --> pdb=" O PRO C 571 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 623 through 636 removed outlier: 4.164A pdb=" N ASP C 627 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 654 through 677 removed outlier: 3.783A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 695 Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.952A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'C' and resid 724 through 727 removed outlier: 3.581A pdb=" N ASP C 727 " --> pdb=" O SER C 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.519A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 219 through 234 removed outlier: 3.760A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 261 through 278 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 302 through 314 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.542A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.690A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 393 through 412 Processing helix chain 'D' and resid 422 through 435 removed outlier: 3.684A pdb=" N ILE D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 460 removed outlier: 4.555A pdb=" N GLY D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP D 454 " --> pdb=" O LYS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 480 removed outlier: 3.533A pdb=" N ILE D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.991A pdb=" N LEU D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 572 through 583 removed outlier: 4.159A pdb=" N ILE D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 577 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 Processing helix chain 'D' and resid 626 through 636 Processing helix chain 'D' and resid 637 through 643 removed outlier: 3.536A pdb=" N ARG D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 677 removed outlier: 3.574A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.799A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.736A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.578A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 219 through 234 removed outlier: 3.839A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 261 through 277 Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.248A pdb=" N ILE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 293 " --> pdb=" O THR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.813A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 370 removed outlier: 3.807A pdb=" N THR E 354 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 374 through 389 Processing helix chain 'E' and resid 393 through 412 Processing helix chain 'E' and resid 422 through 435 removed outlier: 3.543A pdb=" N ILE E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 460 removed outlier: 4.338A pdb=" N GLY E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP E 454 " --> pdb=" O LYS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 479 Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 529 through 535 removed outlier: 3.981A pdb=" N LEU E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.538A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 569 Processing helix chain 'E' and resid 570 through 583 removed outlier: 3.501A pdb=" N PHE E 574 " --> pdb=" O HIS E 570 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 3.761A pdb=" N ARG E 610 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 636 Processing helix chain 'E' and resid 637 through 644 Processing helix chain 'E' and resid 654 through 677 removed outlier: 3.734A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 695 removed outlier: 3.680A pdb=" N ARG E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN E 688 " --> pdb=" O GLN E 684 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 693 " --> pdb=" O TRP E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 712 removed outlier: 4.419A pdb=" N ALA E 705 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP E 710 " --> pdb=" O ARG E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 191 through 203 removed outlier: 4.320A pdb=" N ARG F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 234 removed outlier: 4.238A pdb=" N THR F 221 " --> pdb=" O GLY F 217 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP F 229 " --> pdb=" O GLU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.713A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 270 Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 287 through 290 Processing helix chain 'F' and resid 306 through 314 removed outlier: 3.505A pdb=" N LEU F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY F 314 " --> pdb=" O LEU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.530A pdb=" N ILE F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.901A pdb=" N ILE F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY F 360 " --> pdb=" O GLN F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 Processing helix chain 'F' and resid 375 through 383 removed outlier: 4.004A pdb=" N VAL F 382 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU F 383 " --> pdb=" O ALA F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 412 removed outlier: 3.648A pdb=" N ASP F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP F 403 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 404 " --> pdb=" O ASP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.593A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 removed outlier: 3.653A pdb=" N VAL F 441 " --> pdb=" O PRO F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 460 removed outlier: 4.199A pdb=" N GLY F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 480 removed outlier: 4.021A pdb=" N GLY F 480 " --> pdb=" O MET F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 513 removed outlier: 3.908A pdb=" N VAL F 504 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL F 506 " --> pdb=" O THR F 502 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.743A pdb=" N SER F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 556 removed outlier: 3.631A pdb=" N HIS F 556 " --> pdb=" O VAL F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 584 removed outlier: 3.510A pdb=" N LEU F 577 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 578 " --> pdb=" O PHE F 574 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN F 579 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 599 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.145A pdb=" N GLU F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE F 632 " --> pdb=" O ALA F 628 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 644 Processing helix chain 'F' and resid 654 through 677 removed outlier: 3.591A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 removed outlier: 3.692A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 705 Processing helix chain 'F' and resid 706 through 711 removed outlier: 3.665A pdb=" N ASP F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN F 711 " --> pdb=" O VAL F 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 706 through 711' Processing helix chain 'F' and resid 712 through 722 removed outlier: 3.559A pdb=" N LEU F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 720 " --> pdb=" O LEU F 716 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.541A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.715A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 131 through 158 removed outlier: 3.615A pdb=" N ILE H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.594A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.883A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.846A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 Processing helix chain 'I' and resid 131 through 158 Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 175 through 183 Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 36 through 54 removed outlier: 3.751A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE J 43 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.680A pdb=" N GLY J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 158 removed outlier: 3.537A pdb=" N ILE J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 175 through 183 removed outlier: 3.680A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU J 181 " --> pdb=" O PRO J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.610A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.534A pdb=" N GLY K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 131 through 158 removed outlier: 3.527A pdb=" N HIS K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 170 removed outlier: 3.533A pdb=" N GLU K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.536A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 25 Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.599A pdb=" N PHE L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.754A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE L 82 " --> pdb=" O ASP L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.635A pdb=" N GLY L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 158 removed outlier: 3.819A pdb=" N ASN L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 155 " --> pdb=" O GLU L 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 169 removed outlier: 3.731A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.817A pdb=" N GLU L 181 " --> pdb=" O PRO L 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR L 182 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 25 Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.580A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 79 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 131 through 158 removed outlier: 3.543A pdb=" N GLU M 151 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 175 through 183 Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 36 through 54 removed outlier: 3.766A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.509A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 131 through 158 removed outlier: 3.656A pdb=" N HIS N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 157 " --> pdb=" O MET N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 176 through 183 removed outlier: 3.595A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.616A pdb=" N LEU A 282 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N SER A 321 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 213 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 515 through 520 removed outlier: 3.961A pdb=" N LEU A 561 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 492 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.540A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.157A pdb=" N TYR B 246 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP B 285 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 321 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373 removed outlier: 7.066A pdb=" N ARG B 372 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 515 through 518 removed outlier: 7.145A pdb=" N GLU B 515 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU B 562 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 559 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 602 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AA8, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.845A pdb=" N GLU B 681 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N LEU B 735 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.168A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER C 280 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE C 319 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 282 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER C 321 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 284 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR C 322 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU C 212 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN C 209 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE C 344 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 211 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 346 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 213 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 515 through 520 removed outlier: 7.303A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE C 491 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR C 605 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE C 493 " --> pdb=" O THR C 605 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 585 through 587 removed outlier: 3.684A pdb=" N LEU C 586 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.623A pdb=" N GLU C 681 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LEU C 735 " --> pdb=" O GLU C 681 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.264A pdb=" N TYR D 246 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP D 285 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU D 248 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 372 through 373 removed outlier: 6.997A pdb=" N ARG D 372 " --> pdb=" O VAL D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 515 through 520 removed outlier: 7.245A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.461A pdb=" N GLU D 681 " --> pdb=" O VAL D 733 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU D 735 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.206A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP E 285 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU E 248 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 282 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER E 321 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE E 284 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 372 through 373 removed outlier: 7.342A pdb=" N ARG E 372 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 515 through 520 removed outlier: 7.024A pdb=" N ALA E 559 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 492 " --> pdb=" O ASN E 646 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'E' and resid 678 through 682 removed outlier: 7.276A pdb=" N SER E 679 " --> pdb=" O VAL E 731 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL E 733 " --> pdb=" O SER E 679 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU E 681 " --> pdb=" O VAL E 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 209 through 213 Processing sheet with id=AC5, first strand: chain 'F' and resid 245 through 248 removed outlier: 6.658A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASP F 285 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU F 248 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 561 through 563 removed outlier: 5.628A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR F 604 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 563 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE F 491 " --> pdb=" O MET F 603 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR F 605 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE F 493 " --> pdb=" O THR F 605 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER F 490 " --> pdb=" O ASN F 646 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE F 648 " --> pdb=" O SER F 490 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 492 " --> pdb=" O ILE F 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 735 through 736 removed outlier: 3.572A pdb=" N ASP F 736 " --> pdb=" O GLU F 741 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 28 through 32 removed outlier: 3.547A pdb=" N TYR H 62 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN H 64 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 118 through 121 Processing sheet with id=AD2, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD3, first strand: chain 'I' and resid 28 through 29 removed outlier: 7.073A pdb=" N ILE I 29 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN I 64 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER I 65 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN I 94 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 28 through 29 removed outlier: 7.073A pdb=" N ILE I 29 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN I 64 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER I 65 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN I 94 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG I 118 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE I 121 " --> pdb=" O ARG I 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.543A pdb=" N ARG J 15 " --> pdb=" O GLU J 8 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.124A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.573A pdb=" N ARG K 15 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.648A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 94 through 95 removed outlier: 3.664A pdb=" N VAL K 119 " --> pdb=" O LEU K 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.938A pdb=" N GLU L 8 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 28 through 29 removed outlier: 6.548A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG L 111 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 118 through 121 Processing sheet with id=AE4, first strand: chain 'M' and resid 59 through 60 removed outlier: 6.389A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 63 through 65 removed outlier: 5.672A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'M' and resid 119 through 121 Processing sheet with id=AE7, first strand: chain 'N' and resid 6 through 8 Processing sheet with id=AE8, first strand: chain 'N' and resid 30 through 32 removed outlier: 6.906A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 118 through 121 removed outlier: 3.834A pdb=" N ILE N 121 " --> pdb=" O ARG N 172 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) 1769 hydrogen bonds defined for protein. 5154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.19 Time building geometry restraints manager: 18.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38089 1.06 - 1.28: 6511 1.28 - 1.50: 15369 1.50 - 1.73: 16182 1.73 - 1.95: 307 Bond restraints: 76458 Sorted by residual: bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP E 801 " pdb=" C6 ADP E 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3B AGS E 802 " pdb=" PG AGS E 802 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O3B AGS D 802 " pdb=" PG AGS D 802 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 76453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 138484 6.13 - 12.26: 80 12.26 - 18.38: 4 18.38 - 24.51: 1 24.51 - 30.64: 5 Bond angle restraints: 138574 Sorted by residual: angle pdb="HG21 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG22 ILE F 576 " ideal model delta sigma weight residual 110.00 79.36 30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb="HG22 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 110.00 79.89 30.11 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG21 ILE F 576 " ideal model delta sigma weight residual 109.00 81.58 27.42 3.00e+00 1.11e-01 8.35e+01 angle pdb=" CB ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 109.00 82.60 26.40 3.00e+00 1.11e-01 7.74e+01 angle pdb="HG21 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 110.00 135.11 -25.11 3.00e+00 1.11e-01 7.01e+01 ... (remaining 138569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 34525 35.72 - 71.44: 839 71.44 - 107.15: 43 107.15 - 142.87: 8 142.87 - 178.59: 2 Dihedral angle restraints: 35417 sinusoidal: 19982 harmonic: 15435 Sorted by residual: dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual 300.00 121.41 178.59 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 50.96 -110.96 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 49.12 -109.12 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 35414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4000 0.034 - 0.068: 1306 0.068 - 0.102: 427 0.102 - 0.136: 191 0.136 - 0.170: 27 Chirality restraints: 5951 Sorted by residual: chirality pdb=" CA ILE F 319 " pdb=" N ILE F 319 " pdb=" C ILE F 319 " pdb=" CB ILE F 319 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C3' ADP E 801 " pdb=" C2' ADP E 801 " pdb=" C4' ADP E 801 " pdb=" O3' ADP E 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 5948 not shown) Planarity restraints: 11294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 702 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.73e+00 pdb=" N PRO C 703 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 703 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 703 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 84 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO H 85 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 85 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 85 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 284 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ILE A 284 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 284 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 285 " -0.012 2.00e-02 2.50e+03 ... (remaining 11291 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 8331 2.25 - 2.84: 174879 2.84 - 3.43: 198663 3.43 - 4.01: 273289 4.01 - 4.60: 420912 Nonbonded interactions: 1076074 Sorted by model distance: nonbonded pdb=" O ALA F 381 " pdb=" HZ2 LYS F 397 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLU E 484 " pdb=" H GLU E 484 " model vdw 1.698 2.450 nonbonded pdb=" O ILE E 708 " pdb=" H LYS E 713 " model vdw 1.707 2.450 nonbonded pdb="HH12 ARG A 204 " pdb=" OD2 ASP F 403 " model vdw 1.708 2.450 nonbonded pdb=" HE ARG D 392 " pdb=" OD2 ASP D 396 " model vdw 1.713 2.450 ... (remaining 1076069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 172 through 291 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or \ name HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 533 or (resi \ d 549 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or nam \ e HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 550 throug \ h 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'B' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'C' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'D' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'E' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 435 or resid 438 through 533 or (resid 549 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or \ name HD13 or name HD21 or name HD22 or name HD23)) or resid 550 through 568 or \ resid 572 through 613 or resid 624 through 748)) selection = (chain 'F' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 323 or (resid 324 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 o \ r name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 throu \ gh 748)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = (chain 'N' and (resid 2 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 188 through 191)) } 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: 0.310 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: 1.010 Extract box with map and model: 2.420 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 128.880 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 38343 Z= 0.277 Angle : 0.774 13.427 51789 Z= 0.398 Chirality : 0.042 0.170 5951 Planarity : 0.004 0.054 6683 Dihedral : 14.066 178.591 14628 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 4752 helix: 0.94 (0.10), residues: 2267 sheet: -1.72 (0.19), residues: 679 loop : -0.69 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 7 HIS 0.007 0.001 HIS D 393 PHE 0.023 0.001 PHE A 263 TYR 0.010 0.001 TYR C 324 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1306 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1305 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 GLU cc_start: 0.7699 (tt0) cc_final: 0.7248 (mm-30) REVERT: B 210 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: B 588 ASP cc_start: 0.8164 (p0) cc_final: 0.7934 (p0) REVERT: C 215 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6770 (mm-30) REVERT: C 522 SER cc_start: 0.8723 (p) cc_final: 0.8234 (p) REVERT: D 348 GLU cc_start: 0.7853 (pt0) cc_final: 0.7191 (pt0) REVERT: D 366 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6931 (mt-10) REVERT: D 454 ASP cc_start: 0.7181 (m-30) cc_final: 0.6846 (m-30) REVERT: E 323 THR cc_start: 0.8423 (m) cc_final: 0.7995 (m) REVERT: E 447 ASP cc_start: 0.6750 (p0) cc_final: 0.6357 (p0) REVERT: E 524 TYR cc_start: 0.8250 (m-80) cc_final: 0.7986 (m-80) REVERT: F 192 GLU cc_start: 0.6537 (mp0) cc_final: 0.6270 (mp0) REVERT: F 629 MET cc_start: 0.6650 (ptt) cc_final: 0.6416 (ptt) REVERT: H 2 LEU cc_start: 0.6625 (tp) cc_final: 0.6425 (tp) REVERT: H 5 MET cc_start: 0.7422 (mmt) cc_final: 0.7027 (mmt) REVERT: H 24 LEU cc_start: 0.8416 (tp) cc_final: 0.8033 (tp) REVERT: H 47 MET cc_start: 0.8071 (mtt) cc_final: 0.7778 (mtt) REVERT: H 77 TYR cc_start: 0.7739 (t80) cc_final: 0.7321 (t80) REVERT: H 112 PHE cc_start: 0.6214 (m-80) cc_final: 0.5997 (m-80) REVERT: H 136 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6786 (tm-30) REVERT: H 148 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6777 (tpm170) REVERT: H 165 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7370 (tm-30) REVERT: J 165 GLU cc_start: 0.7649 (tp30) cc_final: 0.7030 (tt0) REVERT: J 174 LEU cc_start: 0.7921 (mt) cc_final: 0.7666 (mt) REVERT: K 104 THR cc_start: 0.7424 (t) cc_final: 0.7157 (t) REVERT: L 14 GLU cc_start: 0.5759 (pp20) cc_final: 0.4800 (pp20) REVERT: L 149 MET cc_start: 0.6338 (mmp) cc_final: 0.6066 (mmp) REVERT: L 153 MET cc_start: 0.6072 (ttm) cc_final: 0.5720 (ttm) REVERT: S 12 GLN cc_start: 0.6432 (tp40) cc_final: 0.6113 (tp40) outliers start: 1 outliers final: 0 residues processed: 1306 average time/residue: 1.1428 time to fit residues: 2335.3319 Evaluate side-chains 1109 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1109 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 403 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 434 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 675 GLN A 688 ASN A 709 GLN B 325 GLN B 558 HIS ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 660 GLN D 528 HIS D 579 GLN D 642 ASN D 711 ASN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 HIS F 305 ASN F 329 ASN F 390 ASN F 583 ASN F 718 ASN H 41 ASN I 41 ASN I 116 ASN I 159 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN L 41 ASN L 156 HIS N 41 ASN N 46 GLN N 150 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38343 Z= 0.317 Angle : 0.609 9.927 51789 Z= 0.332 Chirality : 0.041 0.198 5951 Planarity : 0.005 0.076 6683 Dihedral : 9.109 168.175 5368 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 9.59 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4752 helix: 0.87 (0.10), residues: 2422 sheet: -1.62 (0.19), residues: 664 loop : -0.57 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 689 HIS 0.008 0.001 HIS E 393 PHE 0.030 0.002 PHE K 101 TYR 0.015 0.001 TYR N 128 ARG 0.006 0.001 ARG E 702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1197 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1143 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7302 (mmpt) cc_final: 0.6968 (tttm) REVERT: A 736 ASP cc_start: 0.6518 (t70) cc_final: 0.5413 (t0) REVERT: B 343 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7585 (ttpp) REVERT: B 355 VAL cc_start: 0.8944 (m) cc_final: 0.8736 (t) REVERT: B 588 ASP cc_start: 0.8588 (p0) cc_final: 0.8225 (p0) REVERT: C 565 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7280 (mm-30) REVERT: C 633 LYS cc_start: 0.8512 (mttt) cc_final: 0.8275 (mttt) REVERT: D 264 GLU cc_start: 0.7351 (mp0) cc_final: 0.7000 (mp0) REVERT: D 564 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: E 264 GLU cc_start: 0.7154 (mp0) cc_final: 0.6933 (mp0) REVERT: E 307 ILE cc_start: 0.8984 (pt) cc_final: 0.8612 (tt) REVERT: E 326 GLU cc_start: 0.7026 (mp0) cc_final: 0.6737 (mp0) REVERT: F 664 LYS cc_start: 0.8454 (pttt) cc_final: 0.8173 (ttpt) REVERT: H 5 MET cc_start: 0.7270 (mmt) cc_final: 0.6914 (mmt) REVERT: H 24 LEU cc_start: 0.8542 (tp) cc_final: 0.8270 (tp) REVERT: H 47 MET cc_start: 0.8041 (mtt) cc_final: 0.7834 (mtt) REVERT: H 77 TYR cc_start: 0.7967 (t80) cc_final: 0.7759 (t80) REVERT: H 165 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7490 (tm-30) REVERT: J 165 GLU cc_start: 0.8160 (tp30) cc_final: 0.6994 (tt0) REVERT: K 123 GLN cc_start: 0.7427 (pt0) cc_final: 0.7222 (pt0) REVERT: K 129 GLN cc_start: 0.5170 (mp10) cc_final: 0.4970 (mp10) REVERT: L 14 GLU cc_start: 0.5931 (pp20) cc_final: 0.4914 (pp20) REVERT: L 43 ILE cc_start: 0.6044 (mt) cc_final: 0.5803 (tt) REVERT: L 149 MET cc_start: 0.6594 (mmp) cc_final: 0.6285 (mmp) REVERT: L 153 MET cc_start: 0.6032 (ttm) cc_final: 0.5705 (ttm) REVERT: N 123 GLN cc_start: 0.7943 (pp30) cc_final: 0.7707 (pp30) outliers start: 54 outliers final: 40 residues processed: 1166 average time/residue: 1.1297 time to fit residues: 2051.3721 Evaluate side-chains 1085 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1044 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 693 LYS Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 241 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 361 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 434 optimal weight: 40.0000 chunk 469 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 431 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 579 GLN B 606 ASN C 233 GLN C 325 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN F 718 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN L 54 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38343 Z= 0.293 Angle : 0.552 9.132 51789 Z= 0.294 Chirality : 0.040 0.151 5951 Planarity : 0.004 0.060 6683 Dihedral : 8.878 166.433 5368 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.56 % Allowed : 12.29 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.12), residues: 4752 helix: 0.85 (0.10), residues: 2438 sheet: -1.62 (0.19), residues: 648 loop : -0.64 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 229 HIS 0.008 0.001 HIS A 558 PHE 0.037 0.002 PHE F 327 TYR 0.011 0.001 TYR K 77 ARG 0.013 0.000 ARG H 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1149 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1086 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7448 (mmpt) cc_final: 0.7018 (tttm) REVERT: A 412 MET cc_start: 0.5039 (tmm) cc_final: 0.4811 (tmm) REVERT: A 510 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7996 (mmtp) REVERT: B 623 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7382 (t70) REVERT: C 193 LYS cc_start: 0.7985 (tttm) cc_final: 0.7688 (tttp) REVERT: C 387 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (ttpt) REVERT: C 565 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 699 MET cc_start: 0.7849 (mmp) cc_final: 0.7641 (mmp) REVERT: D 711 ASN cc_start: 0.7960 (m-40) cc_final: 0.7571 (m110) REVERT: E 264 GLU cc_start: 0.7135 (mp0) cc_final: 0.6914 (mp0) REVERT: E 307 ILE cc_start: 0.9022 (pt) cc_final: 0.8634 (tt) REVERT: E 458 MET cc_start: 0.7456 (ppp) cc_final: 0.7009 (tmm) REVERT: F 212 LEU cc_start: 0.3797 (mt) cc_final: 0.3491 (mp) REVERT: F 664 LYS cc_start: 0.8503 (pttt) cc_final: 0.8166 (ttpt) REVERT: H 5 MET cc_start: 0.7401 (mmt) cc_final: 0.7004 (mmt) REVERT: H 74 MET cc_start: 0.7459 (mmp) cc_final: 0.6729 (mmp) REVERT: H 77 TYR cc_start: 0.8002 (t80) cc_final: 0.7785 (t80) REVERT: H 165 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7516 (tm-30) REVERT: J 77 TYR cc_start: 0.8013 (t80) cc_final: 0.6914 (t80) REVERT: J 165 GLU cc_start: 0.8192 (tp30) cc_final: 0.6936 (tt0) REVERT: L 14 GLU cc_start: 0.6047 (pp20) cc_final: 0.4981 (pp20) REVERT: L 149 MET cc_start: 0.6421 (mmp) cc_final: 0.6133 (mmp) REVERT: L 153 MET cc_start: 0.6030 (ttm) cc_final: 0.5738 (ttm) outliers start: 63 outliers final: 41 residues processed: 1107 average time/residue: 1.1524 time to fit residues: 2010.6689 Evaluate side-chains 1078 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1035 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 528 HIS Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 30.0000 chunk 326 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 436 optimal weight: 30.0000 chunk 462 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 413 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN B 606 ASN B 642 ASN C 177 ASN C 233 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN C 718 ASN D 356 GLN D 579 GLN E 342 GLN ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 94 GLN M 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 38343 Z= 0.427 Angle : 0.602 12.167 51789 Z= 0.326 Chirality : 0.043 0.186 5951 Planarity : 0.005 0.062 6683 Dihedral : 9.060 168.853 5368 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 13.55 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 4752 helix: 0.53 (0.10), residues: 2447 sheet: -1.62 (0.18), residues: 678 loop : -0.92 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 689 HIS 0.017 0.001 HIS E 659 PHE 0.023 0.002 PHE F 327 TYR 0.018 0.001 TYR A 695 ARG 0.029 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1163 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1077 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7490 (mmpt) cc_final: 0.7047 (tttm) REVERT: A 558 HIS cc_start: 0.6552 (m90) cc_final: 0.6243 (m-70) REVERT: A 736 ASP cc_start: 0.6736 (t70) cc_final: 0.5890 (t0) REVERT: B 285 ASP cc_start: 0.8324 (p0) cc_final: 0.8092 (p0) REVERT: B 579 GLN cc_start: 0.8085 (pt0) cc_final: 0.7737 (pt0) REVERT: B 714 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8154 (mttp) REVERT: C 193 LYS cc_start: 0.8108 (tttm) cc_final: 0.7834 (tttp) REVERT: C 387 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8495 (ttpt) REVERT: D 472 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7148 (mm-30) REVERT: D 579 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: E 245 ILE cc_start: 0.9184 (mm) cc_final: 0.8954 (mt) REVERT: E 307 ILE cc_start: 0.9078 (pt) cc_final: 0.8723 (tt) REVERT: E 458 MET cc_start: 0.7465 (ppp) cc_final: 0.7239 (tmm) REVERT: F 188 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6317 (tt) REVERT: F 664 LYS cc_start: 0.8564 (pttt) cc_final: 0.8204 (ttpt) REVERT: H 5 MET cc_start: 0.7458 (mmt) cc_final: 0.7228 (mmt) REVERT: H 36 GLU cc_start: 0.5756 (tm-30) cc_final: 0.5385 (tm-30) REVERT: H 74 MET cc_start: 0.7727 (mmp) cc_final: 0.6909 (mmp) REVERT: H 165 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7530 (tm-30) REVERT: I 169 GLU cc_start: 0.5571 (tm-30) cc_final: 0.5253 (tm-30) REVERT: J 77 TYR cc_start: 0.8079 (t80) cc_final: 0.7027 (t80) REVERT: J 165 GLU cc_start: 0.8157 (tp30) cc_final: 0.6982 (tt0) REVERT: L 149 MET cc_start: 0.6383 (mmp) cc_final: 0.6102 (mmp) REVERT: L 153 MET cc_start: 0.6007 (ttm) cc_final: 0.5711 (ttm) REVERT: N 123 GLN cc_start: 0.7900 (pp30) cc_final: 0.7693 (pp30) outliers start: 86 outliers final: 67 residues processed: 1115 average time/residue: 1.0856 time to fit residues: 1893.7636 Evaluate side-chains 1106 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1036 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 384 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 344 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 394 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 235 optimal weight: 9.9990 chunk 414 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN C 233 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 38343 Z= 0.220 Angle : 0.521 7.460 51789 Z= 0.277 Chirality : 0.039 0.158 5951 Planarity : 0.004 0.119 6683 Dihedral : 8.712 159.497 5368 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.88 % Allowed : 14.61 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4752 helix: 0.74 (0.10), residues: 2456 sheet: -1.53 (0.18), residues: 674 loop : -0.83 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 649 HIS 0.010 0.001 HIS E 659 PHE 0.018 0.001 PHE F 267 TYR 0.016 0.001 TYR A 695 ARG 0.008 0.000 ARG L 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1137 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1061 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7490 (mmpt) cc_final: 0.7118 (tttm) REVERT: A 736 ASP cc_start: 0.6728 (t70) cc_final: 0.6507 (t70) REVERT: B 285 ASP cc_start: 0.8263 (p0) cc_final: 0.8024 (p0) REVERT: B 326 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 714 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8151 (mttp) REVERT: C 193 LYS cc_start: 0.8031 (tttm) cc_final: 0.7738 (tttp) REVERT: C 458 MET cc_start: 0.6657 (mmt) cc_final: 0.6350 (mmt) REVERT: E 245 ILE cc_start: 0.9166 (mm) cc_final: 0.8939 (mt) REVERT: E 307 ILE cc_start: 0.9054 (pt) cc_final: 0.8721 (tt) REVERT: F 188 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6305 (tt) REVERT: F 208 ASN cc_start: 0.6817 (p0) cc_final: 0.6615 (p0) REVERT: F 664 LYS cc_start: 0.8537 (pttt) cc_final: 0.8201 (ttpt) REVERT: H 5 MET cc_start: 0.7524 (mmt) cc_final: 0.7305 (mmt) REVERT: H 24 LEU cc_start: 0.8279 (tt) cc_final: 0.8064 (tt) REVERT: H 74 MET cc_start: 0.7660 (mmp) cc_final: 0.6862 (mmp) REVERT: H 165 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7521 (tm-30) REVERT: I 169 GLU cc_start: 0.5540 (tm-30) cc_final: 0.5242 (tm-30) REVERT: J 77 TYR cc_start: 0.8078 (t80) cc_final: 0.7118 (t80) REVERT: J 165 GLU cc_start: 0.8237 (tp30) cc_final: 0.7101 (tt0) REVERT: L 49 PHE cc_start: 0.6841 (t80) cc_final: 0.6572 (t80) REVERT: L 149 MET cc_start: 0.6299 (mmp) cc_final: 0.6048 (mmp) REVERT: L 153 MET cc_start: 0.5969 (ttm) cc_final: 0.5682 (ttm) REVERT: N 123 GLN cc_start: 0.7903 (pp30) cc_final: 0.7671 (pp30) outliers start: 76 outliers final: 61 residues processed: 1095 average time/residue: 1.0896 time to fit residues: 1874.5700 Evaluate side-chains 1089 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1027 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 155 optimal weight: 6.9990 chunk 416 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 462 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN B 606 ASN C 233 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 HIS C 579 GLN D 356 GLN D 730 GLN E 451 ASN F 368 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 38343 Z= 0.335 Angle : 0.556 6.248 51789 Z= 0.298 Chirality : 0.040 0.174 5951 Planarity : 0.004 0.080 6683 Dihedral : 8.829 162.827 5368 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 15.67 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4752 helix: 0.72 (0.10), residues: 2458 sheet: -1.51 (0.19), residues: 667 loop : -0.91 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 689 HIS 0.010 0.001 HIS E 659 PHE 0.019 0.002 PHE E 596 TYR 0.013 0.001 TYR B 524 ARG 0.008 0.001 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1128 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1048 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 GLU cc_start: 0.7583 (mp0) cc_final: 0.7372 (mp0) REVERT: B 285 ASP cc_start: 0.8402 (p0) cc_final: 0.8120 (p0) REVERT: B 326 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 714 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8059 (mttp) REVERT: C 193 LYS cc_start: 0.8104 (tttm) cc_final: 0.7813 (tttp) REVERT: C 458 MET cc_start: 0.6731 (mmt) cc_final: 0.6488 (mmt) REVERT: D 252 SER cc_start: 0.8925 (m) cc_final: 0.8605 (m) REVERT: D 446 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8117 (mtt90) REVERT: D 450 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7631 (tttt) REVERT: E 307 ILE cc_start: 0.9088 (pt) cc_final: 0.8783 (tt) REVERT: F 664 LYS cc_start: 0.8569 (pttt) cc_final: 0.8211 (ttpt) REVERT: H 5 MET cc_start: 0.7565 (mmt) cc_final: 0.7344 (mmt) REVERT: H 74 MET cc_start: 0.7828 (mmp) cc_final: 0.7017 (mmp) REVERT: H 165 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7541 (tm-30) REVERT: J 77 TYR cc_start: 0.8061 (t80) cc_final: 0.7199 (t80) REVERT: K 98 MET cc_start: 0.8155 (tpp) cc_final: 0.7948 (tpp) REVERT: L 153 MET cc_start: 0.6076 (ttm) cc_final: 0.5814 (ttm) REVERT: N 123 GLN cc_start: 0.7980 (pp30) cc_final: 0.7706 (pp30) outliers start: 80 outliers final: 68 residues processed: 1091 average time/residue: 1.1017 time to fit residues: 1888.9073 Evaluate side-chains 1088 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1019 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 579 GLN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 544 ASP Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 445 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 chunk 261 optimal weight: 7.9990 chunk 389 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 460 optimal weight: 6.9990 chunk 288 optimal weight: 40.0000 chunk 280 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN C 233 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN D 730 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 38343 Z= 0.305 Angle : 0.543 6.783 51789 Z= 0.290 Chirality : 0.040 0.161 5951 Planarity : 0.004 0.092 6683 Dihedral : 8.786 159.217 5368 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.25 % Allowed : 16.17 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4752 helix: 0.73 (0.10), residues: 2463 sheet: -1.48 (0.19), residues: 667 loop : -0.93 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 689 HIS 0.008 0.001 HIS E 659 PHE 0.025 0.001 PHE E 263 TYR 0.010 0.001 TYR C 324 ARG 0.012 0.000 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1137 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1046 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.8378 (p0) cc_final: 0.8065 (p0) REVERT: B 326 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 337 LEU cc_start: 0.7400 (mm) cc_final: 0.7145 (mt) REVERT: B 714 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8075 (mttp) REVERT: C 193 LYS cc_start: 0.8096 (tttm) cc_final: 0.7824 (tttp) REVERT: C 458 MET cc_start: 0.6727 (mmt) cc_final: 0.6492 (mmt) REVERT: D 446 ARG cc_start: 0.8346 (mtt90) cc_final: 0.8119 (mtt90) REVERT: D 450 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7620 (tttt) REVERT: D 730 GLN cc_start: 0.8126 (mp10) cc_final: 0.7919 (mp10) REVERT: E 265 LYS cc_start: 0.7421 (tttp) cc_final: 0.7214 (ttpp) REVERT: E 307 ILE cc_start: 0.9110 (pt) cc_final: 0.8810 (tt) REVERT: E 422 ASN cc_start: 0.6565 (t0) cc_final: 0.6307 (t0) REVERT: F 659 HIS cc_start: 0.6929 (m90) cc_final: 0.6723 (m90) REVERT: F 664 LYS cc_start: 0.8575 (pttt) cc_final: 0.8228 (ttpt) REVERT: H 5 MET cc_start: 0.7568 (mmt) cc_final: 0.7331 (mmt) REVERT: H 74 MET cc_start: 0.7836 (mmp) cc_final: 0.6986 (mmp) REVERT: H 156 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6610 (t-90) REVERT: H 165 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7505 (tm-30) REVERT: I 156 HIS cc_start: 0.5447 (OUTLIER) cc_final: 0.5076 (t-90) REVERT: I 169 GLU cc_start: 0.5509 (tm-30) cc_final: 0.5248 (tm-30) REVERT: J 77 TYR cc_start: 0.8092 (t80) cc_final: 0.7228 (t80) REVERT: K 36 GLU cc_start: 0.6236 (mm-30) cc_final: 0.6031 (tm-30) REVERT: K 98 MET cc_start: 0.8128 (tpp) cc_final: 0.7897 (tpp) REVERT: L 149 MET cc_start: 0.6330 (mmp) cc_final: 0.5804 (mmp) REVERT: L 153 MET cc_start: 0.6077 (ttm) cc_final: 0.5812 (ttm) outliers start: 91 outliers final: 75 residues processed: 1092 average time/residue: 1.0996 time to fit residues: 1887.7827 Evaluate side-chains 1107 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1029 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 285 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 275 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 313 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38343 Z= 0.244 Angle : 0.529 7.749 51789 Z= 0.279 Chirality : 0.039 0.160 5951 Planarity : 0.004 0.101 6683 Dihedral : 8.575 151.039 5368 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 16.84 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4752 helix: 0.86 (0.10), residues: 2464 sheet: -1.41 (0.19), residues: 645 loop : -0.91 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 649 HIS 0.009 0.001 HIS E 659 PHE 0.021 0.001 PHE F 267 TYR 0.009 0.001 TYR C 324 ARG 0.010 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1135 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1052 time to evaluate : 4.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.9132 (mt) cc_final: 0.8920 (mp) REVERT: A 704 MET cc_start: 0.6796 (mmm) cc_final: 0.6289 (mmm) REVERT: B 285 ASP cc_start: 0.8378 (p0) cc_final: 0.8087 (p0) REVERT: B 337 LEU cc_start: 0.7426 (mm) cc_final: 0.7188 (mt) REVERT: B 714 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8044 (mttp) REVERT: C 193 LYS cc_start: 0.8078 (tttm) cc_final: 0.7804 (tttp) REVERT: C 458 MET cc_start: 0.6750 (mmt) cc_final: 0.6486 (mmt) REVERT: C 675 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: D 249 ASP cc_start: 0.7919 (t0) cc_final: 0.7621 (t70) REVERT: D 450 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7602 (tttt) REVERT: D 730 GLN cc_start: 0.8122 (mp10) cc_final: 0.7892 (mp10) REVERT: E 265 LYS cc_start: 0.7402 (tttp) cc_final: 0.7197 (ttpp) REVERT: E 268 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8205 (mmtp) REVERT: E 307 ILE cc_start: 0.9106 (pt) cc_final: 0.8813 (tt) REVERT: E 422 ASN cc_start: 0.6600 (t0) cc_final: 0.6347 (t0) REVERT: F 188 LEU cc_start: 0.7558 (mt) cc_final: 0.7070 (mp) REVERT: F 664 LYS cc_start: 0.8583 (pttt) cc_final: 0.8240 (ttpt) REVERT: H 74 MET cc_start: 0.7836 (mmp) cc_final: 0.6987 (mmp) REVERT: H 156 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6596 (t-90) REVERT: H 165 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7514 (tm-30) REVERT: I 169 GLU cc_start: 0.5488 (tm-30) cc_final: 0.5223 (tm-30) REVERT: J 77 TYR cc_start: 0.8021 (t80) cc_final: 0.7363 (t80) REVERT: L 38 HIS cc_start: 0.7386 (m90) cc_final: 0.7081 (m90) REVERT: L 149 MET cc_start: 0.6251 (mmp) cc_final: 0.5742 (mmp) REVERT: L 153 MET cc_start: 0.6135 (ttm) cc_final: 0.5877 (ttm) outliers start: 83 outliers final: 69 residues processed: 1093 average time/residue: 1.1207 time to fit residues: 1927.6582 Evaluate side-chains 1102 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1030 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 419 optimal weight: 9.9990 chunk 441 optimal weight: 20.0000 chunk 402 optimal weight: 5.9990 chunk 429 optimal weight: 0.0970 chunk 258 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 337 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 387 optimal weight: 0.2980 chunk 406 optimal weight: 9.9990 chunk 427 optimal weight: 1.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN B 359 ASN C 233 GLN C 279 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38343 Z= 0.192 Angle : 0.516 7.281 51789 Z= 0.271 Chirality : 0.039 0.158 5951 Planarity : 0.004 0.079 6683 Dihedral : 8.391 141.776 5368 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.85 % Allowed : 17.26 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4752 helix: 0.99 (0.10), residues: 2465 sheet: -1.42 (0.19), residues: 652 loop : -0.85 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 649 HIS 0.007 0.001 HIS E 659 PHE 0.021 0.001 PHE F 267 TYR 0.018 0.001 TYR N 128 ARG 0.016 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1119 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1044 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.9121 (mt) cc_final: 0.8895 (mp) REVERT: A 643 ARG cc_start: 0.5846 (mpt180) cc_final: 0.5614 (mpt-90) REVERT: A 704 MET cc_start: 0.6706 (mmm) cc_final: 0.6248 (mmm) REVERT: B 285 ASP cc_start: 0.8319 (p0) cc_final: 0.8047 (p0) REVERT: B 337 LEU cc_start: 0.7530 (mm) cc_final: 0.7271 (mt) REVERT: C 193 LYS cc_start: 0.8065 (tttm) cc_final: 0.7790 (tttp) REVERT: C 458 MET cc_start: 0.6725 (mmt) cc_final: 0.6390 (mmt) REVERT: C 675 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: D 249 ASP cc_start: 0.7885 (t0) cc_final: 0.7589 (t70) REVERT: D 450 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7581 (tttt) REVERT: D 704 MET cc_start: 0.7762 (mmm) cc_final: 0.7168 (tpp) REVERT: D 711 ASN cc_start: 0.8349 (m-40) cc_final: 0.7805 (m110) REVERT: D 730 GLN cc_start: 0.8091 (mp10) cc_final: 0.7870 (mp10) REVERT: E 200 GLN cc_start: 0.8282 (tt0) cc_final: 0.8035 (tt0) REVERT: E 265 LYS cc_start: 0.7387 (tttp) cc_final: 0.7180 (ttpp) REVERT: E 268 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8197 (mmtp) REVERT: E 307 ILE cc_start: 0.9086 (pt) cc_final: 0.8797 (tt) REVERT: E 422 ASN cc_start: 0.6592 (t0) cc_final: 0.6338 (t0) REVERT: F 188 LEU cc_start: 0.7569 (mt) cc_final: 0.7076 (mp) REVERT: F 208 ASN cc_start: 0.6742 (p0) cc_final: 0.6461 (p0) REVERT: F 664 LYS cc_start: 0.8560 (pttt) cc_final: 0.8247 (ttpt) REVERT: H 74 MET cc_start: 0.7816 (mmp) cc_final: 0.6969 (mmp) REVERT: H 156 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6625 (t-90) REVERT: H 165 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7513 (tm-30) REVERT: I 169 GLU cc_start: 0.5491 (tm-30) cc_final: 0.5236 (tm-30) REVERT: J 77 TYR cc_start: 0.8014 (t80) cc_final: 0.7357 (t80) REVERT: L 38 HIS cc_start: 0.7354 (m90) cc_final: 0.7016 (m90) REVERT: L 149 MET cc_start: 0.6314 (mmp) cc_final: 0.5818 (mmp) REVERT: L 153 MET cc_start: 0.6097 (ttm) cc_final: 0.5843 (ttm) outliers start: 75 outliers final: 68 residues processed: 1082 average time/residue: 1.0988 time to fit residues: 1873.8287 Evaluate side-chains 1105 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1034 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 281 optimal weight: 30.0000 chunk 453 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 315 optimal weight: 40.0000 chunk 476 optimal weight: 7.9990 chunk 438 optimal weight: 8.9990 chunk 379 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 292 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN D 356 GLN D 642 ASN E 305 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38343 Z= 0.279 Angle : 0.544 8.856 51789 Z= 0.286 Chirality : 0.040 0.161 5951 Planarity : 0.004 0.068 6683 Dihedral : 8.455 143.538 5368 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.78 % Allowed : 17.53 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4752 helix: 0.91 (0.10), residues: 2474 sheet: -1.43 (0.19), residues: 650 loop : -0.90 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 689 HIS 0.008 0.001 HIS F 659 PHE 0.024 0.001 PHE I 17 TYR 0.011 0.001 TYR N 128 ARG 0.015 0.000 ARG I 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1113 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1041 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.9134 (mt) cc_final: 0.8907 (mp) REVERT: A 643 ARG cc_start: 0.5883 (mpt180) cc_final: 0.5644 (mpt-90) REVERT: A 704 MET cc_start: 0.6751 (mmm) cc_final: 0.6286 (mmm) REVERT: B 285 ASP cc_start: 0.8380 (p0) cc_final: 0.8078 (p0) REVERT: B 337 LEU cc_start: 0.7511 (mm) cc_final: 0.7257 (mt) REVERT: B 714 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8038 (mttp) REVERT: C 193 LYS cc_start: 0.8098 (tttm) cc_final: 0.7822 (tttp) REVERT: C 458 MET cc_start: 0.6748 (mmt) cc_final: 0.6441 (mmt) REVERT: D 450 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7625 (tttt) REVERT: D 711 ASN cc_start: 0.8366 (m-40) cc_final: 0.7831 (m110) REVERT: E 200 GLN cc_start: 0.8327 (tt0) cc_final: 0.8082 (tt0) REVERT: E 268 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8247 (mmtp) REVERT: E 307 ILE cc_start: 0.9097 (pt) cc_final: 0.8819 (tt) REVERT: F 188 LEU cc_start: 0.7599 (mt) cc_final: 0.7101 (mp) REVERT: F 664 LYS cc_start: 0.8579 (pttt) cc_final: 0.8265 (ttpt) REVERT: H 74 MET cc_start: 0.7875 (mmp) cc_final: 0.7027 (mmp) REVERT: H 156 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6609 (t-90) REVERT: H 165 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7522 (tm-30) REVERT: I 169 GLU cc_start: 0.5494 (tm-30) cc_final: 0.5231 (tm-30) REVERT: J 77 TYR cc_start: 0.8021 (t80) cc_final: 0.7474 (t80) REVERT: L 36 GLU cc_start: 0.6943 (tm-30) cc_final: 0.5585 (tm-30) REVERT: L 38 HIS cc_start: 0.7370 (m90) cc_final: 0.7068 (m90) REVERT: L 149 MET cc_start: 0.6321 (mmp) cc_final: 0.5839 (mmp) REVERT: L 153 MET cc_start: 0.6102 (ttm) cc_final: 0.5843 (ttm) outliers start: 72 outliers final: 67 residues processed: 1082 average time/residue: 1.0664 time to fit residues: 1806.0538 Evaluate side-chains 1094 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1025 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 301 optimal weight: 50.0000 chunk 403 optimal weight: 5.9990 chunk 116 optimal weight: 0.2980 chunk 349 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN B 709 GLN C 279 ASN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 GLN I 156 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.193963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143585 restraints weight = 139823.059| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.50 r_work: 0.3153 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38343 Z= 0.239 Angle : 0.534 7.456 51789 Z= 0.280 Chirality : 0.039 0.163 5951 Planarity : 0.004 0.070 6683 Dihedral : 8.370 143.082 5368 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 17.55 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 4752 helix: 0.94 (0.10), residues: 2475 sheet: -1.43 (0.19), residues: 650 loop : -0.86 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 689 HIS 0.009 0.001 HIS I 156 PHE 0.024 0.001 PHE F 267 TYR 0.011 0.001 TYR D 373 ARG 0.014 0.000 ARG I 15 =============================================================================== Job complete usr+sys time: 26931.65 seconds wall clock time: 455 minutes 28.60 seconds (27328.60 seconds total)