Starting phenix.real_space_refine on Sun Sep 29 21:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/09_2024/7uiv_26554_trim.cif" } resolution = 3.38 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 169 5.16 5 C 23781 2.51 5 N 6708 2.21 5 O 7206 1.98 5 H 38252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 303 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: 76152 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 8908 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 18, 'TRANS': 542} Chain breaks: 2 Chain: "B" 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: "C" Number of atoms: 9191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9191 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 18, 'TRANS': 564} 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: 9133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9133 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} Chain: "F" Number of atoms: 9006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 9006 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 18, 'TRANS': 548} Chain breaks: 1 Chain: "S" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 294 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain breaks: 1 Chain: "H" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} 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: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'AGS': 1} 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} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.49, per 1000 atoms: 0.40 Number of scatterers: 76152 At special positions: 0 Unit cell: (152.25, 149.64, 163.56, 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 169 16.00 P 29 15.00 Mg 7 11.99 O 7206 8.00 N 6708 7.00 C 23781 6.00 H 38252 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: 14.63 Conformation dependent library (CDL) restraints added in 5.7 seconds 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8892 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 52 sheets defined 57.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.539A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 261 through 275 removed outlier: 3.885A pdb=" N LYS A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.739A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.542A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.685A pdb=" N SER A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.614A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 4.029A pdb=" N ALA A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 3.523A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 374 through 389 Processing helix chain 'A' and resid 393 through 412 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.604A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 3.674A pdb=" N GLY A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.706A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.888A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.270A pdb=" N PHE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 654 through 677 removed outlier: 3.578A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 663 " --> pdb=" O HIS A 659 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.520A pdb=" N ASN A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.629A pdb=" N ALA A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 724 through 727 removed outlier: 3.547A pdb=" N ASP A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) No H-bonds generated for '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: 3.838A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.993A pdb=" N ASP B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.513A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.369A 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 288 through 292 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 334 through 341 Processing helix chain 'B' and resid 350 through 370 Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 393 through 412 removed outlier: 3.613A pdb=" N VAL B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.575A 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 500 through 513 removed outlier: 3.755A pdb=" N VAL B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.634A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (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: 3.944A pdb=" N PHE B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 removed outlier: 3.844A pdb=" N THR B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) 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: 3.724A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.671A pdb=" N ALA B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 723 through 727 removed outlier: 4.157A 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: 3.573A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 261 through 278 Processing helix chain 'C' and resid 287 through 293 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: 3.601A 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 removed outlier: 3.540A pdb=" N HIS C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'C' and resid 393 through 412 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 500 through 513 removed outlier: 3.538A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (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: 4.191A pdb=" N LEU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 removed outlier: 4.275A pdb=" N ASP C 544 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 566 through 569 Processing helix chain 'C' and resid 570 through 583 removed outlier: 3.982A pdb=" N PHE C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 4.342A 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 624 through 636 removed outlier: 3.601A pdb=" N ALA C 628 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 removed outlier: 3.504A pdb=" N LEU C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 676 removed outlier: 3.533A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.984A 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: 4.050A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 723 through 727 removed outlier: 3.915A pdb=" N ASP C 727 " --> pdb=" O SER C 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.502A 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: 4.167A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 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: 3.673A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.928A 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 432 removed outlier: 3.501A pdb=" N ILE D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 460 removed outlier: 4.353A pdb=" N GLY D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP D 454 " --> pdb=" O LYS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 480 removed outlier: 3.687A pdb=" N ILE D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 513 removed outlier: 3.976A pdb=" N THR D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) 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: 4.171A pdb=" N LEU D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 570 through 584 removed outlier: 4.057A pdb=" N PHE D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN D 575 " --> pdb=" O PRO D 571 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 577 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 4.558A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU D 611 " --> pdb=" O ALA D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 removed outlier: 4.346A pdb=" N MET D 629 " --> pdb=" O SER D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 654 through 677 removed outlier: 3.645A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 694 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.832A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.578A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.807A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.568A pdb=" N VAL E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 219 through 233 removed outlier: 3.818A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (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 287 through 294 removed outlier: 3.904A pdb=" N ILE E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY E 292 " --> pdb=" O HIS E 288 " (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 324 through 330 Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.697A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 370 removed outlier: 3.580A pdb=" N THR E 354 " --> pdb=" O SER E 350 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.531A pdb=" N VAL E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 412 removed outlier: 3.505A pdb=" N GLY E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 435 Processing helix chain 'E' and resid 445 through 451 Processing helix chain 'E' and resid 451 through 459 removed outlier: 3.602A pdb=" N MET E 458 " --> pdb=" O ASP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 479 Processing helix chain 'E' and resid 500 through 513 removed outlier: 3.901A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 511 " --> pdb=" O GLN E 507 " (cutoff:3.500A) 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: 3.896A pdb=" N LEU E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 534 " --> pdb=" O VAL E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 removed outlier: 4.064A pdb=" N ASP E 544 " --> pdb=" O VAL E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 Processing helix chain 'E' and resid 566 through 569 Processing helix chain 'E' and resid 570 through 584 removed outlier: 3.586A pdb=" N PHE E 574 " --> pdb=" O HIS E 570 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 4.374A pdb=" N ARG E 610 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 612 " --> pdb=" O GLY E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 636 Processing helix chain 'E' and resid 637 through 644 removed outlier: 3.546A pdb=" N ARG E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 677 Processing helix chain 'E' and resid 683 through 695 Processing helix chain 'E' and resid 701 through 712 removed outlier: 4.290A pdb=" N ALA E 705 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.540A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 219 through 234 Processing helix chain 'F' and resid 237 through 242 removed outlier: 4.153A pdb=" N ASP F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'F' and resid 261 through 277 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.191A pdb=" N ILE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 314 Processing helix chain 'F' and resid 323 through 330 Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 350 through 370 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.575A pdb=" N GLU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 412 removed outlier: 3.607A pdb=" N ALA F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.595A pdb=" N LYS F 416 " --> pdb=" O PRO F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 435 removed outlier: 4.166A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 Processing helix chain 'F' and resid 446 through 460 removed outlier: 4.280A pdb=" N LYS F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 480 removed outlier: 3.532A pdb=" N MET F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 513 Processing helix chain 'F' and resid 522 through 524 No H-bonds generated for 'chain 'F' and resid 522 through 524' Processing helix chain 'F' and resid 526 through 532 removed outlier: 3.740A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 556 removed outlier: 3.543A pdb=" N VAL F 553 " --> pdb=" O LEU F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 584 removed outlier: 3.834A pdb=" N ILE F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU F 577 " --> pdb=" O VAL F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 removed outlier: 4.393A pdb=" N ARG F 610 " --> pdb=" O ASN F 606 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 611 " --> pdb=" O ALA F 607 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 614 " --> pdb=" O ARG F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.512A pdb=" N GLU F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 644 removed outlier: 3.758A pdb=" N ARG F 641 " --> pdb=" O THR F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 677 removed outlier: 3.624A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 removed outlier: 3.834A pdb=" N LYS F 693 " --> pdb=" O TRP F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 722 removed outlier: 3.556A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.697A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 727 removed outlier: 3.920A pdb=" N ASP F 727 " --> pdb=" O SER F 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.734A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.679A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.602A 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 Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.664A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.548A 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: 3.578A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 131 through 158 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 183 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.660A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.695A pdb=" N GLY J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.783A pdb=" N LEU J 102 " --> pdb=" O MET J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 158 Processing helix chain 'J' and resid 160 through 170 removed outlier: 4.036A pdb=" N ARG J 170 " --> pdb=" O ARG J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 131 through 158 Processing helix chain 'K' and resid 160 through 170 removed outlier: 4.207A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.752A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 25 Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.736A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 131 through 158 Processing helix chain 'L' and resid 160 through 170 removed outlier: 3.561A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG L 170 " --> pdb=" O ARG L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.544A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.560A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.551A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 82 " --> pdb=" O ASP M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 106 removed outlier: 3.539A pdb=" N GLY M 106 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 175 through 182 Processing helix chain 'N' and resid 19 through 25 Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.698A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 106 Processing helix chain 'N' and resid 131 through 158 Processing helix chain 'N' and resid 160 through 170 removed outlier: 4.074A pdb=" N ARG N 170 " --> pdb=" O ARG N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 183 removed outlier: 3.775A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.199A pdb=" N TYR A 246 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR A 322 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE A 344 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 211 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 515 through 520 removed outlier: 7.501A pdb=" N GLU A 515 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 562 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A 517 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 564 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 519 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA A 559 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 602 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU A 561 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 604 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 563 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 491 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR A 605 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 493 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.689A 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: 6.108A pdb=" N SER A 679 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 733 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU A 681 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N LEU A 735 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.700A pdb=" N THR B 244 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE B 283 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 246 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASP B 285 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 248 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.619A 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: 6.694A 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: 6.792A pdb=" N ALA B 559 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 602 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY B 489 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET B 603 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 491 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 605 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE B 493 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.709A 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 removed outlier: 3.590A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 679 through 682 removed outlier: 6.381A pdb=" N SER B 679 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL B 733 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 681 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.792A 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: 6.073A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER C 280 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE C 319 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 282 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER C 321 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 284 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 322 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN C 209 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 344 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 211 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 346 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 213 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 372 through 373 removed outlier: 6.765A pdb=" N ARG C 372 " --> pdb=" O VAL C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 515 through 520 removed outlier: 6.666A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 491 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR C 605 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 493 " --> pdb=" O THR C 605 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 494 " --> pdb=" O ILE C 648 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 585 through 587 Processing sheet with id=AB4, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.795A pdb=" N GLU C 681 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N LEU C 735 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.440A pdb=" N THR D 244 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE D 283 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR D 246 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP D 285 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU D 248 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER D 280 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE D 319 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 372 through 373 removed outlier: 6.827A pdb=" N ARG D 372 " --> pdb=" O VAL D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 515 through 516 removed outlier: 7.095A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE D 519 " --> pdb=" O ASP D 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 515 through 516 removed outlier: 7.095A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 492 " --> pdb=" O ASN D 646 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 585 through 587 removed outlier: 3.718A pdb=" N LEU D 586 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 679 through 682 removed outlier: 6.652A pdb=" N SER D 679 " --> pdb=" O VAL D 731 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL D 733 " --> pdb=" O SER D 679 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU D 681 " --> pdb=" O VAL D 733 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LEU D 735 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.228A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP E 285 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU E 248 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E 282 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N SER E 321 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE E 284 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N THR E 323 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 372 through 373 removed outlier: 6.935A pdb=" N ARG E 372 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 515 through 520 removed outlier: 6.859A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 600 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 561 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER E 490 " --> pdb=" O ASN E 646 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE E 648 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU E 492 " --> pdb=" O ILE E 648 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 585 through 587 Processing sheet with id=AC6, first strand: chain 'E' and resid 679 through 682 removed outlier: 6.076A pdb=" N SER E 679 " --> pdb=" O VAL E 731 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL E 733 " --> pdb=" O SER E 679 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU E 681 " --> pdb=" O VAL E 733 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LEU E 735 " --> pdb=" O GLU E 681 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 173 through 175 removed outlier: 3.674A pdb=" N THR F 174 " --> pdb=" O SER F 247 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER F 280 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE F 319 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU F 282 " --> pdb=" O ILE F 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 209 through 213 removed outlier: 6.871A pdb=" N ASN F 209 " --> pdb=" O GLN F 342 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE F 344 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU F 211 " --> pdb=" O ILE F 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 372 through 373 removed outlier: 8.137A pdb=" N ARG F 372 " --> pdb=" O VAL F 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 489 through 494 removed outlier: 3.993A pdb=" N ASP F 564 " --> pdb=" O PHE F 519 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 585 through 587 Processing sheet with id=AD3, first strand: chain 'F' and resid 679 through 682 removed outlier: 6.546A pdb=" N SER F 679 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL F 733 " --> pdb=" O SER F 679 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU F 681 " --> pdb=" O VAL F 733 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU F 735 " --> pdb=" O GLU F 681 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN F 730 " --> pdb=" O GLN F 747 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN F 747 " --> pdb=" O GLN F 730 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.486A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS H 113 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.330A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 121 " --> pdb=" O ARG H 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD8, first strand: chain 'I' and resid 28 through 32 removed outlier: 5.300A pdb=" N SER I 65 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN I 94 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 28 through 32 removed outlier: 5.300A pdb=" N SER I 65 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN I 94 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG I 111 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AE2, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.545A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG J 111 " --> pdb=" O SER J 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.505A pdb=" N ARG K 15 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.281A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG K 111 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 94 through 95 removed outlier: 6.465A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.514A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.660A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN L 64 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU L 31 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER L 187 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 94 through 95 removed outlier: 6.011A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AF2, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.964A pdb=" N ILE M 29 " --> pdb=" O TYR M 62 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 90 through 91 Processing sheet with id=AF4, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AF5, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.648A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 28 through 32 removed outlier: 7.333A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.552A pdb=" N ARG N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) 1876 hydrogen bonds defined for protein. 5514 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: 31.57 Time building geometry restraints manager: 18.42 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: 38226 1.06 - 1.28: 6521 1.28 - 1.50: 15435 1.50 - 1.73: 16240 1.73 - 1.95: 305 Bond restraints: 76727 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 2.96e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP D 802 " pdb=" C5 ADP D 802 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C5 ADP A 801 " pdb=" C6 ADP A 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 76722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 138878 4.75 - 9.50: 179 9.50 - 14.25: 22 14.25 - 19.00: 0 19.00 - 23.75: 3 Bond angle restraints: 139082 Sorted by residual: angle pdb=" CB LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 109.00 85.25 23.75 3.00e+00 1.11e-01 6.27e+01 angle pdb=" CD2 LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 108.00 84.75 23.25 3.00e+00 1.11e-01 6.00e+01 angle pdb=" CD1 LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 108.00 85.08 22.92 3.00e+00 1.11e-01 5.84e+01 angle pdb=" PA AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sigma weight residual 119.76 133.62 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" PB AGS E 802 " pdb=" O3B AGS E 802 " pdb=" PG AGS E 802 " ideal model delta sigma weight residual 120.12 133.82 -13.70 3.00e+00 1.11e-01 2.09e+01 ... (remaining 139077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 34311 32.24 - 64.48: 1130 64.48 - 96.72: 68 96.72 - 128.96: 10 128.96 - 161.20: 7 Dihedral angle restraints: 35526 sinusoidal: 20054 harmonic: 15472 Sorted by residual: dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual 300.00 165.91 134.09 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 72.14 -132.14 1 2.00e+01 2.50e-03 4.01e+01 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 -60.00 68.95 -128.96 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 35523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 5969 0.353 - 0.705: 0 0.705 - 1.058: 0 1.058 - 1.410: 0 1.410 - 1.763: 1 Chirality restraints: 5970 Sorted by residual: chirality pdb=" CG LEU F 517 " pdb=" CB LEU F 517 " pdb=" CD1 LEU F 517 " pdb=" CD2 LEU F 517 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.77e+01 chirality pdb=" C3' ADP A 801 " pdb=" C2' ADP A 801 " pdb=" C4' ADP A 801 " pdb=" O3' ADP A 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA MET D 412 " pdb=" N MET D 412 " pdb=" C MET D 412 " pdb=" CB MET D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 5967 not shown) Planarity restraints: 11332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 702 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO B 703 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 703 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 703 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 308 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO F 309 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 309 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 309 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 394 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO F 395 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 395 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 395 " 0.039 5.00e-02 4.00e+02 ... (remaining 11329 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 10773 2.27 - 2.85: 177461 2.85 - 3.43: 201939 3.43 - 4.02: 278657 4.02 - 4.60: 426033 Nonbonded interactions: 1094863 Sorted by model distance: nonbonded pdb=" O SER F 531 " pdb=" H GLY F 535 " model vdw 1.687 2.450 nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.700 2.450 nonbonded pdb=" O GLU C 526 " pdb=" HG1 THR C 529 " model vdw 1.705 2.450 nonbonded pdb=" HG1 THR D 502 " pdb="MG MG D 804 " model vdw 1.705 1.700 nonbonded pdb=" O TYR C 246 " pdb=" H PHE C 283 " model vdw 1.711 2.450 ... (remaining 1094858 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 173 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or resid 305 \ through 501 or (resid 502 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name H or name HA or name HB or name HG21 or name HG \ 22 or name HG23)) or resid 503 through 747)) selection = (chain 'B' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'C' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 291 or resid 305 through 431 or (resid \ 432 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 o \ r name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH \ 11 or name HH21)) or resid 433 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ or na \ me NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or n \ ame HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH2 \ 2)) or resid 456 through 539 or resid 548 through 747)) selection = (chain 'D' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'E' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'F' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 431 or (r \ esid 432 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH21)) or resid 433 through 454 or (resid 455 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or nam \ e HH22)) or resid 456 through 501 or (resid 502 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 503 through 539 or resid 548 thr \ ough 747)) } 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' and resid 2 through 191) selection = chain 'N' } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.970 Extract box with map and model: 2.080 Check model and map are aligned: 0.430 Set scattering table: 0.530 Process input model: 131.460 Find NCS groups from input model: 2.910 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 38475 Z= 0.295 Angle : 0.808 13.862 51976 Z= 0.412 Chirality : 0.048 1.763 5970 Planarity : 0.004 0.075 6704 Dihedral : 15.035 161.196 14675 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 4769 helix: 1.62 (0.09), residues: 2395 sheet: -0.06 (0.18), residues: 726 loop : -0.22 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 689 HIS 0.011 0.001 HIS D 528 PHE 0.033 0.001 PHE A 267 TYR 0.012 0.001 TYR D 324 ARG 0.015 0.000 ARG N 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1436 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1436 time to evaluate : 4.267 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: A 327 PHE cc_start: 0.7390 (t80) cc_final: 0.6891 (t80) REVERT: A 684 GLN cc_start: 0.7726 (tp40) cc_final: 0.7476 (tp40) REVERT: B 370 ASP cc_start: 0.7421 (t0) cc_final: 0.7126 (t0) REVERT: B 523 GLU cc_start: 0.7953 (mp0) cc_final: 0.7685 (mp0) REVERT: B 575 ASN cc_start: 0.8094 (m-40) cc_final: 0.7850 (m-40) REVERT: C 208 ASN cc_start: 0.8739 (p0) cc_final: 0.8409 (p0) REVERT: C 240 MET cc_start: 0.8447 (mmm) cc_final: 0.8235 (mmp) REVERT: C 370 ASP cc_start: 0.7304 (t0) cc_final: 0.6991 (t0) REVERT: C 459 LEU cc_start: 0.8798 (mm) cc_final: 0.8595 (mm) REVERT: C 515 GLU cc_start: 0.7682 (tp30) cc_final: 0.7348 (tp30) REVERT: C 740 ASN cc_start: 0.8057 (t0) cc_final: 0.6934 (t0) REVERT: D 182 VAL cc_start: 0.8221 (m) cc_final: 0.7998 (t) REVERT: D 339 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8738 (ttp80) REVERT: D 503 GLU cc_start: 0.7771 (tp30) cc_final: 0.7457 (tp30) REVERT: E 250 ILE cc_start: 0.8309 (mm) cc_final: 0.8067 (mt) REVERT: E 361 LEU cc_start: 0.8320 (mp) cc_final: 0.8093 (mp) REVERT: E 403 ASP cc_start: 0.8091 (t70) cc_final: 0.7859 (t0) REVERT: E 465 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7931 (mmtm) REVERT: E 553 VAL cc_start: 0.8374 (m) cc_final: 0.8152 (p) REVERT: E 556 HIS cc_start: 0.7850 (m-70) cc_final: 0.7231 (m-70) REVERT: E 627 ASP cc_start: 0.8220 (m-30) cc_final: 0.7907 (m-30) REVERT: F 218 VAL cc_start: 0.7947 (p) cc_final: 0.7739 (p) REVERT: F 265 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8003 (pttt) REVERT: H 57 LYS cc_start: 0.8482 (mttt) cc_final: 0.8260 (mtpp) REVERT: I 10 THR cc_start: 0.7141 (m) cc_final: 0.6911 (p) REVERT: J 8 GLU cc_start: 0.7188 (tt0) cc_final: 0.6982 (tt0) REVERT: K 122 HIS cc_start: 0.6971 (p-80) cc_final: 0.6764 (p-80) REVERT: M 8 GLU cc_start: 0.6575 (tt0) cc_final: 0.5823 (tt0) REVERT: M 144 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8555 (ttmm) REVERT: N 22 ARG cc_start: 0.7967 (tpt90) cc_final: 0.7662 (tpt90) REVERT: N 148 ARG cc_start: 0.7197 (tpt170) cc_final: 0.6967 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 1436 average time/residue: 1.1953 time to fit residues: 2658.8046 Evaluate side-chains 1177 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1177 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 433 optimal weight: 6.9990 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 356 GLN A 583 ASN B 209 ASN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN C 329 ASN C 422 ASN D 233 GLN D 589 ASN D 660 GLN D 740 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 HIS E 558 HIS E 642 ASN F 390 ASN F 558 HIS F 583 ASN F 590 ASN F 670 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 122 HIS J 116 ASN J 129 GLN K 41 ASN L 41 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 81 GLN M 138 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 38475 Z= 0.325 Angle : 0.628 10.176 51976 Z= 0.337 Chirality : 0.047 1.704 5970 Planarity : 0.005 0.077 6704 Dihedral : 9.683 154.148 5378 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.31 % Allowed : 10.65 % Favored : 88.05 % 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: 0.95 (0.11), residues: 4769 helix: 1.45 (0.10), residues: 2512 sheet: -0.26 (0.18), residues: 776 loop : -0.11 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 689 HIS 0.012 0.001 HIS C 528 PHE 0.021 0.002 PHE A 267 TYR 0.019 0.001 TYR I 128 ARG 0.012 0.001 ARG L 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1331 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1278 time to evaluate : 4.394 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: A 181 ARG cc_start: 0.5508 (mtt180) cc_final: 0.4702 (mpt-90) REVERT: A 191 ARG cc_start: 0.6917 (mmt180) cc_final: 0.6645 (mmt180) REVERT: A 327 PHE cc_start: 0.7428 (t80) cc_final: 0.6937 (t80) REVERT: A 343 LYS cc_start: 0.6558 (ttpp) cc_final: 0.6043 (ptmm) REVERT: A 555 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8176 (mmmt) REVERT: A 641 ARG cc_start: 0.5908 (ttp80) cc_final: 0.5629 (ttp80) REVERT: B 370 ASP cc_start: 0.7543 (t0) cc_final: 0.7308 (t0) REVERT: B 400 ASP cc_start: 0.7868 (m-30) cc_final: 0.7647 (m-30) REVERT: C 285 ASP cc_start: 0.8338 (t0) cc_final: 0.7934 (m-30) REVERT: C 370 ASP cc_start: 0.7393 (t0) cc_final: 0.7107 (t0) REVERT: C 589 ASN cc_start: 0.6653 (p0) cc_final: 0.6411 (p0) REVERT: C 740 ASN cc_start: 0.8059 (t0) cc_final: 0.7219 (t0) REVERT: D 286 GLU cc_start: 0.7132 (mp0) cc_final: 0.6898 (mp0) REVERT: D 300 GLN cc_start: 0.7023 (tp40) cc_final: 0.6678 (tp40) REVERT: D 503 GLU cc_start: 0.8013 (tp30) cc_final: 0.7675 (tp30) REVERT: E 250 ILE cc_start: 0.8194 (mm) cc_final: 0.7976 (mt) REVERT: E 361 LEU cc_start: 0.8439 (mp) cc_final: 0.8100 (mp) REVERT: E 403 ASP cc_start: 0.8232 (t70) cc_final: 0.7951 (t70) REVERT: E 454 ASP cc_start: 0.7487 (m-30) cc_final: 0.7069 (m-30) REVERT: E 465 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8013 (mmtm) REVERT: E 556 HIS cc_start: 0.7708 (m90) cc_final: 0.6768 (m90) REVERT: E 627 ASP cc_start: 0.8309 (m-30) cc_final: 0.8054 (m-30) REVERT: E 631 GLU cc_start: 0.8047 (tp30) cc_final: 0.7782 (tp30) REVERT: F 351 ILE cc_start: 0.7311 (mp) cc_final: 0.6948 (mt) REVERT: H 22 ARG cc_start: 0.8828 (tpt90) cc_final: 0.8541 (tpt90) REVERT: H 57 LYS cc_start: 0.8639 (mttt) cc_final: 0.8414 (mtpp) REVERT: H 98 MET cc_start: 0.7691 (mmm) cc_final: 0.7134 (tmm) REVERT: I 25 LYS cc_start: 0.8441 (tttt) cc_final: 0.8176 (ttmm) REVERT: I 175 SER cc_start: 0.8365 (m) cc_final: 0.7241 (t) REVERT: K 149 MET cc_start: 0.7842 (mmm) cc_final: 0.7482 (mmm) REVERT: M 144 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8484 (ttmm) REVERT: N 116 ASN cc_start: 0.7636 (m-40) cc_final: 0.7398 (m110) outliers start: 53 outliers final: 39 residues processed: 1301 average time/residue: 1.1745 time to fit residues: 2374.9230 Evaluate side-chains 1231 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1192 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 GLN Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 440 SER Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 670 GLN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 7 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 433 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 386 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 590 ASN B 642 ASN C 178 GLN ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN C 624 ASN D 390 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** L 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 38475 Z= 0.301 Angle : 0.577 10.324 51976 Z= 0.305 Chirality : 0.046 1.706 5970 Planarity : 0.004 0.059 6704 Dihedral : 9.481 149.371 5378 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.36 % Allowed : 13.80 % Favored : 84.84 % 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: 0.73 (0.12), residues: 4769 helix: 1.28 (0.10), residues: 2528 sheet: -0.43 (0.17), residues: 790 loop : -0.20 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 229 HIS 0.012 0.001 HIS C 528 PHE 0.020 0.001 PHE E 596 TYR 0.011 0.001 TYR J 60 ARG 0.007 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1263 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1208 time to evaluate : 4.351 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 181 ARG cc_start: 0.5378 (mtt180) cc_final: 0.4798 (mpt-90) REVERT: A 327 PHE cc_start: 0.7423 (t80) cc_final: 0.7002 (t80) REVERT: A 343 LYS cc_start: 0.6608 (ttpp) cc_final: 0.6058 (ptmm) REVERT: A 362 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8385 (tttp) REVERT: A 372 ARG cc_start: 0.6386 (tpt170) cc_final: 0.6151 (tpt90) REVERT: A 641 ARG cc_start: 0.5942 (ttp80) cc_final: 0.5665 (ttp80) REVERT: B 370 ASP cc_start: 0.7555 (t0) cc_final: 0.7323 (t0) REVERT: B 400 ASP cc_start: 0.7882 (m-30) cc_final: 0.7671 (m-30) REVERT: C 285 ASP cc_start: 0.8338 (t0) cc_final: 0.7965 (m-30) REVERT: C 740 ASN cc_start: 0.8046 (t0) cc_final: 0.7365 (t0) REVERT: D 300 GLN cc_start: 0.7153 (tp40) cc_final: 0.6788 (tp40) REVERT: D 685 GLU cc_start: 0.7571 (pt0) cc_final: 0.7266 (pt0) REVERT: E 250 ILE cc_start: 0.8207 (mm) cc_final: 0.7953 (mt) REVERT: E 361 LEU cc_start: 0.8481 (mp) cc_final: 0.8122 (mp) REVERT: E 403 ASP cc_start: 0.8269 (t70) cc_final: 0.7988 (t70) REVERT: E 447 ASP cc_start: 0.7538 (p0) cc_final: 0.7274 (p0) REVERT: E 465 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7992 (mmtm) REVERT: E 627 ASP cc_start: 0.8290 (m-30) cc_final: 0.8046 (m-30) REVERT: F 240 MET cc_start: 0.7435 (mmp) cc_final: 0.7141 (mmp) REVERT: F 351 ILE cc_start: 0.7260 (mp) cc_final: 0.6877 (mt) REVERT: F 410 ARG cc_start: 0.6392 (ptp90) cc_final: 0.6109 (ptm-80) REVERT: H 22 ARG cc_start: 0.8874 (tpt90) cc_final: 0.8641 (tpt90) REVERT: H 57 LYS cc_start: 0.8649 (mttt) cc_final: 0.8438 (mtpp) REVERT: H 98 MET cc_start: 0.7726 (mmm) cc_final: 0.7143 (tmm) REVERT: K 182 TYR cc_start: 0.8513 (t80) cc_final: 0.8160 (t80) REVERT: M 144 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8470 (ttmm) outliers start: 55 outliers final: 45 residues processed: 1227 average time/residue: 1.1771 time to fit residues: 2250.8414 Evaluate side-chains 1230 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1185 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 GLN Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 133 THR Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 428 optimal weight: 0.6980 chunk 326 optimal weight: 50.0000 chunk 225 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 435 optimal weight: 7.9990 chunk 461 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 412 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN B 369 HIS B 575 ASN B 583 ASN B 590 ASN B 606 ASN C 178 GLN ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 329 ASN ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 709 GLN D 390 ASN E 305 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 575 ASN H 46 GLN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS J 116 ASN J 159 GLN K 116 ASN ** L 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 38475 Z= 0.395 Angle : 0.602 10.064 51976 Z= 0.318 Chirality : 0.047 1.710 5970 Planarity : 0.004 0.059 6704 Dihedral : 9.484 148.706 5378 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 15.28 % Favored : 82.82 % 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: 0.42 (0.12), residues: 4769 helix: 1.07 (0.10), residues: 2545 sheet: -0.67 (0.18), residues: 708 loop : -0.43 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 649 HIS 0.015 0.002 HIS E 556 PHE 0.019 0.002 PHE F 172 TYR 0.016 0.001 TYR J 60 ARG 0.013 0.001 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1295 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1218 time to evaluate : 4.357 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: A 181 ARG cc_start: 0.5671 (mtt180) cc_final: 0.5102 (mpt-90) REVERT: A 327 PHE cc_start: 0.7430 (t80) cc_final: 0.7001 (t80) REVERT: A 343 LYS cc_start: 0.6688 (ttpp) cc_final: 0.6128 (ptmm) REVERT: A 362 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8420 (tttp) REVERT: A 461 PHE cc_start: 0.8032 (m-80) cc_final: 0.7827 (m-80) REVERT: A 555 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8240 (mmmt) REVERT: A 629 MET cc_start: 0.6996 (mmt) cc_final: 0.6654 (mmt) REVERT: A 641 ARG cc_start: 0.5982 (ttp80) cc_final: 0.5724 (ttp80) REVERT: B 370 ASP cc_start: 0.7651 (t0) cc_final: 0.7365 (t0) REVERT: B 400 ASP cc_start: 0.7976 (m-30) cc_final: 0.7722 (m-30) REVERT: C 285 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: C 408 ARG cc_start: 0.8424 (mtm110) cc_final: 0.8156 (mtm110) REVERT: C 678 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 740 ASN cc_start: 0.8059 (t0) cc_final: 0.7500 (t0) REVERT: D 300 GLN cc_start: 0.7549 (tp40) cc_final: 0.7161 (tp40) REVERT: D 455 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7902 (mtm-85) REVERT: D 685 GLU cc_start: 0.7627 (pt0) cc_final: 0.7286 (pt0) REVERT: D 699 MET cc_start: 0.8040 (mmp) cc_final: 0.7776 (mmm) REVERT: E 178 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 250 ILE cc_start: 0.8263 (mm) cc_final: 0.8057 (mt) REVERT: E 361 LEU cc_start: 0.8557 (mp) cc_final: 0.8184 (mp) REVERT: E 465 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8020 (mmtm) REVERT: E 627 ASP cc_start: 0.8313 (m-30) cc_final: 0.8058 (m-30) REVERT: F 351 ILE cc_start: 0.7221 (mp) cc_final: 0.7012 (mt) REVERT: F 549 LEU cc_start: 0.7771 (mt) cc_final: 0.7350 (tp) REVERT: F 704 MET cc_start: 0.6061 (mmm) cc_final: 0.5781 (mmm) REVERT: H 57 LYS cc_start: 0.8719 (mttt) cc_final: 0.8518 (mtpp) REVERT: J 141 GLU cc_start: 0.7309 (tp30) cc_final: 0.7048 (tp30) REVERT: K 149 MET cc_start: 0.7943 (mmm) cc_final: 0.7682 (mmm) REVERT: L 22 ARG cc_start: 0.8441 (tpt90) cc_final: 0.8179 (tpt-90) REVERT: L 26 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7730 (mp0) REVERT: M 16 SER cc_start: 0.8758 (t) cc_final: 0.8359 (p) REVERT: M 82 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5726 (p90) REVERT: M 144 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8458 (ttmm) REVERT: M 172 ARG cc_start: 0.6938 (tpp80) cc_final: 0.6351 (tpp80) REVERT: N 57 LYS cc_start: 0.6910 (mtpp) cc_final: 0.6654 (mtpt) outliers start: 77 outliers final: 60 residues processed: 1239 average time/residue: 1.1902 time to fit residues: 2306.3073 Evaluate side-chains 1233 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1170 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 461 PHE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 534 ILE Chi-restraints excluded: chain E residue 554 ILE Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 383 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 343 optimal weight: 40.0000 chunk 190 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 235 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN B 583 ASN B 606 ASN D 390 ASN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 HIS N 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 38475 Z= 0.342 Angle : 0.580 10.039 51976 Z= 0.306 Chirality : 0.046 1.705 5970 Planarity : 0.004 0.092 6704 Dihedral : 9.400 148.377 5378 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.97 % Allowed : 16.51 % Favored : 81.52 % 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: 4769 helix: 1.02 (0.10), residues: 2559 sheet: -0.83 (0.18), residues: 690 loop : -0.49 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 649 HIS 0.017 0.002 HIS E 556 PHE 0.024 0.002 PHE B 327 TYR 0.032 0.001 TYR L 128 ARG 0.009 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1270 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1190 time to evaluate : 4.394 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: A 181 ARG cc_start: 0.5757 (mtt180) cc_final: 0.5110 (mpt-90) REVERT: A 327 PHE cc_start: 0.7426 (t80) cc_final: 0.7039 (t80) REVERT: A 343 LYS cc_start: 0.6743 (ttpp) cc_final: 0.6296 (ptmm) REVERT: A 372 ARG cc_start: 0.6594 (tpt170) cc_final: 0.6238 (tpt90) REVERT: A 373 TYR cc_start: 0.6109 (m-80) cc_final: 0.5830 (m-80) REVERT: A 555 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8251 (mmmt) REVERT: A 641 ARG cc_start: 0.5899 (ttp80) cc_final: 0.5668 (ttp80) REVERT: B 370 ASP cc_start: 0.7784 (t0) cc_final: 0.7457 (t0) REVERT: B 400 ASP cc_start: 0.8027 (m-30) cc_final: 0.7755 (m-30) REVERT: C 285 ASP cc_start: 0.8404 (t0) cc_final: 0.8066 (m-30) REVERT: C 678 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8847 (p) REVERT: C 740 ASN cc_start: 0.8105 (t0) cc_final: 0.7526 (t0) REVERT: D 300 GLN cc_start: 0.7726 (tp40) cc_final: 0.7390 (tp40) REVERT: D 455 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7872 (mtm-85) REVERT: E 178 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 225 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 235 ASP cc_start: 0.6152 (t70) cc_final: 0.5841 (t0) REVERT: E 250 ILE cc_start: 0.8298 (mm) cc_final: 0.8069 (mt) REVERT: E 264 GLU cc_start: 0.7998 (mp0) cc_final: 0.7609 (mp0) REVERT: E 361 LEU cc_start: 0.8573 (mp) cc_final: 0.8204 (mp) REVERT: E 447 ASP cc_start: 0.7627 (p0) cc_final: 0.7383 (p0) REVERT: E 627 ASP cc_start: 0.8266 (m-30) cc_final: 0.8058 (m-30) REVERT: F 351 ILE cc_start: 0.7197 (mp) cc_final: 0.6994 (mt) REVERT: F 459 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7807 (mm) REVERT: F 549 LEU cc_start: 0.7789 (mt) cc_final: 0.7342 (tt) REVERT: H 57 LYS cc_start: 0.8743 (mttt) cc_final: 0.8524 (mtpp) REVERT: J 141 GLU cc_start: 0.7333 (tp30) cc_final: 0.7092 (tp30) REVERT: K 149 MET cc_start: 0.8020 (mmm) cc_final: 0.7672 (mmm) REVERT: K 162 GLU cc_start: 0.7706 (mp0) cc_final: 0.7468 (mp0) REVERT: L 22 ARG cc_start: 0.8468 (tpt90) cc_final: 0.8217 (tpt-90) REVERT: L 26 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7691 (mp0) REVERT: L 151 GLU cc_start: 0.7258 (mp0) cc_final: 0.6898 (mp0) REVERT: M 16 SER cc_start: 0.8777 (t) cc_final: 0.8416 (p) REVERT: M 82 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.5678 (p90) REVERT: M 144 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8427 (ttmm) REVERT: M 178 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7474 (mp0) REVERT: N 57 LYS cc_start: 0.6894 (mtpp) cc_final: 0.6669 (mtpt) outliers start: 80 outliers final: 66 residues processed: 1215 average time/residue: 1.1306 time to fit residues: 2141.4630 Evaluate side-chains 1227 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1158 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 642 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 534 ILE Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 155 optimal weight: 2.9990 chunk 415 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 461 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN C 422 ASN C 545 GLN C 652 HIS D 545 GLN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS J 116 ASN M 138 HIS N 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38475 Z= 0.215 Angle : 0.540 10.055 51976 Z= 0.280 Chirality : 0.045 1.701 5970 Planarity : 0.004 0.064 6704 Dihedral : 9.164 147.906 5378 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.65 % Allowed : 17.52 % Favored : 80.83 % 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: 0.49 (0.12), residues: 4769 helix: 1.15 (0.10), residues: 2569 sheet: -0.79 (0.18), residues: 689 loop : -0.39 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 649 HIS 0.010 0.001 HIS F 393 PHE 0.025 0.001 PHE B 327 TYR 0.011 0.001 TYR M 77 ARG 0.011 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1237 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1170 time to evaluate : 4.408 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: A 181 ARG cc_start: 0.5782 (mtt180) cc_final: 0.5138 (mpt-90) REVERT: A 286 GLU cc_start: 0.6086 (pm20) cc_final: 0.5785 (pm20) REVERT: A 327 PHE cc_start: 0.7429 (t80) cc_final: 0.6898 (t80) REVERT: A 362 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8413 (tttp) REVERT: A 372 ARG cc_start: 0.6520 (tpt170) cc_final: 0.6212 (tpt90) REVERT: A 641 ARG cc_start: 0.5858 (ttp80) cc_final: 0.5645 (ttp80) REVERT: B 370 ASP cc_start: 0.7806 (t0) cc_final: 0.7418 (t0) REVERT: B 400 ASP cc_start: 0.7957 (m-30) cc_final: 0.7663 (m-30) REVERT: B 634 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8072 (ttpp) REVERT: C 408 ARG cc_start: 0.8620 (mtp85) cc_final: 0.8299 (mtp85) REVERT: C 678 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8836 (p) REVERT: C 740 ASN cc_start: 0.8139 (t0) cc_final: 0.7567 (t0) REVERT: D 300 GLN cc_start: 0.7738 (tp40) cc_final: 0.7431 (tp40) REVERT: D 410 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.8078 (tmm-80) REVERT: D 455 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7846 (mtm-85) REVERT: D 685 GLU cc_start: 0.7603 (pt0) cc_final: 0.7173 (pt0) REVERT: E 225 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7447 (mt-10) REVERT: E 250 ILE cc_start: 0.8292 (mm) cc_final: 0.8063 (mt) REVERT: E 264 GLU cc_start: 0.7966 (mp0) cc_final: 0.7528 (mp0) REVERT: E 361 LEU cc_start: 0.8531 (mp) cc_final: 0.8175 (mp) REVERT: E 403 ASP cc_start: 0.8014 (t70) cc_final: 0.7122 (t70) REVERT: E 447 ASP cc_start: 0.7570 (p0) cc_final: 0.7301 (p0) REVERT: E 598 ASN cc_start: 0.7449 (m110) cc_final: 0.7156 (m-40) REVERT: E 627 ASP cc_start: 0.8240 (m-30) cc_final: 0.8018 (m-30) REVERT: F 240 MET cc_start: 0.7446 (mmp) cc_final: 0.7168 (mmp) REVERT: F 351 ILE cc_start: 0.7170 (mp) cc_final: 0.6963 (mt) REVERT: H 173 PHE cc_start: 0.8113 (m-80) cc_final: 0.7908 (m-80) REVERT: J 141 GLU cc_start: 0.7322 (tp30) cc_final: 0.7085 (tp30) REVERT: K 149 MET cc_start: 0.7979 (mmm) cc_final: 0.7639 (mmm) REVERT: L 22 ARG cc_start: 0.8408 (tpt90) cc_final: 0.8185 (tpt-90) REVERT: L 26 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7569 (mp0) REVERT: M 16 SER cc_start: 0.8767 (t) cc_final: 0.8426 (p) REVERT: M 82 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5597 (p90) REVERT: M 144 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8356 (ttmm) outliers start: 67 outliers final: 57 residues processed: 1187 average time/residue: 1.1514 time to fit residues: 2129.0769 Evaluate side-chains 1193 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1134 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 485 HIS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 642 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 138 HIS Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 444 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 459 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 233 GLN B 583 ASN B 642 ASN C 422 ASN C 652 HIS D 390 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 38475 Z= 0.376 Angle : 0.587 10.011 51976 Z= 0.309 Chirality : 0.046 1.708 5970 Planarity : 0.004 0.111 6704 Dihedral : 9.322 153.864 5378 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.05 % Allowed : 17.77 % Favored : 80.19 % 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: 4769 helix: 1.02 (0.10), residues: 2575 sheet: -0.87 (0.19), residues: 678 loop : -0.49 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 649 HIS 0.010 0.001 HIS L 138 PHE 0.026 0.002 PHE B 327 TYR 0.018 0.001 TYR J 60 ARG 0.015 0.001 ARG D 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1248 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1165 time to evaluate : 4.328 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: A 181 ARG cc_start: 0.5871 (mtt180) cc_final: 0.5150 (mpt-90) REVERT: A 327 PHE cc_start: 0.7489 (t80) cc_final: 0.7092 (t80) REVERT: A 343 LYS cc_start: 0.6813 (ttpp) cc_final: 0.6087 (ptmm) REVERT: A 362 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8452 (tttp) REVERT: A 372 ARG cc_start: 0.6634 (tpt170) cc_final: 0.6313 (tpt90) REVERT: A 425 ASP cc_start: 0.6807 (m-30) cc_final: 0.6477 (m-30) REVERT: A 492 LEU cc_start: 0.8146 (tp) cc_final: 0.7874 (tt) REVERT: A 629 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6484 (ttm) REVERT: A 641 ARG cc_start: 0.5931 (ttp80) cc_final: 0.5722 (ttp80) REVERT: B 370 ASP cc_start: 0.7824 (t0) cc_final: 0.7431 (t0) REVERT: B 400 ASP cc_start: 0.8013 (m-30) cc_final: 0.7745 (m-30) REVERT: B 427 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 634 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8310 (ttpp) REVERT: B 642 ASN cc_start: 0.7893 (m110) cc_final: 0.7654 (m110) REVERT: C 285 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: C 408 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8310 (mtp85) REVERT: C 678 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8863 (p) REVERT: C 740 ASN cc_start: 0.8137 (t0) cc_final: 0.7536 (t0) REVERT: D 455 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7903 (mtm-85) REVERT: D 685 GLU cc_start: 0.7662 (pt0) cc_final: 0.7297 (pt0) REVERT: E 178 GLN cc_start: 0.8238 (tm-30) cc_final: 0.8010 (tm-30) REVERT: E 225 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7492 (mt-10) REVERT: E 250 ILE cc_start: 0.8345 (mm) cc_final: 0.8107 (mt) REVERT: E 264 GLU cc_start: 0.8050 (mp0) cc_final: 0.7630 (mp0) REVERT: E 361 LEU cc_start: 0.8626 (mp) cc_final: 0.8277 (mp) REVERT: E 403 ASP cc_start: 0.8094 (t0) cc_final: 0.7216 (t70) REVERT: E 447 ASP cc_start: 0.7591 (p0) cc_final: 0.7380 (p0) REVERT: E 465 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8122 (mmtm) REVERT: F 283 PHE cc_start: 0.8468 (t80) cc_final: 0.8169 (t80) REVERT: F 351 ILE cc_start: 0.7122 (mp) cc_final: 0.6921 (mt) REVERT: J 141 GLU cc_start: 0.7389 (tp30) cc_final: 0.7134 (tp30) REVERT: K 149 MET cc_start: 0.8047 (mmm) cc_final: 0.7708 (mmm) REVERT: K 162 GLU cc_start: 0.7687 (mp0) cc_final: 0.7440 (mp0) REVERT: L 22 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8261 (tpt-90) REVERT: L 26 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7597 (mp0) REVERT: M 16 SER cc_start: 0.8791 (t) cc_final: 0.8502 (p) REVERT: M 82 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.5594 (p90) REVERT: M 120 MET cc_start: 0.6240 (tpp) cc_final: 0.5958 (tpp) REVERT: M 144 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8361 (ttmm) REVERT: N 77 TYR cc_start: 0.8583 (t80) cc_final: 0.8372 (t80) outliers start: 83 outliers final: 65 residues processed: 1193 average time/residue: 1.1236 time to fit residues: 2092.5895 Evaluate side-chains 1212 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1143 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 534 ILE Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 284 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 292 optimal weight: 20.0000 chunk 313 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 361 optimal weight: 4.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 ASN B 583 ASN C 422 ASN D 390 ASN D 558 HIS E 329 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38475 Z= 0.270 Angle : 0.558 9.965 51976 Z= 0.292 Chirality : 0.046 1.706 5970 Planarity : 0.004 0.062 6704 Dihedral : 9.169 151.124 5378 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.63 % Allowed : 18.38 % Favored : 79.99 % 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: 0.39 (0.12), residues: 4769 helix: 1.10 (0.10), residues: 2572 sheet: -0.89 (0.19), residues: 678 loop : -0.47 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.009 0.001 HIS L 138 PHE 0.018 0.001 PHE K 17 TYR 0.014 0.001 TYR J 60 ARG 0.012 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1233 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1167 time to evaluate : 4.349 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: A 181 ARG cc_start: 0.5873 (mtt180) cc_final: 0.5315 (mpt-90) REVERT: A 327 PHE cc_start: 0.7453 (t80) cc_final: 0.7090 (t80) REVERT: A 343 LYS cc_start: 0.6702 (ttpp) cc_final: 0.6333 (ptmm) REVERT: A 362 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8439 (tttp) REVERT: A 629 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6617 (ttm) REVERT: A 641 ARG cc_start: 0.5952 (ttp80) cc_final: 0.5742 (ttp80) REVERT: B 370 ASP cc_start: 0.7851 (t0) cc_final: 0.7445 (t0) REVERT: B 400 ASP cc_start: 0.7971 (m-30) cc_final: 0.7714 (m-30) REVERT: B 427 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 634 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8300 (ttpp) REVERT: B 642 ASN cc_start: 0.7770 (m110) cc_final: 0.7492 (m110) REVERT: C 408 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8337 (mtp85) REVERT: C 678 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 740 ASN cc_start: 0.8136 (t0) cc_final: 0.7585 (t0) REVERT: D 455 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7870 (mtm-85) REVERT: D 685 GLU cc_start: 0.7648 (pt0) cc_final: 0.7277 (pt0) REVERT: E 225 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7405 (mt-10) REVERT: E 264 GLU cc_start: 0.7979 (mp0) cc_final: 0.7530 (mp0) REVERT: E 361 LEU cc_start: 0.8599 (mp) cc_final: 0.8235 (mp) REVERT: E 446 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7278 (mtm-85) REVERT: E 447 ASP cc_start: 0.7566 (p0) cc_final: 0.7334 (p0) REVERT: F 283 PHE cc_start: 0.8476 (t80) cc_final: 0.8190 (t80) REVERT: J 141 GLU cc_start: 0.7385 (tp30) cc_final: 0.7134 (tp30) REVERT: K 149 MET cc_start: 0.8068 (mmm) cc_final: 0.7726 (mmm) REVERT: K 162 GLU cc_start: 0.7699 (mp0) cc_final: 0.7457 (mp0) REVERT: L 26 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7602 (mp0) REVERT: M 16 SER cc_start: 0.8792 (t) cc_final: 0.8515 (p) REVERT: M 82 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5553 (p90) REVERT: M 120 MET cc_start: 0.6092 (tpp) cc_final: 0.5819 (tpp) REVERT: M 144 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8354 (ttmm) REVERT: M 178 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7516 (mp0) outliers start: 66 outliers final: 60 residues processed: 1190 average time/residue: 1.0883 time to fit residues: 2005.1902 Evaluate side-chains 1209 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1146 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 418 optimal weight: 0.7980 chunk 440 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 chunk 428 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 336 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 387 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 426 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN C 422 ASN C 545 GLN C 652 HIS D 390 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN N 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 38475 Z= 0.226 Angle : 0.549 11.090 51976 Z= 0.285 Chirality : 0.041 0.928 5970 Planarity : 0.004 0.071 6704 Dihedral : 9.072 151.468 5378 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.53 % Allowed : 18.85 % Favored : 79.62 % 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: 0.49 (0.12), residues: 4769 helix: 1.19 (0.10), residues: 2573 sheet: -0.90 (0.19), residues: 678 loop : -0.42 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.008 0.001 HIS F 393 PHE 0.034 0.001 PHE H 173 TYR 0.018 0.001 TYR N 77 ARG 0.012 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1231 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1169 time to evaluate : 4.566 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: A 286 GLU cc_start: 0.6109 (pm20) cc_final: 0.5828 (pm20) REVERT: A 327 PHE cc_start: 0.7434 (t80) cc_final: 0.7037 (t80) REVERT: A 343 LYS cc_start: 0.6686 (ttpp) cc_final: 0.6037 (ptmm) REVERT: A 362 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8424 (tttp) REVERT: A 372 ARG cc_start: 0.6617 (tpt170) cc_final: 0.6286 (tpt90) REVERT: A 492 LEU cc_start: 0.8144 (tp) cc_final: 0.7906 (tt) REVERT: A 629 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6674 (ttm) REVERT: A 641 ARG cc_start: 0.5919 (ttp80) cc_final: 0.5717 (ttp80) REVERT: B 370 ASP cc_start: 0.7845 (t0) cc_final: 0.7397 (t0) REVERT: B 400 ASP cc_start: 0.7913 (m-30) cc_final: 0.7658 (m-30) REVERT: B 427 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 634 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8157 (ttpp) REVERT: B 642 ASN cc_start: 0.7759 (m110) cc_final: 0.7509 (m110) REVERT: C 678 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8848 (p) REVERT: C 740 ASN cc_start: 0.8134 (t0) cc_final: 0.7572 (t0) REVERT: D 455 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7853 (mtm-85) REVERT: D 685 GLU cc_start: 0.7675 (pt0) cc_final: 0.7289 (pt0) REVERT: E 225 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7362 (mt-10) REVERT: E 264 GLU cc_start: 0.7986 (mp0) cc_final: 0.7538 (mp0) REVERT: E 361 LEU cc_start: 0.8605 (mp) cc_final: 0.8245 (mp) REVERT: E 446 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7292 (mtm-85) REVERT: E 447 ASP cc_start: 0.7578 (p0) cc_final: 0.7328 (p0) REVERT: F 176 LEU cc_start: 0.8512 (mp) cc_final: 0.8261 (mt) REVERT: F 283 PHE cc_start: 0.8501 (t80) cc_final: 0.8200 (t80) REVERT: F 644 LEU cc_start: 0.4179 (tp) cc_final: 0.3762 (tp) REVERT: J 141 GLU cc_start: 0.7365 (tp30) cc_final: 0.7126 (tp30) REVERT: K 149 MET cc_start: 0.8071 (mmm) cc_final: 0.7727 (mmm) REVERT: K 162 GLU cc_start: 0.7677 (mp0) cc_final: 0.7451 (mp0) REVERT: M 16 SER cc_start: 0.8783 (t) cc_final: 0.8491 (p) REVERT: M 82 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.5569 (p90) REVERT: M 120 MET cc_start: 0.6028 (tpp) cc_final: 0.5739 (tpp) REVERT: M 144 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8327 (ttmm) REVERT: M 178 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7501 (mp0) outliers start: 62 outliers final: 57 residues processed: 1190 average time/residue: 1.0792 time to fit residues: 1988.3705 Evaluate side-chains 1204 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1144 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 281 optimal weight: 40.0000 chunk 453 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 314 optimal weight: 30.0000 chunk 475 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 292 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN B 583 ASN C 422 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 38475 Z= 0.329 Angle : 0.586 9.232 51976 Z= 0.306 Chirality : 0.043 1.201 5970 Planarity : 0.004 0.064 6704 Dihedral : 9.201 163.767 5378 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.58 % Allowed : 19.22 % Favored : 79.20 % 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: 0.34 (0.12), residues: 4769 helix: 1.09 (0.10), residues: 2570 sheet: -0.97 (0.19), residues: 673 loop : -0.52 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.011 0.001 HIS A 570 PHE 0.017 0.002 PHE E 596 TYR 0.019 0.001 TYR J 60 ARG 0.019 0.001 ARG A 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1217 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1153 time to evaluate : 4.439 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: A 286 GLU cc_start: 0.6183 (pm20) cc_final: 0.5902 (pm20) REVERT: A 327 PHE cc_start: 0.7446 (t80) cc_final: 0.7079 (t80) REVERT: A 343 LYS cc_start: 0.6725 (ttpp) cc_final: 0.6327 (ptmm) REVERT: A 362 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8456 (tttp) REVERT: A 372 ARG cc_start: 0.6657 (tpt170) cc_final: 0.6333 (tpt90) REVERT: A 492 LEU cc_start: 0.8213 (tp) cc_final: 0.7980 (tt) REVERT: A 629 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6703 (ttm) REVERT: A 641 ARG cc_start: 0.5966 (ttp80) cc_final: 0.5757 (ttp80) REVERT: B 370 ASP cc_start: 0.7854 (t0) cc_final: 0.7277 (t0) REVERT: B 400 ASP cc_start: 0.7988 (m-30) cc_final: 0.7737 (m-30) REVERT: B 642 ASN cc_start: 0.7752 (m110) cc_final: 0.7497 (m110) REVERT: C 408 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8315 (mtp85) REVERT: C 678 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 740 ASN cc_start: 0.8126 (t0) cc_final: 0.7560 (t0) REVERT: D 455 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7898 (mtm-85) REVERT: E 225 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7516 (mt-10) REVERT: E 264 GLU cc_start: 0.8022 (mp0) cc_final: 0.7578 (mp0) REVERT: E 361 LEU cc_start: 0.8638 (mp) cc_final: 0.8278 (mp) REVERT: E 446 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7299 (mtm-85) REVERT: E 447 ASP cc_start: 0.7595 (p0) cc_final: 0.7359 (p0) REVERT: F 283 PHE cc_start: 0.8525 (t80) cc_final: 0.8214 (t80) REVERT: H 146 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8152 (tttt) REVERT: I 172 ARG cc_start: 0.7588 (ttm110) cc_final: 0.7106 (ttm110) REVERT: J 141 GLU cc_start: 0.7427 (tp30) cc_final: 0.7175 (tp30) REVERT: K 149 MET cc_start: 0.8115 (mmm) cc_final: 0.7766 (mmm) REVERT: K 162 GLU cc_start: 0.7697 (mp0) cc_final: 0.7490 (mp0) REVERT: L 172 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7314 (tpt170) REVERT: M 16 SER cc_start: 0.8792 (t) cc_final: 0.8539 (p) REVERT: M 82 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.5607 (p90) REVERT: M 120 MET cc_start: 0.6175 (tpp) cc_final: 0.5892 (tpp) REVERT: M 144 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8368 (ttmm) REVERT: M 178 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7490 (mp0) outliers start: 64 outliers final: 55 residues processed: 1174 average time/residue: 1.1169 time to fit residues: 2040.0334 Evaluate side-chains 1203 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1145 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 743 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 534 ILE Chi-restraints excluded: chain E residue 642 ASN Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 279 ASN Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 113 CYS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 300 optimal weight: 20.0000 chunk 403 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 348 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 379 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 389 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN C 422 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS K 191 HIS ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN N 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.177295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130835 restraints weight = 142425.261| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.49 r_work: 0.3055 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38475 Z= 0.198 Angle : 0.550 9.827 51976 Z= 0.284 Chirality : 0.042 1.276 5970 Planarity : 0.004 0.063 6704 Dihedral : 9.011 164.636 5378 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.43 % Allowed : 19.59 % Favored : 78.98 % 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: 0.53 (0.12), residues: 4769 helix: 1.24 (0.10), residues: 2569 sheet: -0.91 (0.19), residues: 684 loop : -0.41 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.008 0.001 HIS C 528 PHE 0.030 0.001 PHE H 173 TYR 0.016 0.001 TYR N 77 ARG 0.012 0.000 ARG H 15 =============================================================================== Job complete usr+sys time: 29142.48 seconds wall clock time: 492 minutes 20.33 seconds (29540.33 seconds total)