Starting phenix.real_space_refine on Tue Feb 20 01:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0v_25582/02_2024/7t0v_25582_updated.pdb" } resolution = 3.67 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= 0.048 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 9 5.21 5 S 124 5.16 5 C 16462 2.51 5 N 4698 2.21 5 O 5073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26397 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4365 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4387 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4121 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4251 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 526} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 161 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 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, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 14.47, per 1000 atoms: 0.55 Number of scatterers: 26397 At special positions: 0 Unit cell: (114.895, 150.088, 152.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 31 15.00 Mg 9 11.99 O 5073 8.00 N 4698 7.00 C 16462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.75 Conformation dependent library (CDL) restraints added in 5.2 seconds 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 12 sheets defined 50.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.74 Creating SS restraints... Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.952A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 277 through 293 removed outlier: 4.265A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.859A pdb=" N VAL A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 357 through 362 removed outlier: 4.517A pdb=" N ARG A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.760A pdb=" N ARG A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.682A pdb=" N LEU A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.833A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 524 through 530 removed outlier: 4.025A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 578 through 590 removed outlier: 3.781A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 615 through 631 removed outlier: 3.789A pdb=" N ALA A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 671 through 685 removed outlier: 3.674A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 removed outlier: 3.749A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 733 through 757 Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.838A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 removed outlier: 3.561A pdb=" N TYR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.249A pdb=" N LYS B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.633A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.998A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.035A pdb=" N ARG B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.514A pdb=" N ARG B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.642A pdb=" N LYS B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.512A pdb=" N SER B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'B' and resid 473 through 482 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.824A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 578 through 592 removed outlier: 3.741A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 671 through 685 removed outlier: 3.870A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 724 Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 733 through 760 Processing helix chain 'B' and resid 777 through 786 removed outlier: 3.655A pdb=" N LYS B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 209 through 217 removed outlier: 4.077A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 269 through 272 Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.682A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 318 through 336 removed outlier: 4.177A pdb=" N ARG C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 357 through 362 removed outlier: 4.382A pdb=" N ARG C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.514A pdb=" N GLN C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 435 removed outlier: 4.150A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.514A pdb=" N GLU C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 482 removed outlier: 3.951A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 507 through 516 Processing helix chain 'C' and resid 518 through 522 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 548 through 558 Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.519A pdb=" N VAL C 583 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 605 No H-bonds generated for 'chain 'C' and resid 603 through 605' Processing helix chain 'C' and resid 616 through 629 removed outlier: 3.903A pdb=" N VAL C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 622 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.597A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 726 through 728 No H-bonds generated for 'chain 'C' and resid 726 through 728' Processing helix chain 'C' and resid 733 through 761 Processing helix chain 'C' and resid 777 through 784 removed outlier: 3.550A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 798 Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 208 through 217 removed outlier: 4.138A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 277 through 293 removed outlier: 4.623A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 318 through 336 removed outlier: 4.349A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 357 through 362 removed outlier: 4.005A pdb=" N ARG D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.556A pdb=" N GLN D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 422 Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.754A pdb=" N LEU D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 473 through 482 removed outlier: 3.553A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 524 through 529 Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.519A pdb=" N ASN D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 603 through 605 No H-bonds generated for 'chain 'D' and resid 603 through 605' Processing helix chain 'D' and resid 617 through 629 removed outlier: 3.853A pdb=" N VAL D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 671 through 683 removed outlier: 3.689A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 733 through 753 Processing helix chain 'D' and resid 777 through 786 removed outlier: 3.975A pdb=" N ASN D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.972A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 277 through 293 removed outlier: 4.425A pdb=" N GLU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 317 through 336 removed outlier: 3.988A pdb=" N VAL E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 357 through 362 removed outlier: 4.411A pdb=" N ARG E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 386 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 437 removed outlier: 4.416A pdb=" N ALA E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.827A pdb=" N HIS E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 482 Processing helix chain 'E' and resid 507 through 516 Processing helix chain 'E' and resid 519 through 522 No H-bonds generated for 'chain 'E' and resid 519 through 522' Processing helix chain 'E' and resid 524 through 530 removed outlier: 4.082A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 558 Processing helix chain 'E' and resid 569 through 571 No H-bonds generated for 'chain 'E' and resid 569 through 571' Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.825A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 605 No H-bonds generated for 'chain 'E' and resid 603 through 605' Processing helix chain 'E' and resid 619 through 630 removed outlier: 3.629A pdb=" N THR E 624 " --> pdb=" O ARG E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 685 removed outlier: 3.516A pdb=" N THR E 685 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 724 removed outlier: 3.551A pdb=" N LYS E 721 " --> pdb=" O ALA E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 728 No H-bonds generated for 'chain 'E' and resid 726 through 728' Processing helix chain 'E' and resid 733 through 754 Processing helix chain 'E' and resid 777 through 785 removed outlier: 3.901A pdb=" N ASN E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 208 through 217 removed outlier: 3.880A pdb=" N LYS F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 270 through 272 No H-bonds generated for 'chain 'F' and resid 270 through 272' Processing helix chain 'F' and resid 277 through 293 removed outlier: 4.352A pdb=" N GLU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 317 through 335 removed outlier: 3.998A pdb=" N VAL F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 331 " --> pdb=" O MET F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 357 through 362 removed outlier: 4.375A pdb=" N ARG F 362 " --> pdb=" O ALA F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.678A pdb=" N GLN F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 386 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 401 No H-bonds generated for 'chain 'F' and resid 398 through 401' Processing helix chain 'F' and resid 408 through 422 Processing helix chain 'F' and resid 424 through 437 removed outlier: 3.617A pdb=" N LEU F 430 " --> pdb=" O ASN F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.824A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 482 Processing helix chain 'F' and resid 486 through 490 removed outlier: 3.582A pdb=" N GLU F 490 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 516 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.774A pdb=" N THR F 528 " --> pdb=" O PRO F 524 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 558 Processing helix chain 'F' and resid 578 through 592 removed outlier: 3.681A pdb=" N VAL F 583 " --> pdb=" O SER F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 605 No H-bonds generated for 'chain 'F' and resid 603 through 605' Processing helix chain 'F' and resid 615 through 630 removed outlier: 5.068A pdb=" N ARG F 620 " --> pdb=" O ASP F 616 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 684 removed outlier: 3.626A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 724 removed outlier: 3.734A pdb=" N LYS F 721 " --> pdb=" O ALA F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 728 No H-bonds generated for 'chain 'F' and resid 726 through 728' Processing helix chain 'F' and resid 733 through 757 Processing helix chain 'F' and resid 777 through 785 removed outlier: 3.565A pdb=" N LYS F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.294A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 662 through 665 removed outlier: 3.567A pdb=" N ALA A 536 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A 562 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE A 599 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 564 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP A 601 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 566 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 368 removed outlier: 7.874A pdb=" N VAL B 239 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 345 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU B 241 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 347 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 267 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 662 through 665 removed outlier: 3.894A pdb=" N ALA B 536 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 562 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE B 599 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 564 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP B 601 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 566 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 368 removed outlier: 7.942A pdb=" N VAL C 239 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 345 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 241 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 347 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 263 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE C 300 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 265 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP C 302 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 267 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 662 through 665 removed outlier: 8.274A pdb=" N ILE C 538 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL C 640 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 540 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLY C 642 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 368 removed outlier: 7.812A pdb=" N VAL D 239 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 345 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU D 241 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA D 347 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA D 263 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE D 300 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 265 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP D 302 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL D 267 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 662 through 665 removed outlier: 8.382A pdb=" N ILE D 538 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 640 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU D 540 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY D 642 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 369 removed outlier: 8.146A pdb=" N VAL E 239 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 345 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 241 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA E 347 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY E 243 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR E 349 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 662 through 665 removed outlier: 4.041A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE E 538 " --> pdb=" O ILE E 638 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 640 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU E 540 " --> pdb=" O VAL E 640 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY E 642 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS E 596 " --> pdb=" O TYR E 639 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE E 641 " --> pdb=" O CYS E 596 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU E 598 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA E 643 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE E 600 " --> pdb=" O ALA E 643 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 366 through 368 removed outlier: 6.597A pdb=" N LEU F 240 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 348 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE F 265 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE F 300 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 267 " --> pdb=" O PHE F 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 663 through 665 removed outlier: 5.729A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE F 538 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY F 642 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP F 601 " --> pdb=" O ILE F 564 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 566 " --> pdb=" O ASP F 601 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2889 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: 9.19 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8888 1.34 - 1.46: 4625 1.46 - 1.58: 13055 1.58 - 1.69: 51 1.69 - 1.81: 206 Bond restraints: 26825 Sorted by residual: bond pdb=" O5' ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.78e+00 bond pdb=" O5' ATP B 901 " pdb=" PA ATP B 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.32e+00 bond pdb=" O5' ATP D 902 " pdb=" PA ATP D 902 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.97e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.96e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.87e+00 ... (remaining 26820 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.48: 1000 106.48 - 113.90: 15702 113.90 - 121.32: 12967 121.32 - 128.74: 6540 128.74 - 136.15: 152 Bond angle restraints: 36361 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 118.58 18.25 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 123.01 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 121.16 15.67 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 121.21 15.62 1.00e+00 1.00e+00 2.44e+02 ... (remaining 36356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 16207 25.86 - 51.72: 389 51.72 - 77.58: 83 77.58 - 103.44: 3 103.44 - 129.29: 3 Dihedral angle restraints: 16685 sinusoidal: 6946 harmonic: 9739 Sorted by residual: dihedral pdb=" C5' ADP F 901 " pdb=" O5' ADP F 901 " pdb=" PA ADP F 901 " pdb=" O2A ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 170.71 129.29 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 63.78 -123.78 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 61.71 -121.72 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 16682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2498 0.032 - 0.065: 1137 0.065 - 0.097: 354 0.097 - 0.129: 152 0.129 - 0.162: 24 Chirality restraints: 4165 Sorted by residual: chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE E 495 " pdb=" N ILE E 495 " pdb=" C ILE E 495 " pdb=" CB ILE E 495 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 4162 not shown) Planarity restraints: 4679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 568 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO F 569 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 569 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 569 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO F 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.020 5.00e-02 4.00e+02 ... (remaining 4676 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 204 2.47 - 3.07: 18320 3.07 - 3.68: 39803 3.68 - 4.29: 60645 4.29 - 4.90: 99580 Nonbonded interactions: 218552 Sorted by model distance: nonbonded pdb=" O1B ATP A 902 " pdb="MG MG A 904 " model vdw 1.857 2.170 nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.890 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.892 2.170 nonbonded pdb=" O1B ATP C 901 " pdb="MG MG C 903 " model vdw 1.898 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.907 2.170 ... (remaining 218547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 193 through 460 or (resid 461 through 463 and (name N or n \ ame CA or name C or name O or name CB )) or resid 464 through 487 or resid 493 t \ hrough 573 or (resid 574 through 576 and (name N or name CA or name C or name O \ or name CB )) or resid 577 or (resid 578 and (name N or name CA or name C or nam \ e O or name CB )) or resid 579 through 631 or resid 637 through 754 or (resid 75 \ 5 through 757 and (name N or name CA or name C or name O or name CB )) or resid \ 773 through 790)) selection = (chain 'B' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'C' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'D' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'E' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 573 or (resid 574 through \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 th \ rough 790)) selection = (chain 'F' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 631 or resid 637 through 754 or (resid 755 through 75 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 773 through \ 790)) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.300 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 71.270 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 0.053 26825 Z= 0.271 Angle : 0.726 18.497 36361 Z= 0.474 Chirality : 0.043 0.162 4165 Planarity : 0.004 0.053 4679 Dihedral : 11.583 129.295 10373 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 1.71 % Allowed : 3.02 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.13 (0.15), residues: 3343 helix: -0.33 (0.12), residues: 1786 sheet: 0.70 (0.26), residues: 402 loop : 0.37 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 500 HIS 0.003 0.001 HIS C 254 PHE 0.017 0.002 PHE B 600 TYR 0.017 0.001 TYR B 752 ARG 0.007 0.001 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 814 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8414 (t) cc_final: 0.8181 (p) REVERT: A 508 ASP cc_start: 0.8354 (t70) cc_final: 0.7946 (t0) REVERT: A 795 GLU cc_start: 0.8101 (mp0) cc_final: 0.7689 (mp0) REVERT: A 798 MET cc_start: 0.4504 (ptt) cc_final: 0.3980 (tpp) REVERT: A 799 HIS cc_start: 0.5790 (m170) cc_final: 0.4712 (t70) REVERT: B 294 LEU cc_start: 0.9236 (tp) cc_final: 0.8890 (tp) REVERT: B 472 THR cc_start: 0.7875 (p) cc_final: 0.7660 (m) REVERT: B 530 VAL cc_start: 0.8971 (m) cc_final: 0.8753 (t) REVERT: B 578 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7891 (tp30) REVERT: C 201 ILE cc_start: 0.9145 (tp) cc_final: 0.8943 (tp) REVERT: C 538 ILE cc_start: 0.8748 (mm) cc_final: 0.8399 (tt) REVERT: C 754 GLN cc_start: 0.8039 (mt0) cc_final: 0.7798 (mm110) REVERT: D 321 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7523 (mtm-85) REVERT: D 431 LEU cc_start: 0.8904 (mt) cc_final: 0.8590 (tt) REVERT: D 472 THR cc_start: 0.7915 (m) cc_final: 0.7354 (p) REVERT: D 511 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7762 (ttmm) REVERT: D 584 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7382 (mtm110) REVERT: D 739 LEU cc_start: 0.8857 (tp) cc_final: 0.8652 (tt) REVERT: E 350 ASN cc_start: 0.7588 (p0) cc_final: 0.7348 (p0) REVERT: F 368 ASP cc_start: 0.6158 (t0) cc_final: 0.5779 (p0) REVERT: F 402 MET cc_start: 0.7645 (ptp) cc_final: 0.6792 (mmm) REVERT: F 508 ASP cc_start: 0.7508 (t0) cc_final: 0.6872 (m-30) REVERT: F 515 MET cc_start: 0.8455 (ttp) cc_final: 0.8162 (ttm) REVERT: F 601 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: F 718 ASP cc_start: 0.7270 (m-30) cc_final: 0.6770 (m-30) outliers start: 48 outliers final: 10 residues processed: 850 average time/residue: 0.4211 time to fit residues: 537.0925 Evaluate side-chains 449 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 438 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 50.0000 chunk 255 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 196 optimal weight: 0.0670 chunk 306 optimal weight: 8.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 438 HIS A 557 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 756 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN C 602 GLN D 212 GLN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 HIS D 585 GLN D 741 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 741 GLN F 242 HIS F 303 GLN F 438 HIS ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26825 Z= 0.197 Angle : 0.617 10.447 36361 Z= 0.305 Chirality : 0.044 0.287 4165 Planarity : 0.004 0.056 4679 Dihedral : 11.065 124.232 4022 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.85 % Allowed : 11.74 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.43 (0.15), residues: 3343 helix: 0.31 (0.12), residues: 1807 sheet: 0.52 (0.26), residues: 397 loop : 0.49 (0.21), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 466 HIS 0.007 0.001 HIS F 438 PHE 0.019 0.001 PHE B 731 TYR 0.016 0.001 TYR B 797 ARG 0.008 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 492 time to evaluate : 3.320 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: A 272 VAL cc_start: 0.8406 (t) cc_final: 0.8088 (p) REVERT: A 628 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 795 GLU cc_start: 0.8103 (mp0) cc_final: 0.7707 (mp0) REVERT: A 798 MET cc_start: 0.4597 (ptt) cc_final: 0.4028 (tpp) REVERT: A 799 HIS cc_start: 0.5771 (m170) cc_final: 0.4670 (t70) REVERT: B 294 LEU cc_start: 0.9216 (tp) cc_final: 0.8833 (tp) REVERT: B 731 PHE cc_start: 0.7550 (m-80) cc_final: 0.7243 (m-80) REVERT: B 735 ASP cc_start: 0.7232 (m-30) cc_final: 0.6910 (m-30) REVERT: B 740 MET cc_start: 0.6947 (tmm) cc_final: 0.6629 (tmm) REVERT: C 380 ILE cc_start: 0.9457 (mt) cc_final: 0.9229 (pt) REVERT: C 482 LEU cc_start: 0.8735 (mm) cc_final: 0.8456 (tp) REVERT: C 513 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8714 (mt) REVERT: C 754 GLN cc_start: 0.7949 (mt0) cc_final: 0.7717 (mm-40) REVERT: D 318 MET cc_start: 0.7806 (tpp) cc_final: 0.7150 (tpp) REVERT: D 390 LEU cc_start: 0.8486 (mt) cc_final: 0.8165 (mt) REVERT: D 431 LEU cc_start: 0.8888 (mt) cc_final: 0.8589 (tt) REVERT: D 452 ASP cc_start: 0.6428 (m-30) cc_final: 0.6176 (m-30) REVERT: D 511 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7810 (ttmm) REVERT: D 585 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.7096 (tp40) REVERT: E 350 ASN cc_start: 0.7676 (p0) cc_final: 0.7407 (p0) REVERT: E 603 MET cc_start: 0.8262 (ttp) cc_final: 0.8015 (ttm) REVERT: E 649 MET cc_start: 0.5865 (mmt) cc_final: 0.5643 (mmt) REVERT: E 752 TYR cc_start: 0.6866 (m-10) cc_final: 0.6649 (m-80) REVERT: E 780 TRP cc_start: 0.8212 (m100) cc_final: 0.7892 (m100) REVERT: F 212 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8611 (pp30) REVERT: F 368 ASP cc_start: 0.5965 (t0) cc_final: 0.5551 (p0) REVERT: F 515 MET cc_start: 0.8830 (ttp) cc_final: 0.8507 (ttt) outliers start: 80 outliers final: 47 residues processed: 550 average time/residue: 0.3922 time to fit residues: 337.1724 Evaluate side-chains 417 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 367 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 306 optimal weight: 0.8980 chunk 331 optimal weight: 50.0000 chunk 273 optimal weight: 40.0000 chunk 304 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 245 optimal weight: 40.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 585 GLN B 328 ASN B 379 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN F 438 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 HIS ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26825 Z= 0.210 Angle : 0.591 9.262 36361 Z= 0.288 Chirality : 0.043 0.241 4165 Planarity : 0.004 0.052 4679 Dihedral : 10.633 124.807 4017 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 3.63 % Allowed : 12.74 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.70 (0.15), residues: 3343 helix: 0.63 (0.12), residues: 1794 sheet: 0.35 (0.25), residues: 394 loop : 0.54 (0.21), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 453 HIS 0.006 0.001 HIS F 254 PHE 0.013 0.001 PHE D 288 TYR 0.018 0.001 TYR E 682 ARG 0.017 0.001 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 398 time to evaluate : 3.814 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: A 272 VAL cc_start: 0.8283 (t) cc_final: 0.7962 (p) REVERT: A 401 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8540 (ptpp) REVERT: A 466 TRP cc_start: 0.7387 (m-90) cc_final: 0.6950 (m-90) REVERT: A 515 MET cc_start: 0.7392 (mtm) cc_final: 0.7153 (ptp) REVERT: A 628 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 726 LEU cc_start: 0.8764 (mt) cc_final: 0.8537 (pt) REVERT: A 795 GLU cc_start: 0.8107 (mp0) cc_final: 0.7693 (mp0) REVERT: A 798 MET cc_start: 0.4601 (ptt) cc_final: 0.4032 (tpp) REVERT: A 799 HIS cc_start: 0.5757 (m170) cc_final: 0.4701 (t70) REVERT: B 294 LEU cc_start: 0.9219 (tp) cc_final: 0.8975 (tp) REVERT: B 515 MET cc_start: 0.7012 (ttp) cc_final: 0.6427 (ttp) REVERT: B 731 PHE cc_start: 0.7665 (m-80) cc_final: 0.7190 (m-80) REVERT: B 735 ASP cc_start: 0.7153 (m-30) cc_final: 0.6714 (m-30) REVERT: B 740 MET cc_start: 0.6920 (tmm) cc_final: 0.6573 (tmm) REVERT: C 523 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8042 (p0) REVERT: C 754 GLN cc_start: 0.7977 (mt0) cc_final: 0.7768 (mm-40) REVERT: D 318 MET cc_start: 0.7574 (tpp) cc_final: 0.6716 (tpp) REVERT: D 321 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7120 (mtm-85) REVERT: D 431 LEU cc_start: 0.8893 (mt) cc_final: 0.8619 (tt) REVERT: D 452 ASP cc_start: 0.6455 (m-30) cc_final: 0.6211 (m-30) REVERT: E 350 ASN cc_start: 0.7777 (p0) cc_final: 0.7568 (p0) REVERT: E 427 ILE cc_start: 0.8379 (mm) cc_final: 0.8070 (tp) REVERT: E 527 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6820 (t80) REVERT: E 603 MET cc_start: 0.8222 (ttp) cc_final: 0.7958 (ttm) REVERT: E 625 LEU cc_start: 0.8836 (tt) cc_final: 0.8522 (tp) REVERT: E 649 MET cc_start: 0.6023 (mmt) cc_final: 0.5775 (mmt) REVERT: E 752 TYR cc_start: 0.6716 (m-10) cc_final: 0.6499 (m-80) REVERT: E 775 ILE cc_start: 0.7623 (mp) cc_final: 0.7275 (mt) REVERT: F 212 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8596 (pp30) REVERT: F 318 MET cc_start: 0.4701 (tpp) cc_final: 0.4279 (tpt) REVERT: F 330 MET cc_start: 0.7478 (mpp) cc_final: 0.6850 (mpp) REVERT: F 351 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7883 (mmm160) REVERT: F 620 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8085 (mtp-110) REVERT: F 745 GLN cc_start: 0.8135 (mt0) cc_final: 0.5985 (mt0) outliers start: 102 outliers final: 67 residues processed: 464 average time/residue: 0.3584 time to fit residues: 267.5051 Evaluate side-chains 419 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 347 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 654 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 20.0000 chunk 230 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 146 optimal weight: 0.0060 chunk 205 optimal weight: 9.9990 chunk 307 optimal weight: 0.0570 chunk 325 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN A 585 GLN B 328 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN D 756 GLN F 242 HIS ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 HIS ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26825 Z= 0.156 Angle : 0.550 8.976 36361 Z= 0.267 Chirality : 0.042 0.218 4165 Planarity : 0.004 0.048 4679 Dihedral : 10.226 128.019 4017 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 3.42 % Allowed : 14.23 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.82 (0.15), residues: 3343 helix: 0.85 (0.12), residues: 1781 sheet: 0.38 (0.25), residues: 396 loop : 0.36 (0.20), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 466 HIS 0.004 0.001 HIS F 438 PHE 0.019 0.001 PHE D 354 TYR 0.017 0.001 TYR F 665 ARG 0.012 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 403 time to evaluate : 3.477 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: A 272 VAL cc_start: 0.8299 (t) cc_final: 0.7975 (p) REVERT: A 330 MET cc_start: 0.8124 (mtm) cc_final: 0.7828 (mtm) REVERT: A 466 TRP cc_start: 0.7317 (m-90) cc_final: 0.6713 (m-90) REVERT: A 795 GLU cc_start: 0.8066 (mp0) cc_final: 0.7635 (mp0) REVERT: A 798 MET cc_start: 0.4504 (ptt) cc_final: 0.3983 (tpp) REVERT: A 799 HIS cc_start: 0.5723 (m170) cc_final: 0.4660 (t70) REVERT: B 294 LEU cc_start: 0.9196 (tp) cc_final: 0.8909 (tp) REVERT: B 515 MET cc_start: 0.7011 (ttp) cc_final: 0.6437 (ttp) REVERT: B 731 PHE cc_start: 0.7588 (m-80) cc_final: 0.6979 (m-80) REVERT: B 735 ASP cc_start: 0.7058 (m-30) cc_final: 0.6652 (m-30) REVERT: B 740 MET cc_start: 0.6844 (tmm) cc_final: 0.6411 (tmm) REVERT: C 380 ILE cc_start: 0.9479 (mt) cc_final: 0.9274 (pt) REVERT: C 523 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 603 MET cc_start: 0.7970 (ppp) cc_final: 0.7491 (ppp) REVERT: C 754 GLN cc_start: 0.8043 (mt0) cc_final: 0.7729 (mm-40) REVERT: D 318 MET cc_start: 0.7936 (tpp) cc_final: 0.7134 (tpp) REVERT: D 321 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7210 (mtm-85) REVERT: D 378 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: D 431 LEU cc_start: 0.8699 (mt) cc_final: 0.8482 (tt) REVERT: D 452 ASP cc_start: 0.6447 (m-30) cc_final: 0.6171 (m-30) REVERT: E 350 ASN cc_start: 0.7761 (p0) cc_final: 0.7518 (p0) REVERT: E 473 MET cc_start: 0.7197 (tmm) cc_final: 0.6761 (tmm) REVERT: E 603 MET cc_start: 0.8189 (ttp) cc_final: 0.7907 (ttm) REVERT: E 625 LEU cc_start: 0.8765 (tt) cc_final: 0.8518 (tp) REVERT: E 649 MET cc_start: 0.6015 (mmt) cc_final: 0.5755 (mmt) REVERT: F 215 LEU cc_start: 0.8015 (tt) cc_final: 0.7681 (pp) REVERT: F 318 MET cc_start: 0.4744 (tpp) cc_final: 0.4184 (tpp) REVERT: F 330 MET cc_start: 0.7528 (mpp) cc_final: 0.6911 (mpp) REVERT: F 652 GLU cc_start: 0.8206 (mp0) cc_final: 0.7951 (mp0) REVERT: F 745 GLN cc_start: 0.8159 (mt0) cc_final: 0.6083 (mt0) outliers start: 96 outliers final: 62 residues processed: 466 average time/residue: 0.3762 time to fit residues: 280.4959 Evaluate side-chains 404 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 340 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 654 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 166 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 379 GLN B 424 GLN B 785 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26825 Z= 0.295 Angle : 0.601 9.250 36361 Z= 0.294 Chirality : 0.044 0.186 4165 Planarity : 0.004 0.055 4679 Dihedral : 10.131 132.337 4013 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 3.88 % Allowed : 14.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.84 (0.15), residues: 3343 helix: 0.89 (0.12), residues: 1776 sheet: 0.20 (0.25), residues: 387 loop : 0.42 (0.20), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 453 HIS 0.017 0.001 HIS E 254 PHE 0.017 0.002 PHE A 600 TYR 0.012 0.001 TYR F 406 ARG 0.011 0.001 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 358 time to evaluate : 3.395 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: A 272 VAL cc_start: 0.8407 (t) cc_final: 0.8095 (p) REVERT: A 515 MET cc_start: 0.7322 (ptp) cc_final: 0.7084 (ptp) REVERT: A 795 GLU cc_start: 0.8119 (mp0) cc_final: 0.7666 (mp0) REVERT: A 798 MET cc_start: 0.4528 (ptt) cc_final: 0.4028 (tpp) REVERT: A 799 HIS cc_start: 0.5739 (m170) cc_final: 0.4653 (t-170) REVERT: B 294 LEU cc_start: 0.9281 (tp) cc_final: 0.9002 (tp) REVERT: B 731 PHE cc_start: 0.8018 (m-80) cc_final: 0.7359 (m-80) REVERT: B 735 ASP cc_start: 0.6984 (m-30) cc_final: 0.6504 (m-30) REVERT: B 740 MET cc_start: 0.6988 (tmm) cc_final: 0.6560 (tmm) REVERT: C 423 PHE cc_start: 0.8292 (m-80) cc_final: 0.7921 (m-80) REVERT: C 523 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8057 (p0) REVERT: C 754 GLN cc_start: 0.8090 (mt0) cc_final: 0.7742 (mm-40) REVERT: C 792 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7745 (mppt) REVERT: D 318 MET cc_start: 0.8148 (tpp) cc_final: 0.7036 (tpp) REVERT: D 321 ARG cc_start: 0.7887 (mtm110) cc_final: 0.6796 (mtm-85) REVERT: D 431 LEU cc_start: 0.8719 (mt) cc_final: 0.8468 (tt) REVERT: D 452 ASP cc_start: 0.6565 (m-30) cc_final: 0.6323 (m-30) REVERT: E 231 MET cc_start: 0.6079 (ttm) cc_final: 0.5820 (ttm) REVERT: E 237 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6676 (m-40) REVERT: E 316 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7615 (ptpp) REVERT: E 350 ASN cc_start: 0.7799 (p0) cc_final: 0.7573 (p0) REVERT: E 427 ILE cc_start: 0.8350 (mm) cc_final: 0.8087 (tp) REVERT: E 515 MET cc_start: 0.8102 (ptt) cc_final: 0.7833 (ptp) REVERT: E 752 TYR cc_start: 0.6777 (m-10) cc_final: 0.5949 (m-80) REVERT: F 215 LEU cc_start: 0.7962 (tt) cc_final: 0.7688 (pp) REVERT: F 330 MET cc_start: 0.7546 (mpp) cc_final: 0.6848 (mpp) REVERT: F 620 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8197 (mtp180) REVERT: F 652 GLU cc_start: 0.8235 (mp0) cc_final: 0.7994 (mp0) REVERT: F 745 GLN cc_start: 0.7903 (mt0) cc_final: 0.7053 (mt0) outliers start: 109 outliers final: 80 residues processed: 439 average time/residue: 0.3674 time to fit residues: 259.6606 Evaluate side-chains 414 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 331 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 356 ASP Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 565 SER Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 4.9990 chunk 293 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 326 optimal weight: 40.0000 chunk 270 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26825 Z= 0.202 Angle : 0.556 8.942 36361 Z= 0.268 Chirality : 0.043 0.217 4165 Planarity : 0.004 0.048 4679 Dihedral : 9.971 135.467 4012 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 3.42 % Allowed : 15.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3343 helix: 0.95 (0.12), residues: 1793 sheet: 0.20 (0.25), residues: 399 loop : 0.37 (0.20), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 453 HIS 0.014 0.001 HIS E 254 PHE 0.011 0.001 PHE D 354 TYR 0.019 0.001 TYR F 665 ARG 0.009 0.000 ARG E 727 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 353 time to evaluate : 3.128 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: A 272 VAL cc_start: 0.8383 (t) cc_final: 0.8102 (p) REVERT: A 330 MET cc_start: 0.7963 (mtm) cc_final: 0.7489 (mpp) REVERT: A 466 TRP cc_start: 0.7430 (m-90) cc_final: 0.7098 (m-90) REVERT: A 515 MET cc_start: 0.7299 (ptp) cc_final: 0.7005 (ptt) REVERT: A 795 GLU cc_start: 0.8085 (mp0) cc_final: 0.7627 (mp0) REVERT: A 798 MET cc_start: 0.4485 (ptt) cc_final: 0.4019 (tpp) REVERT: A 799 HIS cc_start: 0.5742 (m170) cc_final: 0.4649 (t-170) REVERT: B 294 LEU cc_start: 0.9247 (tp) cc_final: 0.8982 (tp) REVERT: B 375 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7740 (tpt90) REVERT: B 490 GLU cc_start: 0.7313 (mp0) cc_final: 0.7111 (mp0) REVERT: B 515 MET cc_start: 0.7056 (ttp) cc_final: 0.6452 (ttp) REVERT: B 731 PHE cc_start: 0.7925 (m-80) cc_final: 0.7188 (m-80) REVERT: B 735 ASP cc_start: 0.6964 (m-30) cc_final: 0.6444 (m-30) REVERT: B 740 MET cc_start: 0.6979 (tmm) cc_final: 0.6562 (tmm) REVERT: C 423 PHE cc_start: 0.8218 (m-80) cc_final: 0.7891 (m-80) REVERT: C 513 LEU cc_start: 0.9114 (mp) cc_final: 0.8908 (mt) REVERT: C 523 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8098 (p0) REVERT: C 754 GLN cc_start: 0.8041 (mt0) cc_final: 0.7729 (mm-40) REVERT: C 792 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7828 (mppt) REVERT: C 798 MET cc_start: 0.5510 (ptp) cc_final: 0.5287 (tmm) REVERT: D 318 MET cc_start: 0.8247 (tpp) cc_final: 0.7211 (tpp) REVERT: D 321 ARG cc_start: 0.7766 (mtm110) cc_final: 0.6766 (mtm-85) REVERT: D 431 LEU cc_start: 0.8699 (mt) cc_final: 0.8446 (tt) REVERT: D 452 ASP cc_start: 0.6625 (m-30) cc_final: 0.6344 (m-30) REVERT: E 237 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6703 (m-40) REVERT: E 350 ASN cc_start: 0.7767 (p0) cc_final: 0.7478 (p0) REVERT: E 427 ILE cc_start: 0.8280 (mm) cc_final: 0.8018 (tp) REVERT: E 515 MET cc_start: 0.8038 (ptt) cc_final: 0.7744 (ptp) REVERT: E 541 TRP cc_start: 0.7856 (p-90) cc_final: 0.7513 (p-90) REVERT: F 215 LEU cc_start: 0.7913 (tt) cc_final: 0.7648 (pp) REVERT: F 240 LEU cc_start: 0.7849 (tp) cc_final: 0.7253 (pp) REVERT: F 330 MET cc_start: 0.7606 (mpp) cc_final: 0.7356 (mpp) REVERT: F 438 HIS cc_start: 0.5801 (OUTLIER) cc_final: 0.5556 (t-90) REVERT: F 620 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8296 (mtp180) REVERT: F 745 GLN cc_start: 0.7905 (mt0) cc_final: 0.7154 (mt0) outliers start: 96 outliers final: 71 residues processed: 420 average time/residue: 0.3541 time to fit residues: 242.0790 Evaluate side-chains 407 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 332 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 438 HIS Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 238 optimal weight: 40.0000 chunk 184 optimal weight: 9.9990 chunk 274 optimal weight: 0.0470 chunk 182 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 203 optimal weight: 0.6980 chunk 198 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN B 328 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26825 Z= 0.158 Angle : 0.554 12.753 36361 Z= 0.261 Chirality : 0.042 0.197 4165 Planarity : 0.004 0.050 4679 Dihedral : 9.732 135.745 4012 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 2.74 % Allowed : 17.00 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 1.08 (0.15), residues: 3343 helix: 1.19 (0.13), residues: 1767 sheet: 0.24 (0.25), residues: 395 loop : 0.37 (0.20), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 466 HIS 0.018 0.001 HIS F 438 PHE 0.009 0.001 PHE D 354 TYR 0.016 0.001 TYR E 752 ARG 0.006 0.000 ARG C 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 367 time to evaluate : 3.242 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: A 272 VAL cc_start: 0.8358 (t) cc_final: 0.8069 (p) REVERT: A 330 MET cc_start: 0.8216 (mtm) cc_final: 0.7738 (mpp) REVERT: A 515 MET cc_start: 0.7344 (ptp) cc_final: 0.7095 (ptt) REVERT: A 795 GLU cc_start: 0.8148 (mp0) cc_final: 0.7694 (mp0) REVERT: A 798 MET cc_start: 0.4362 (ptt) cc_final: 0.3937 (tpp) REVERT: A 799 HIS cc_start: 0.5736 (m170) cc_final: 0.4652 (t-170) REVERT: B 294 LEU cc_start: 0.9212 (tp) cc_final: 0.8928 (tp) REVERT: B 515 MET cc_start: 0.7111 (ttp) cc_final: 0.6540 (ttp) REVERT: B 731 PHE cc_start: 0.7900 (m-80) cc_final: 0.7211 (m-80) REVERT: B 735 ASP cc_start: 0.6943 (m-30) cc_final: 0.6444 (m-30) REVERT: B 740 MET cc_start: 0.6897 (tmm) cc_final: 0.6454 (tmm) REVERT: C 423 PHE cc_start: 0.8213 (m-80) cc_final: 0.7885 (m-80) REVERT: C 523 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8027 (p0) REVERT: C 754 GLN cc_start: 0.7969 (mt0) cc_final: 0.7690 (mm-40) REVERT: C 792 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7706 (mppt) REVERT: C 798 MET cc_start: 0.5471 (ptp) cc_final: 0.5073 (tmm) REVERT: D 281 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 318 MET cc_start: 0.8226 (tpp) cc_final: 0.7204 (tpp) REVERT: D 321 ARG cc_start: 0.7766 (mtm110) cc_final: 0.6897 (mtm-85) REVERT: D 431 LEU cc_start: 0.8715 (mt) cc_final: 0.8473 (tt) REVERT: D 452 ASP cc_start: 0.6508 (m-30) cc_final: 0.6193 (m-30) REVERT: E 235 TYR cc_start: 0.7363 (t80) cc_final: 0.7104 (t80) REVERT: E 237 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6474 (m-40) REVERT: E 316 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7541 (ptpp) REVERT: E 350 ASN cc_start: 0.7874 (p0) cc_final: 0.7556 (p0) REVERT: E 427 ILE cc_start: 0.8267 (mm) cc_final: 0.7997 (tp) REVERT: E 498 THR cc_start: 0.8551 (m) cc_final: 0.8295 (p) REVERT: E 541 TRP cc_start: 0.7845 (p-90) cc_final: 0.7521 (p-90) REVERT: E 625 LEU cc_start: 0.8713 (tt) cc_final: 0.8491 (tp) REVERT: F 215 LEU cc_start: 0.7836 (tt) cc_final: 0.7616 (pp) REVERT: F 240 LEU cc_start: 0.7815 (tp) cc_final: 0.7189 (pp) REVERT: F 620 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (mtp180) REVERT: F 660 LEU cc_start: 0.8118 (mt) cc_final: 0.7770 (mp) REVERT: F 745 GLN cc_start: 0.7889 (mt0) cc_final: 0.7125 (mt0) outliers start: 77 outliers final: 63 residues processed: 418 average time/residue: 0.3577 time to fit residues: 241.2099 Evaluate side-chains 406 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 340 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 63 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26825 Z= 0.151 Angle : 0.552 10.306 36361 Z= 0.263 Chirality : 0.042 0.189 4165 Planarity : 0.004 0.050 4679 Dihedral : 9.462 134.238 4012 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 2.77 % Allowed : 17.36 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 1.14 (0.15), residues: 3343 helix: 1.24 (0.13), residues: 1784 sheet: 0.25 (0.25), residues: 397 loop : 0.38 (0.20), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 466 HIS 0.010 0.001 HIS E 254 PHE 0.012 0.001 PHE E 288 TYR 0.008 0.001 TYR C 233 ARG 0.010 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 374 time to evaluate : 2.999 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: A 272 VAL cc_start: 0.8303 (t) cc_final: 0.8002 (p) REVERT: A 330 MET cc_start: 0.8092 (mtm) cc_final: 0.7556 (mpp) REVERT: A 515 MET cc_start: 0.7351 (ptp) cc_final: 0.7070 (ptt) REVERT: A 795 GLU cc_start: 0.8063 (mp0) cc_final: 0.7603 (mp0) REVERT: A 798 MET cc_start: 0.4339 (ptt) cc_final: 0.3953 (tpp) REVERT: A 799 HIS cc_start: 0.5743 (m170) cc_final: 0.3961 (t70) REVERT: B 294 LEU cc_start: 0.9178 (tp) cc_final: 0.8914 (tp) REVERT: B 515 MET cc_start: 0.7093 (ttp) cc_final: 0.6511 (ttp) REVERT: B 731 PHE cc_start: 0.7910 (m-80) cc_final: 0.7216 (m-80) REVERT: B 735 ASP cc_start: 0.6878 (m-30) cc_final: 0.6389 (m-30) REVERT: B 740 MET cc_start: 0.6846 (tmm) cc_final: 0.6409 (tmm) REVERT: C 423 PHE cc_start: 0.8187 (m-80) cc_final: 0.7875 (m-80) REVERT: C 523 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7979 (p0) REVERT: C 754 GLN cc_start: 0.7973 (mt0) cc_final: 0.7684 (mm-40) REVERT: C 792 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7709 (mppt) REVERT: D 209 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7815 (p0) REVERT: D 281 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7859 (mm-30) REVERT: D 318 MET cc_start: 0.8174 (tpp) cc_final: 0.7554 (tpp) REVERT: D 431 LEU cc_start: 0.8718 (mt) cc_final: 0.8472 (tt) REVERT: D 452 ASP cc_start: 0.6346 (m-30) cc_final: 0.5983 (m-30) REVERT: D 798 MET cc_start: 0.7670 (mmm) cc_final: 0.7022 (mmt) REVERT: E 237 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6504 (m-40) REVERT: E 316 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7515 (ptpp) REVERT: E 350 ASN cc_start: 0.7793 (p0) cc_final: 0.7529 (p0) REVERT: E 427 ILE cc_start: 0.8270 (mm) cc_final: 0.8013 (tp) REVERT: E 515 MET cc_start: 0.7909 (ptm) cc_final: 0.7668 (ptm) REVERT: E 541 TRP cc_start: 0.7894 (p-90) cc_final: 0.7601 (p-90) REVERT: E 625 LEU cc_start: 0.8659 (tt) cc_final: 0.8453 (tp) REVERT: E 752 TYR cc_start: 0.6919 (m-80) cc_final: 0.6708 (m-80) REVERT: F 303 GLN cc_start: 0.7293 (tp-100) cc_final: 0.6856 (tp40) REVERT: F 620 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8161 (mtp180) REVERT: F 660 LEU cc_start: 0.8032 (mt) cc_final: 0.7661 (mp) REVERT: F 745 GLN cc_start: 0.7877 (mt0) cc_final: 0.7088 (mt0) outliers start: 78 outliers final: 60 residues processed: 429 average time/residue: 0.3571 time to fit residues: 246.0718 Evaluate side-chains 404 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 340 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 302 optimal weight: 30.0000 chunk 182 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 chunk 286 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN B 379 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26825 Z= 0.358 Angle : 0.667 11.880 36361 Z= 0.323 Chirality : 0.045 0.224 4165 Planarity : 0.004 0.054 4679 Dihedral : 9.870 143.891 4012 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 2.92 % Allowed : 17.57 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.90 (0.15), residues: 3343 helix: 1.02 (0.12), residues: 1773 sheet: 0.07 (0.25), residues: 394 loop : 0.36 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 466 HIS 0.008 0.001 HIS F 254 PHE 0.018 0.002 PHE A 600 TYR 0.025 0.002 TYR C 797 ARG 0.010 0.001 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 339 time to evaluate : 3.583 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: A 330 MET cc_start: 0.7975 (mtm) cc_final: 0.7382 (mpp) REVERT: A 515 MET cc_start: 0.7281 (ptp) cc_final: 0.7004 (ptt) REVERT: A 795 GLU cc_start: 0.8184 (mp0) cc_final: 0.7722 (mp0) REVERT: A 798 MET cc_start: 0.4549 (ptt) cc_final: 0.4020 (tpp) REVERT: A 799 HIS cc_start: 0.5279 (m170) cc_final: 0.4321 (t-170) REVERT: B 294 LEU cc_start: 0.9266 (tp) cc_final: 0.9031 (tp) REVERT: B 515 MET cc_start: 0.7197 (ttp) cc_final: 0.6704 (ttp) REVERT: B 735 ASP cc_start: 0.7000 (m-30) cc_final: 0.6595 (m-30) REVERT: B 740 MET cc_start: 0.7169 (tmm) cc_final: 0.6691 (tmm) REVERT: C 423 PHE cc_start: 0.8329 (m-80) cc_final: 0.8032 (m-80) REVERT: C 635 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6046 (ppt-90) REVERT: C 754 GLN cc_start: 0.7957 (mt0) cc_final: 0.7700 (mm110) REVERT: C 792 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7792 (mppt) REVERT: D 318 MET cc_start: 0.8393 (tpp) cc_final: 0.7762 (tpp) REVERT: D 431 LEU cc_start: 0.8732 (mt) cc_final: 0.8495 (tt) REVERT: D 452 ASP cc_start: 0.6649 (m-30) cc_final: 0.6332 (m-30) REVERT: E 237 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6940 (m-40) REVERT: E 316 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7620 (ptpp) REVERT: E 350 ASN cc_start: 0.7926 (p0) cc_final: 0.7589 (p0) REVERT: E 427 ILE cc_start: 0.8299 (mm) cc_final: 0.8033 (tp) REVERT: E 515 MET cc_start: 0.7869 (ptm) cc_final: 0.7585 (ptt) REVERT: E 541 TRP cc_start: 0.8008 (p-90) cc_final: 0.7664 (p-90) REVERT: F 620 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8166 (mtp180) REVERT: F 745 GLN cc_start: 0.7950 (mt0) cc_final: 0.7193 (mt0) outliers start: 82 outliers final: 71 residues processed: 394 average time/residue: 0.3625 time to fit residues: 230.2375 Evaluate side-chains 398 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 324 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 330 MET Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 565 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.9980 chunk 320 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 335 optimal weight: 40.0000 chunk 309 optimal weight: 50.0000 chunk 267 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26825 Z= 0.174 Angle : 0.600 12.042 36361 Z= 0.285 Chirality : 0.043 0.218 4165 Planarity : 0.004 0.047 4679 Dihedral : 9.544 137.578 4010 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 2.42 % Allowed : 18.32 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 1.03 (0.15), residues: 3343 helix: 1.24 (0.13), residues: 1772 sheet: -0.02 (0.24), residues: 399 loop : 0.28 (0.20), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 466 HIS 0.009 0.001 HIS E 254 PHE 0.010 0.001 PHE C 288 TYR 0.013 0.001 TYR C 797 ARG 0.007 0.000 ARG F 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 353 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8429 (t) cc_final: 0.8120 (p) REVERT: A 330 MET cc_start: 0.7885 (mtm) cc_final: 0.7325 (mpp) REVERT: A 515 MET cc_start: 0.7258 (ptp) cc_final: 0.6967 (ptt) REVERT: A 795 GLU cc_start: 0.8183 (mp0) cc_final: 0.7712 (mp0) REVERT: A 798 MET cc_start: 0.4420 (ptt) cc_final: 0.3978 (tpp) REVERT: A 799 HIS cc_start: 0.5265 (m170) cc_final: 0.4311 (t-170) REVERT: B 294 LEU cc_start: 0.9181 (tp) cc_final: 0.8935 (tp) REVERT: B 515 MET cc_start: 0.7195 (ttp) cc_final: 0.6629 (ttp) REVERT: B 731 PHE cc_start: 0.8060 (m-80) cc_final: 0.7303 (m-80) REVERT: B 735 ASP cc_start: 0.7003 (m-30) cc_final: 0.6436 (m-30) REVERT: B 740 MET cc_start: 0.6996 (tmm) cc_final: 0.6534 (tmm) REVERT: C 754 GLN cc_start: 0.7921 (mt0) cc_final: 0.7651 (mp10) REVERT: C 792 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7799 (mppt) REVERT: D 208 ASP cc_start: 0.7050 (t0) cc_final: 0.6825 (t0) REVERT: D 209 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (p0) REVERT: D 318 MET cc_start: 0.8343 (tpp) cc_final: 0.7759 (tpp) REVERT: D 431 LEU cc_start: 0.8727 (mt) cc_final: 0.8501 (tt) REVERT: D 452 ASP cc_start: 0.6480 (m-30) cc_final: 0.6095 (m-30) REVERT: E 237 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6723 (m-40) REVERT: E 316 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7543 (ptpp) REVERT: E 326 ILE cc_start: 0.8279 (mt) cc_final: 0.7985 (tp) REVERT: E 350 ASN cc_start: 0.7790 (p0) cc_final: 0.7332 (t0) REVERT: E 427 ILE cc_start: 0.8246 (mm) cc_final: 0.7983 (tp) REVERT: E 515 MET cc_start: 0.7864 (ptm) cc_final: 0.7584 (ptt) REVERT: E 541 TRP cc_start: 0.7946 (p-90) cc_final: 0.7609 (p-90) REVERT: E 625 LEU cc_start: 0.8679 (tt) cc_final: 0.8458 (tp) REVERT: E 752 TYR cc_start: 0.6829 (m-80) cc_final: 0.6606 (m-80) REVERT: F 620 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (mtp180) REVERT: F 745 GLN cc_start: 0.7895 (mt0) cc_final: 0.7334 (mt0) outliers start: 68 outliers final: 59 residues processed: 399 average time/residue: 0.3941 time to fit residues: 255.5309 Evaluate side-chains 399 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 337 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 9.9990 chunk 284 optimal weight: 40.0000 chunk 81 optimal weight: 0.0060 chunk 246 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 112 optimal weight: 0.2980 chunk 274 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 overall best weight: 4.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108615 restraints weight = 53081.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109940 restraints weight = 32992.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109886 restraints weight = 23314.066| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26825 Z= 0.229 Angle : 0.614 12.079 36361 Z= 0.292 Chirality : 0.043 0.200 4165 Planarity : 0.004 0.051 4679 Dihedral : 9.514 136.035 4010 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.56 % Allowed : 18.36 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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 (0.15), residues: 3343 helix: 1.25 (0.13), residues: 1747 sheet: -0.04 (0.24), residues: 398 loop : 0.34 (0.20), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 466 HIS 0.008 0.001 HIS E 254 PHE 0.009 0.001 PHE A 600 TYR 0.010 0.001 TYR E 682 ARG 0.006 0.000 ARG F 362 =============================================================================== Job complete usr+sys time: 5594.90 seconds wall clock time: 102 minutes 43.43 seconds (6163.43 seconds total)