Starting phenix.real_space_refine on Thu Apr 11 22:37:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/04_2024/7swl_25474_updated.pdb" } resolution = 2.88 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= 0.049 sd= 0.336 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 29 5.49 5 Mg 9 5.21 5 S 115 5.16 5 C 14929 2.51 5 N 4252 2.21 5 O 4573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23907 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4238 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4262 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4294 Chain: "C" Number of atoms: 4320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4357 Chain: "D" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4259 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 3652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3652 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Chain breaks: 6 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2684 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 329} Chain breaks: 7 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 177 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 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} Time building chain proxies: 15.97, per 1000 atoms: 0.67 Number of scatterers: 23907 At special positions: 0 Unit cell: (127.595, 146.575, 158.175, 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 115 16.00 P 29 15.00 Mg 9 11.99 O 4573 8.00 N 4252 7.00 C 14929 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: 9.19 Conformation dependent library (CDL) restraints added in 6.0 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 11 sheets defined 51.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 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: 3.844A 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: 4.274A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.872A 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 318 through 335 removed outlier: 3.965A pdb=" N VAL A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.734A 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: 4.402A pdb=" N ARG A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.655A 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 437 removed outlier: 4.464A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) 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: 3.977A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 3.523A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) 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: 4.182A 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 592 removed outlier: 3.646A 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: 3.834A pdb=" N ALA A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.658A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 removed outlier: 3.624A 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 754 Processing helix chain 'A' and resid 756 through 759 No H-bonds generated for 'chain 'A' and resid 756 through 759' Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.578A pdb=" N LYS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.585A pdb=" N MET A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 798' 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: 4.201A 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: 3.658A 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: 3.964A 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: 4.175A pdb=" N ARG B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.538A pdb=" N ARG B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.650A 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: 3.697A 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: 3.766A 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 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: 3.834A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.708A 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 783 removed outlier: 3.635A pdb=" N LYS B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 797 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: 4.089A 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 removed outlier: 3.507A pdb=" N GLY C 258 " --> pdb=" O HIS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 272 Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.697A 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: 4.173A pdb=" N ARG C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 3.632A 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: 4.340A pdb=" N ARG C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.506A 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: 4.120A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 473 through 482 removed outlier: 3.903A 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 530 removed outlier: 3.820A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 Processing helix chain 'C' and resid 578 through 592 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: 3.868A pdb=" N VAL C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.649A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.665A 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 760 Processing helix chain 'C' and resid 777 through 784 removed outlier: 3.572A 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: 4.167A 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 231 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 279 through 293 removed outlier: 3.609A 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: 3.526A pdb=" N ILE D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 335 " --> pdb=" O ASP D 331 " (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: 4.117A pdb=" N ARG D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 384 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: 3.679A 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: 3.554A 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: 3.514A pdb=" N VAL D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 578 through 592 removed outlier: 3.603A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) 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: 3.876A pdb=" N VAL D 621 " --> pdb=" O ALA D 617 " (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: 3.737A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.910A pdb=" N ASN D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.744A pdb=" N MET D 798 " --> pdb=" O GLU D 795 " (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: 3.727A pdb=" N LEU E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 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 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 278 through 293 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 335 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: 3.849A pdb=" N ARG E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 423 Processing helix chain 'E' and resid 473 through 482 removed outlier: 3.629A pdb=" N SER E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 516 removed outlier: 3.550A pdb=" N MET E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) 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 529 Processing helix chain 'E' and resid 548 through 559 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: 3.731A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 588 " --> pdb=" O ARG E 584 " (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 617 through 631 removed outlier: 3.631A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 652 through 655 Processing helix chain 'E' and resid 673 through 684 removed outlier: 3.849A pdb=" N ASN E 684 " --> pdb=" O THR E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 723 removed outlier: 3.598A pdb=" N VAL E 722 " --> pdb=" O ASP E 718 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 723 " --> pdb=" O LEU E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 749 removed outlier: 3.585A pdb=" N GLN E 741 " --> pdb=" O GLY E 737 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 785 removed outlier: 4.120A pdb=" N GLU E 781 " --> pdb=" O GLU E 778 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS E 782 " --> pdb=" O ASP E 779 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN E 785 " --> pdb=" O LYS E 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.771A pdb=" N ILE F 380 " --> pdb=" O ALA F 376 " (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 435 removed outlier: 3.889A pdb=" N TYR F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.959A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 482 removed outlier: 3.560A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 507 through 516 removed outlier: 3.980A pdb=" N LYS F 511 " --> pdb=" O GLU F 507 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 512 " --> pdb=" O ASP F 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET F 515 " --> pdb=" O LYS F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 522 No H-bonds generated for 'chain 'F' and resid 519 through 522' Processing helix chain 'F' and resid 527 through 530 Processing helix chain 'F' and resid 548 through 558 Processing helix chain 'F' and resid 568 through 571 No H-bonds generated for 'chain 'F' and resid 568 through 571' Processing helix chain 'F' and resid 581 through 592 removed outlier: 3.503A pdb=" N PHE F 587 " --> pdb=" O VAL F 583 " (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 621 through 630 removed outlier: 3.680A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 628 " --> pdb=" O THR F 624 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 684 removed outlier: 4.002A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 681 " --> pdb=" O ILE F 677 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN F 684 " --> pdb=" O THR F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 722 No H-bonds generated for 'chain 'F' and resid 719 through 722' Processing helix chain 'F' and resid 733 through 753 removed outlier: 3.583A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN F 738 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 739 " --> pdb=" O ASP F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 784 removed outlier: 3.762A pdb=" N LYS F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 783 " --> pdb=" O ASP F 779 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.493A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.638A 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: 3.666A pdb=" N ALA A 536 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 562 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE A 599 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 564 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP A 601 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.516A 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 369 removed outlier: 7.967A pdb=" N VAL B 239 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 345 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 241 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 347 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY B 243 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 349 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.844A 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: 3.814A pdb=" N ALA B 536 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 562 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE B 599 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 564 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP B 601 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.698A 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 369 removed outlier: 8.054A pdb=" N VAL C 239 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 345 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU C 241 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 347 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLY C 243 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 349 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 263 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE C 300 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 265 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP C 302 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.747A 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: 3.748A pdb=" N ALA C 536 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.502A 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 369 removed outlier: 8.050A pdb=" N VAL D 239 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 345 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU D 241 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA D 347 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLY D 243 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR D 349 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA D 263 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE D 300 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE D 265 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP D 302 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.875A 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: 8.336A pdb=" N ILE D 538 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 640 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU D 540 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY D 642 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.496A 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 368 removed outlier: 3.598A pdb=" N ASN E 237 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 562 through 566 removed outlier: 4.025A pdb=" N GLY E 661 " --> pdb=" O GLY E 537 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU E 539 " --> pdb=" O GLY E 661 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER E 663 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP E 541 " --> pdb=" O SER E 663 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 665 " --> pdb=" O TRP E 541 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 663 through 665 removed outlier: 9.485A pdb=" N ILE F 664 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL F 640 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY F 642 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 639 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 598 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2603 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: 8.32 Time building geometry restraints manager: 9.88 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: 8024 1.34 - 1.46: 4124 1.46 - 1.58: 11891 1.58 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24279 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 7.98e+00 bond pdb=" O5' ATP A 901 " pdb=" PA ATP A 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.43e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.33e+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 7.24e+00 ... (remaining 24274 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.61: 860 106.61 - 113.94: 14084 113.94 - 121.28: 11787 121.28 - 128.62: 5995 128.62 - 135.96: 147 Bond angle restraints: 32873 Sorted by residual: angle pdb=" PB ATP E 902 " pdb=" O3B ATP E 902 " pdb=" PG ATP E 902 " ideal model delta sigma weight residual 139.87 129.42 10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 129.59 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 130.23 9.64 1.00e+00 1.00e+00 9.30e+01 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 130.92 8.95 1.00e+00 1.00e+00 8.01e+01 ... (remaining 32868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14690 24.83 - 49.65: 329 49.65 - 74.48: 85 74.48 - 99.31: 9 99.31 - 124.13: 1 Dihedral angle restraints: 15114 sinusoidal: 6318 harmonic: 8796 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 175.87 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA ARG D 635 " pdb=" CB ARG D 635 " pdb=" CG ARG D 635 " pdb=" CD ARG D 635 " ideal model delta sinusoidal sigma weight residual 60.00 118.64 -58.64 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2259 0.029 - 0.058: 1036 0.058 - 0.087: 220 0.087 - 0.116: 211 0.116 - 0.144: 36 Chirality restraints: 3762 Sorted by residual: 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 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 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 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 3759 not shown) Planarity restraints: 4214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 357 " -0.061 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 GLY A 519 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.43e+00 pdb=" N PRO A 520 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 220 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 221 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.016 5.00e-02 4.00e+02 ... (remaining 4211 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 173 2.54 - 3.13: 18237 3.13 - 3.72: 36810 3.72 - 4.31: 54091 4.31 - 4.90: 89423 Nonbonded interactions: 198734 Sorted by model distance: nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.953 2.170 nonbonded pdb=" O1B ATP C 902 " pdb="MG MG C 904 " model vdw 1.970 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 903 " model vdw 1.994 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.995 2.170 ... (remaining 198729 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 200 through 302 or resid 304 through 388 or resid 394 thro \ ugh 425 or resid 470 through 483 or (resid 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 487 or resid 494 through 588 or res \ id 590 through 634 or (resid 635 and (name N or name CA or name C or name O or n \ ame CB )) or resid 636 through 654 or resid 656 through 726 or resid 732 through \ 751 or resid 775 through 788 or resid 904)) selection = (chain 'B' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'C' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'D' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'E' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 588 or resid 590 through 654 or resid 656 through 788 or resid 903)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.010 Extract box with map and model: 2.090 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 68.950 Find NCS groups from input model: 1.700 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24279 Z= 0.214 Angle : 0.509 10.455 32873 Z= 0.305 Chirality : 0.040 0.144 3762 Planarity : 0.003 0.035 4214 Dihedral : 11.234 124.134 9416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 0.95 % Allowed : 2.88 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.12 (0.16), residues: 3006 helix: -0.21 (0.13), residues: 1583 sheet: 0.79 (0.28), residues: 365 loop : 0.65 (0.21), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 541 HIS 0.003 0.001 HIS C 242 PHE 0.008 0.001 PHE C 264 TYR 0.009 0.001 TYR B 406 ARG 0.003 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 541 time to evaluate : 2.830 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 208 ASP cc_start: 0.7875 (m-30) cc_final: 0.7465 (m-30) REVERT: A 401 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8180 (tptt) REVERT: A 735 ASP cc_start: 0.8623 (m-30) cc_final: 0.8321 (m-30) REVERT: B 351 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7691 (mmt90) REVERT: B 649 MET cc_start: 0.8070 (mmm) cc_final: 0.7754 (mmp) REVERT: B 777 MET cc_start: 0.8479 (tpt) cc_final: 0.8260 (tpt) REVERT: C 286 ASP cc_start: 0.7882 (m-30) cc_final: 0.7607 (m-30) REVERT: C 635 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (ppt170) REVERT: C 757 GLN cc_start: 0.6926 (tt0) cc_final: 0.6534 (mt0) REVERT: D 401 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8220 (tttp) REVERT: D 778 GLU cc_start: 0.8054 (pt0) cc_final: 0.7683 (tp30) REVERT: E 416 LYS cc_start: 0.7499 (mttt) cc_final: 0.7083 (mmtt) REVERT: E 472 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7080 (t) REVERT: E 473 MET cc_start: 0.6010 (tmm) cc_final: 0.5747 (ppp) REVERT: E 475 GLN cc_start: 0.6054 (mt0) cc_final: 0.5675 (mt0) REVERT: E 526 LEU cc_start: 0.8078 (tp) cc_final: 0.7530 (tp) REVERT: E 639 TYR cc_start: 0.7789 (m-80) cc_final: 0.7388 (m-80) REVERT: E 776 THR cc_start: 0.6000 (p) cc_final: 0.5736 (t) REVERT: F 424 GLN cc_start: 0.7342 (tp40) cc_final: 0.6571 (tt0) REVERT: F 586 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7038 (mp) REVERT: F 601 ASP cc_start: 0.6872 (p0) cc_final: 0.6355 (t0) REVERT: F 649 MET cc_start: 0.6171 (mmm) cc_final: 0.5468 (mmm) REVERT: F 754 GLN cc_start: 0.6943 (mt0) cc_final: 0.6285 (pp30) REVERT: F 782 LYS cc_start: 0.6716 (ptpp) cc_final: 0.6147 (tttp) outliers start: 24 outliers final: 7 residues processed: 559 average time/residue: 1.7183 time to fit residues: 1074.9823 Evaluate side-chains 339 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 328 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 123 optimal weight: 50.0000 chunk 238 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.0980 chunk 177 optimal weight: 10.0000 chunk 276 optimal weight: 50.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 424 GLN C 562 ASN C 585 GLN D 433 GLN D 741 GLN E 335 GLN E 523 ASN E 602 GLN E 745 GLN E 785 ASN F 433 GLN F 484 GLN F 785 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24279 Z= 0.173 Angle : 0.518 9.175 32873 Z= 0.261 Chirality : 0.042 0.260 3762 Planarity : 0.004 0.033 4214 Dihedral : 11.095 106.902 3662 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 2.29 % Allowed : 11.91 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.16), residues: 3006 helix: 0.43 (0.13), residues: 1587 sheet: 0.58 (0.27), residues: 374 loop : 0.70 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 466 HIS 0.003 0.001 HIS A 242 PHE 0.014 0.001 PHE E 527 TYR 0.014 0.001 TYR A 752 ARG 0.006 0.000 ARG C 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 386 time to evaluate : 3.538 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7601 (mmp-170) cc_final: 0.7378 (tpp-160) REVERT: A 355 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7283 (mp) REVERT: A 401 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8399 (tptt) REVERT: A 716 ASP cc_start: 0.7645 (t0) cc_final: 0.6991 (m-30) REVERT: A 735 ASP cc_start: 0.8546 (m-30) cc_final: 0.8182 (m-30) REVERT: A 786 GLU cc_start: 0.7718 (pt0) cc_final: 0.7490 (pt0) REVERT: A 796 LYS cc_start: 0.5336 (tmtp) cc_final: 0.4827 (mmpt) REVERT: B 320 SER cc_start: 0.8553 (t) cc_final: 0.8330 (m) REVERT: B 325 GLU cc_start: 0.7336 (tp30) cc_final: 0.7063 (tp30) REVERT: B 433 GLN cc_start: 0.7476 (tp40) cc_final: 0.7227 (tm-30) REVERT: B 777 MET cc_start: 0.8340 (tpt) cc_final: 0.7991 (mmm) REVERT: C 286 ASP cc_start: 0.7772 (m-30) cc_final: 0.7375 (m-30) REVERT: C 635 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8021 (ppt170) REVERT: C 757 GLN cc_start: 0.7130 (tt0) cc_final: 0.6723 (mt0) REVERT: D 778 GLU cc_start: 0.7977 (pt0) cc_final: 0.7453 (tp30) REVERT: D 781 GLU cc_start: 0.7285 (mp0) cc_final: 0.6945 (mp0) REVERT: E 282 LYS cc_start: 0.7494 (tttt) cc_final: 0.7289 (tmtm) REVERT: E 318 MET cc_start: 0.7298 (ttp) cc_final: 0.6964 (ttt) REVERT: E 320 SER cc_start: 0.7903 (t) cc_final: 0.7575 (m) REVERT: E 382 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7509 (mmt180) REVERT: E 416 LYS cc_start: 0.7629 (mttt) cc_final: 0.7183 (mmtt) REVERT: E 472 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6948 (t) REVERT: E 475 GLN cc_start: 0.5854 (mt0) cc_final: 0.5449 (mm-40) REVERT: E 477 ARG cc_start: 0.7279 (mtm180) cc_final: 0.6855 (mtm110) REVERT: E 526 LEU cc_start: 0.8165 (tp) cc_final: 0.7875 (tp) REVERT: E 741 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: E 750 ARG cc_start: 0.5244 (ttp80) cc_final: 0.4118 (tpt90) REVERT: F 424 GLN cc_start: 0.7450 (tp40) cc_final: 0.6692 (tt0) REVERT: F 601 ASP cc_start: 0.6999 (p0) cc_final: 0.6433 (t0) REVERT: F 603 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6249 (ptm) REVERT: F 678 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6121 (tm) REVERT: F 740 MET cc_start: 0.6875 (ttp) cc_final: 0.6294 (tmm) REVERT: F 754 GLN cc_start: 0.6882 (mt0) cc_final: 0.6213 (pp30) REVERT: G 17 LEU cc_start: 0.8035 (mp) cc_final: 0.7806 (mp) outliers start: 58 outliers final: 24 residues processed: 419 average time/residue: 1.7063 time to fit residues: 802.5374 Evaluate side-chains 364 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 298 optimal weight: 50.0000 chunk 246 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN E 502 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24279 Z= 0.257 Angle : 0.528 8.629 32873 Z= 0.262 Chirality : 0.042 0.198 3762 Planarity : 0.004 0.049 4214 Dihedral : 11.098 99.209 3655 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 2.96 % Allowed : 12.97 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 3006 helix: 0.69 (0.13), residues: 1584 sheet: 0.47 (0.27), residues: 370 loop : 0.61 (0.21), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 466 HIS 0.004 0.001 HIS C 254 PHE 0.016 0.002 PHE E 527 TYR 0.012 0.001 TYR B 406 ARG 0.009 0.001 ARG C 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 345 time to evaluate : 2.777 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 371 MET cc_start: 0.8874 (mtt) cc_final: 0.8445 (mtt) REVERT: A 401 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8431 (tptt) REVERT: A 735 ASP cc_start: 0.8588 (m-30) cc_final: 0.8215 (m-30) REVERT: A 796 LYS cc_start: 0.5369 (tmtp) cc_final: 0.4903 (mmpt) REVERT: B 320 SER cc_start: 0.8482 (t) cc_final: 0.8278 (m) REVERT: B 325 GLU cc_start: 0.7407 (tp30) cc_final: 0.7042 (tp30) REVERT: B 433 GLN cc_start: 0.7498 (tp40) cc_final: 0.7282 (tm-30) REVERT: B 777 MET cc_start: 0.8379 (tpt) cc_final: 0.8049 (tpt) REVERT: C 286 ASP cc_start: 0.7622 (m-30) cc_final: 0.7206 (m-30) REVERT: C 757 GLN cc_start: 0.7100 (tt0) cc_final: 0.6701 (mt0) REVERT: D 217 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6476 (mt-10) REVERT: D 330 MET cc_start: 0.8888 (mtp) cc_final: 0.8591 (mtm) REVERT: D 533 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7700 (mptp) REVERT: D 778 GLU cc_start: 0.8115 (pt0) cc_final: 0.7532 (tp30) REVERT: D 781 GLU cc_start: 0.7468 (mp0) cc_final: 0.7087 (mp0) REVERT: E 318 MET cc_start: 0.7300 (ttp) cc_final: 0.6987 (ttt) REVERT: E 416 LYS cc_start: 0.7487 (mttt) cc_final: 0.6974 (mmtt) REVERT: E 475 GLN cc_start: 0.5819 (mt0) cc_final: 0.5355 (mm-40) REVERT: E 526 LEU cc_start: 0.8179 (tp) cc_final: 0.7909 (tp) REVERT: E 567 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7280 (tptt) REVERT: E 639 TYR cc_start: 0.7857 (m-80) cc_final: 0.7523 (m-80) REVERT: E 741 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: F 424 GLN cc_start: 0.7502 (tp40) cc_final: 0.6710 (tt0) REVERT: F 601 ASP cc_start: 0.6877 (p0) cc_final: 0.6357 (t0) REVERT: F 603 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6545 (ptm) REVERT: F 678 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6076 (tm) REVERT: F 740 MET cc_start: 0.7034 (ttp) cc_final: 0.6748 (tmm) REVERT: F 741 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: F 754 GLN cc_start: 0.7008 (mt0) cc_final: 0.6290 (pp30) REVERT: G 17 LEU cc_start: 0.8121 (mp) cc_final: 0.7870 (mp) outliers start: 75 outliers final: 32 residues processed: 385 average time/residue: 1.6515 time to fit residues: 716.7169 Evaluate side-chains 361 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 321 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain F residue 775 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 277 optimal weight: 30.0000 chunk 293 optimal weight: 30.0000 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 GLN E 412 GLN E 502 HIS F 557 ASN ** F 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24279 Z= 0.209 Angle : 0.510 9.005 32873 Z= 0.251 Chirality : 0.042 0.271 3762 Planarity : 0.003 0.039 4214 Dihedral : 10.901 97.096 3652 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 2.72 % Allowed : 14.00 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.99 (0.16), residues: 3006 helix: 0.91 (0.13), residues: 1574 sheet: 0.39 (0.27), residues: 369 loop : 0.63 (0.21), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 466 HIS 0.003 0.001 HIS C 242 PHE 0.018 0.001 PHE E 527 TYR 0.009 0.001 TYR B 406 ARG 0.012 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 332 time to evaluate : 2.739 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6390 (mmp80) cc_final: 0.6112 (mmp80) REVERT: A 355 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 401 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8438 (tptt) REVERT: A 560 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8693 (mttp) REVERT: A 735 ASP cc_start: 0.8547 (m-30) cc_final: 0.8167 (m-30) REVERT: A 796 LYS cc_start: 0.5725 (tmtp) cc_final: 0.5157 (mmpt) REVERT: B 320 SER cc_start: 0.8448 (t) cc_final: 0.8248 (m) REVERT: B 325 GLU cc_start: 0.7389 (tp30) cc_final: 0.7034 (tp30) REVERT: B 335 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: B 777 MET cc_start: 0.8341 (tpt) cc_final: 0.7993 (mmm) REVERT: C 286 ASP cc_start: 0.7652 (m-30) cc_final: 0.7382 (m-30) REVERT: D 217 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: D 290 GLU cc_start: 0.7444 (tt0) cc_final: 0.7186 (tt0) REVERT: D 330 MET cc_start: 0.8885 (mtp) cc_final: 0.8598 (mtm) REVERT: D 533 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7732 (mptp) REVERT: D 778 GLU cc_start: 0.8118 (pt0) cc_final: 0.7485 (tp30) REVERT: D 781 GLU cc_start: 0.7526 (mp0) cc_final: 0.7190 (mp0) REVERT: E 318 MET cc_start: 0.7264 (ttp) cc_final: 0.6965 (ttt) REVERT: E 526 LEU cc_start: 0.8160 (tp) cc_final: 0.7935 (tp) REVERT: E 550 LEU cc_start: 0.8336 (tp) cc_final: 0.8134 (tt) REVERT: E 567 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7233 (tptt) REVERT: E 639 TYR cc_start: 0.7841 (m-80) cc_final: 0.7505 (m-80) REVERT: E 741 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7121 (mm-40) REVERT: F 424 GLN cc_start: 0.7438 (tp40) cc_final: 0.6621 (tt0) REVERT: F 601 ASP cc_start: 0.6671 (p0) cc_final: 0.6347 (t0) REVERT: F 603 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6634 (ptm) REVERT: F 678 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.6059 (tm) REVERT: F 740 MET cc_start: 0.6959 (ttp) cc_final: 0.6755 (tmm) REVERT: F 741 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6913 (tp40) REVERT: F 754 GLN cc_start: 0.7017 (mt0) cc_final: 0.6282 (pp30) REVERT: G 17 LEU cc_start: 0.8087 (mp) cc_final: 0.7829 (mp) outliers start: 69 outliers final: 36 residues processed: 367 average time/residue: 1.6434 time to fit residues: 681.5334 Evaluate side-chains 363 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 317 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 604 ASP Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 250 optimal weight: 0.4980 chunk 203 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 263 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 523 ASN E 412 GLN E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN ** F 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24279 Z= 0.150 Angle : 0.480 8.582 32873 Z= 0.236 Chirality : 0.041 0.199 3762 Planarity : 0.003 0.036 4214 Dihedral : 10.489 95.085 3652 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 2.60 % Allowed : 14.43 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.22 (0.16), residues: 3006 helix: 1.13 (0.13), residues: 1590 sheet: 0.49 (0.27), residues: 369 loop : 0.67 (0.21), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 500 HIS 0.003 0.001 HIS C 242 PHE 0.012 0.001 PHE E 527 TYR 0.008 0.001 TYR C 235 ARG 0.011 0.000 ARG E 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 348 time to evaluate : 3.026 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6435 (mmp80) cc_final: 0.6158 (tpm170) REVERT: A 355 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 359 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7496 (mm) REVERT: A 735 ASP cc_start: 0.8523 (m-30) cc_final: 0.8137 (m-30) REVERT: A 796 LYS cc_start: 0.5741 (tmtp) cc_final: 0.5179 (mmpt) REVERT: B 325 GLU cc_start: 0.7347 (tp30) cc_final: 0.7012 (tp30) REVERT: B 777 MET cc_start: 0.8353 (tpt) cc_final: 0.8065 (mmm) REVERT: C 755 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6883 (ttm170) REVERT: D 217 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6096 (mt-10) REVERT: D 330 MET cc_start: 0.8886 (mtp) cc_final: 0.8614 (mtm) REVERT: D 533 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7746 (mptp) REVERT: E 234 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7751 (ttp-110) REVERT: E 318 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6942 (ttt) REVERT: E 341 LYS cc_start: 0.8298 (mptt) cc_final: 0.8087 (mmmt) REVERT: E 526 LEU cc_start: 0.8200 (tp) cc_final: 0.7886 (tp) REVERT: E 567 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7576 (tptp) REVERT: E 720 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6939 (pp20) REVERT: F 424 GLN cc_start: 0.7431 (tp40) cc_final: 0.6634 (tt0) REVERT: F 601 ASP cc_start: 0.6791 (p0) cc_final: 0.6313 (t0) REVERT: F 603 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6720 (ptm) REVERT: F 741 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6463 (tp40) REVERT: F 754 GLN cc_start: 0.6963 (mt0) cc_final: 0.6080 (pt0) REVERT: F 786 GLU cc_start: 0.5655 (mp0) cc_final: 0.4871 (mt-10) REVERT: G 17 LEU cc_start: 0.7962 (mp) cc_final: 0.7724 (mp) outliers start: 66 outliers final: 33 residues processed: 388 average time/residue: 1.6236 time to fit residues: 711.3513 Evaluate side-chains 353 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 718 ASP Chi-restraints excluded: chain E residue 720 GLU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 604 ASP Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 678 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 294 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 overall best weight: 2.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 412 GLN E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN F 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24279 Z= 0.196 Angle : 0.509 15.800 32873 Z= 0.247 Chirality : 0.041 0.156 3762 Planarity : 0.003 0.039 4214 Dihedral : 10.472 88.518 3651 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 2.56 % Allowed : 15.42 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 3006 helix: 1.17 (0.13), residues: 1589 sheet: 0.40 (0.27), residues: 377 loop : 0.74 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 219 HIS 0.003 0.001 HIS C 242 PHE 0.012 0.001 PHE C 423 TYR 0.009 0.001 TYR B 406 ARG 0.012 0.001 ARG E 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 318 time to evaluate : 2.772 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6434 (mmp80) cc_final: 0.6184 (tpm170) REVERT: A 355 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7290 (mp) REVERT: A 560 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8681 (mttp) REVERT: A 735 ASP cc_start: 0.8536 (m-30) cc_final: 0.8148 (m-30) REVERT: A 795 GLU cc_start: 0.7324 (pp20) cc_final: 0.7104 (pp20) REVERT: A 796 LYS cc_start: 0.5797 (tmtp) cc_final: 0.5186 (mmpt) REVERT: B 325 GLU cc_start: 0.7388 (tp30) cc_final: 0.7037 (tp30) REVERT: B 335 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: B 777 MET cc_start: 0.8360 (tpt) cc_final: 0.8081 (mmm) REVERT: C 231 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7337 (ptm) REVERT: D 217 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: D 330 MET cc_start: 0.8860 (mtp) cc_final: 0.8660 (mtm) REVERT: D 533 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7757 (mptp) REVERT: D 778 GLU cc_start: 0.7988 (pt0) cc_final: 0.7524 (tp30) REVERT: E 234 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7818 (ttp-110) REVERT: E 318 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6960 (ttt) REVERT: E 567 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7617 (tptp) REVERT: E 720 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7001 (pp20) REVERT: F 424 GLN cc_start: 0.7419 (tp40) cc_final: 0.6604 (tt0) REVERT: F 601 ASP cc_start: 0.6741 (p0) cc_final: 0.6282 (t0) REVERT: F 603 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6751 (ptm) REVERT: F 749 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: F 754 GLN cc_start: 0.6966 (mt0) cc_final: 0.6105 (pt0) REVERT: G 17 LEU cc_start: 0.7990 (mp) cc_final: 0.7759 (mp) outliers start: 65 outliers final: 37 residues processed: 353 average time/residue: 1.6459 time to fit residues: 654.8176 Evaluate side-chains 352 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 304 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 720 GLU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 0.0170 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 412 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN F 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24279 Z= 0.143 Angle : 0.497 12.747 32873 Z= 0.240 Chirality : 0.041 0.160 3762 Planarity : 0.003 0.044 4214 Dihedral : 10.117 80.620 3651 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 2.37 % Allowed : 16.01 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.46 (0.16), residues: 3006 helix: 1.38 (0.13), residues: 1582 sheet: 0.54 (0.27), residues: 369 loop : 0.72 (0.21), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 219 HIS 0.002 0.001 HIS C 242 PHE 0.010 0.001 PHE D 220 TYR 0.009 0.001 TYR A 752 ARG 0.013 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 323 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 560 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8688 (mttp) REVERT: A 735 ASP cc_start: 0.8503 (m-30) cc_final: 0.8109 (m-30) REVERT: A 795 GLU cc_start: 0.7200 (pp20) cc_final: 0.6952 (pp20) REVERT: A 796 LYS cc_start: 0.5781 (tmtp) cc_final: 0.5216 (mmpt) REVERT: B 325 GLU cc_start: 0.7298 (tp30) cc_final: 0.6978 (tp30) REVERT: B 777 MET cc_start: 0.8355 (tpt) cc_final: 0.8023 (mmm) REVERT: C 231 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7215 (ptm) REVERT: C 526 LEU cc_start: 0.9023 (tp) cc_final: 0.8643 (tp) REVERT: C 735 ASP cc_start: 0.8191 (m-30) cc_final: 0.7936 (m-30) REVERT: C 755 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6893 (ttm170) REVERT: D 330 MET cc_start: 0.8879 (mtp) cc_final: 0.8602 (mtm) REVERT: D 533 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7746 (mptp) REVERT: D 778 GLU cc_start: 0.7916 (pt0) cc_final: 0.7473 (tp30) REVERT: E 234 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7850 (ttp-110) REVERT: E 318 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6901 (ttt) REVERT: E 398 GLU cc_start: 0.7647 (tt0) cc_final: 0.7275 (mt-10) REVERT: E 567 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7583 (tptp) REVERT: E 639 TYR cc_start: 0.7758 (m-80) cc_final: 0.7519 (m-80) REVERT: E 720 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: F 424 GLN cc_start: 0.7461 (tp40) cc_final: 0.6650 (tt0) REVERT: F 528 THR cc_start: 0.6220 (OUTLIER) cc_final: 0.5910 (p) REVERT: F 601 ASP cc_start: 0.6756 (p0) cc_final: 0.6312 (t0) REVERT: F 603 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6797 (ptm) REVERT: F 754 GLN cc_start: 0.6967 (mt0) cc_final: 0.6124 (pt0) REVERT: F 786 GLU cc_start: 0.5273 (mp0) cc_final: 0.4535 (mt-10) REVERT: G 17 LEU cc_start: 0.7909 (mp) cc_final: 0.7688 (mp) outliers start: 60 outliers final: 31 residues processed: 352 average time/residue: 1.6832 time to fit residues: 667.9656 Evaluate side-chains 344 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 304 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 720 GLU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 88 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN F 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24279 Z= 0.148 Angle : 0.498 12.179 32873 Z= 0.239 Chirality : 0.041 0.158 3762 Planarity : 0.003 0.045 4214 Dihedral : 9.895 79.125 3651 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 17.03 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.57 (0.16), residues: 3006 helix: 1.45 (0.13), residues: 1588 sheet: 0.53 (0.27), residues: 377 loop : 0.81 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 541 HIS 0.002 0.001 HIS A 242 PHE 0.011 0.001 PHE A 288 TYR 0.007 0.001 TYR B 406 ARG 0.014 0.000 ARG E 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 328 time to evaluate : 2.928 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 474 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: A 560 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: A 735 ASP cc_start: 0.8509 (m-30) cc_final: 0.8117 (m-30) REVERT: A 795 GLU cc_start: 0.7204 (pp20) cc_final: 0.6947 (pp20) REVERT: A 796 LYS cc_start: 0.5825 (tmtp) cc_final: 0.5229 (mmpt) REVERT: B 325 GLU cc_start: 0.7326 (tp30) cc_final: 0.7000 (tp30) REVERT: B 333 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7973 (pt) REVERT: B 335 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7251 (mp-120) REVERT: B 777 MET cc_start: 0.8373 (tpt) cc_final: 0.8116 (mmm) REVERT: C 231 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7332 (ptm) REVERT: C 735 ASP cc_start: 0.8190 (m-30) cc_final: 0.7920 (m-30) REVERT: C 755 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6895 (ttm170) REVERT: D 330 MET cc_start: 0.8876 (mtp) cc_final: 0.8612 (mtm) REVERT: D 533 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7735 (mptp) REVERT: D 778 GLU cc_start: 0.7908 (pt0) cc_final: 0.7491 (tp30) REVERT: E 318 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6968 (ttt) REVERT: E 382 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7592 (mpt-90) REVERT: E 398 GLU cc_start: 0.7652 (tt0) cc_final: 0.7289 (mt-10) REVERT: E 567 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7573 (tptp) REVERT: E 718 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: E 741 GLN cc_start: 0.7523 (tp40) cc_final: 0.7045 (mm-40) REVERT: F 424 GLN cc_start: 0.7524 (tp40) cc_final: 0.6730 (tt0) REVERT: F 528 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5878 (p) REVERT: F 601 ASP cc_start: 0.6733 (p0) cc_final: 0.6233 (t0) REVERT: F 603 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6752 (ptm) REVERT: F 749 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: F 754 GLN cc_start: 0.6994 (mt0) cc_final: 0.6151 (pt0) REVERT: F 786 GLU cc_start: 0.5415 (mp0) cc_final: 0.4589 (mt-10) REVERT: G 17 LEU cc_start: 0.7855 (mp) cc_final: 0.7647 (mp) outliers start: 61 outliers final: 32 residues processed: 360 average time/residue: 1.6884 time to fit residues: 683.7438 Evaluate side-chains 350 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 305 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 718 ASP Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 30.0000 chunk 280 optimal weight: 40.0000 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 246 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 272 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 335 GLN E 502 HIS F 433 GLN F 557 ASN F 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 24279 Z= 0.276 Angle : 0.678 59.197 32873 Z= 0.365 Chirality : 0.043 0.194 3762 Planarity : 0.004 0.068 4214 Dihedral : 9.905 78.967 3651 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.09 % Allowed : 17.55 % Favored : 80.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.14 % 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: 1.52 (0.16), residues: 3006 helix: 1.40 (0.13), residues: 1588 sheet: 0.54 (0.27), residues: 377 loop : 0.79 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 780 HIS 0.003 0.001 HIS C 242 PHE 0.030 0.001 PHE D 423 TYR 0.008 0.001 TYR B 406 ARG 0.063 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 309 time to evaluate : 2.838 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 474 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: A 560 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8690 (mttp) REVERT: A 735 ASP cc_start: 0.8521 (m-30) cc_final: 0.8127 (m-30) REVERT: A 795 GLU cc_start: 0.7213 (pp20) cc_final: 0.6949 (pp20) REVERT: A 796 LYS cc_start: 0.5833 (tmtp) cc_final: 0.5235 (mmpt) REVERT: B 325 GLU cc_start: 0.7345 (tp30) cc_final: 0.7015 (tp30) REVERT: B 333 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7985 (pt) REVERT: B 777 MET cc_start: 0.8366 (tpt) cc_final: 0.8102 (mmm) REVERT: C 231 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7348 (ptm) REVERT: C 735 ASP cc_start: 0.8199 (m-30) cc_final: 0.7929 (m-30) REVERT: C 755 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6898 (ttm170) REVERT: D 330 MET cc_start: 0.8884 (mtp) cc_final: 0.8623 (mtm) REVERT: D 533 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7740 (mptp) REVERT: D 778 GLU cc_start: 0.7909 (pt0) cc_final: 0.7499 (tp30) REVERT: E 318 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6968 (ttt) REVERT: E 398 GLU cc_start: 0.7653 (tt0) cc_final: 0.7290 (mt-10) REVERT: E 567 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7582 (tptp) REVERT: E 741 GLN cc_start: 0.7592 (tp40) cc_final: 0.7278 (mm-40) REVERT: F 424 GLN cc_start: 0.7533 (tp40) cc_final: 0.6733 (tt0) REVERT: F 528 THR cc_start: 0.6210 (OUTLIER) cc_final: 0.5882 (p) REVERT: F 601 ASP cc_start: 0.6696 (p0) cc_final: 0.6230 (t0) REVERT: F 603 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6755 (ptm) REVERT: F 749 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: F 754 GLN cc_start: 0.6999 (mt0) cc_final: 0.6166 (pt0) REVERT: F 786 GLU cc_start: 0.5503 (mp0) cc_final: 0.4760 (mt-10) REVERT: G 17 LEU cc_start: 0.7876 (mp) cc_final: 0.7653 (mp) outliers start: 53 outliers final: 36 residues processed: 334 average time/residue: 1.6950 time to fit residues: 642.5507 Evaluate side-chains 349 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 302 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 603 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 302 optimal weight: 40.0000 chunk 278 optimal weight: 3.9990 chunk 241 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS F 433 GLN F 557 ASN F 741 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 24279 Z= 0.276 Angle : 0.678 59.197 32873 Z= 0.365 Chirality : 0.043 0.194 3762 Planarity : 0.004 0.068 4214 Dihedral : 9.905 78.967 3651 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 17.71 % Favored : 80.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.14 % 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: 1.52 (0.16), residues: 3006 helix: 1.40 (0.13), residues: 1588 sheet: 0.54 (0.27), residues: 377 loop : 0.79 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 780 HIS 0.003 0.001 HIS C 242 PHE 0.030 0.001 PHE D 423 TYR 0.008 0.001 TYR B 406 ARG 0.063 0.001 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 304 time to evaluate : 2.895 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 355 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 474 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: A 560 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8690 (mttp) REVERT: A 735 ASP cc_start: 0.8521 (m-30) cc_final: 0.8127 (m-30) REVERT: A 795 GLU cc_start: 0.7213 (pp20) cc_final: 0.6949 (pp20) REVERT: A 796 LYS cc_start: 0.5833 (tmtp) cc_final: 0.5235 (mmpt) REVERT: B 325 GLU cc_start: 0.7346 (tp30) cc_final: 0.7015 (tp30) REVERT: B 333 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7985 (pt) REVERT: B 777 MET cc_start: 0.8365 (tpt) cc_final: 0.8102 (mmm) REVERT: C 231 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7347 (ptm) REVERT: C 735 ASP cc_start: 0.8199 (m-30) cc_final: 0.7929 (m-30) REVERT: C 755 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6898 (ttm170) REVERT: D 330 MET cc_start: 0.8884 (mtp) cc_final: 0.8623 (mtm) REVERT: D 533 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7740 (mptp) REVERT: D 778 GLU cc_start: 0.7910 (pt0) cc_final: 0.7499 (tp30) REVERT: E 318 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6968 (ttt) REVERT: E 398 GLU cc_start: 0.7653 (tt0) cc_final: 0.7290 (mt-10) REVERT: E 567 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7582 (tptp) REVERT: E 741 GLN cc_start: 0.7597 (tp40) cc_final: 0.7278 (mm-40) REVERT: F 424 GLN cc_start: 0.7533 (tp40) cc_final: 0.6733 (tt0) REVERT: F 528 THR cc_start: 0.6211 (OUTLIER) cc_final: 0.5882 (p) REVERT: F 601 ASP cc_start: 0.6696 (p0) cc_final: 0.6230 (t0) REVERT: F 603 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6755 (ptm) REVERT: F 749 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: F 754 GLN cc_start: 0.6999 (mt0) cc_final: 0.6166 (pt0) REVERT: F 786 GLU cc_start: 0.5504 (mp0) cc_final: 0.4761 (mt-10) REVERT: G 17 LEU cc_start: 0.7876 (mp) cc_final: 0.7653 (mp) outliers start: 50 outliers final: 36 residues processed: 329 average time/residue: 1.6698 time to fit residues: 619.4531 Evaluate side-chains 348 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 301 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 603 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS F 433 GLN F 557 ASN F 741 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124981 restraints weight = 54169.071| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.12 r_work: 0.3203 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 24279 Z= 0.276 Angle : 0.678 59.197 32873 Z= 0.365 Chirality : 0.043 0.194 3762 Planarity : 0.004 0.068 4214 Dihedral : 9.905 78.967 3651 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 17.74 % Favored : 80.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.14 % 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: 1.52 (0.16), residues: 3006 helix: 1.40 (0.13), residues: 1588 sheet: 0.54 (0.27), residues: 377 loop : 0.79 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 780 HIS 0.003 0.001 HIS C 242 PHE 0.030 0.001 PHE D 423 TYR 0.008 0.001 TYR B 406 ARG 0.063 0.001 ARG A 362 =============================================================================== Job complete usr+sys time: 10245.33 seconds wall clock time: 184 minutes 58.16 seconds (11098.16 seconds total)