Starting phenix.real_space_refine on Fri Nov 21 00:46:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rax_4786/11_2025/6rax_4786.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 239 5.16 5 C 25619 2.51 5 N 7193 2.21 5 O 7875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 340 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40970 Number of models: 1 Model: "" Number of chains: 19 Chain: "2" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4788 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 28, 'TRANS': 576} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4879 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 22, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "4" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5013 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 26, 'TRANS': 599} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4864 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 592} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4986 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 608} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "7" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4964 Classifications: {'peptide': 636} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 611} Unresolved chain links: 5 Chain breaks: 2 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 19 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 424 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4575 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 14, 'TRANS': 552} Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1583 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1381 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1677 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.78, per 1000 atoms: 0.21 Number of scatterers: 40970 At special positions: 0 Unit cell: (214.92, 182.52, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 239 16.00 P 44 15.00 O 7875 8.00 N 7193 7.00 C 25619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.06 Simple disulfide: pdb=" SG CYS 6 152 " - pdb=" SG CYS 6 179 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 187 " - pdb=" SG CYS 7 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM40909 O3A ATP 5 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.9 seconds 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9610 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 35 sheets defined 36.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain '2' and resid 178 through 189 removed outlier: 3.732A pdb=" N ASN 2 182 " --> pdb=" O THR 2 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 2 189 " --> pdb=" O GLN 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 4.757A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 226 Processing helix chain '2' and resid 236 through 256 removed outlier: 3.947A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 260 Processing helix chain '2' and resid 283 through 287 removed outlier: 3.589A pdb=" N LEU 2 287 " --> pdb=" O LYS 2 284 " (cutoff:3.500A) Processing helix chain '2' and resid 455 through 460 removed outlier: 3.690A pdb=" N ILE 2 458 " --> pdb=" O ASP 2 455 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) Processing helix chain '2' and resid 462 through 466 Processing helix chain '2' and resid 473 through 484 removed outlier: 3.678A pdb=" N LYS 2 477 " --> pdb=" O HIS 2 473 " (cutoff:3.500A) Processing helix chain '2' and resid 516 through 525 removed outlier: 4.438A pdb=" N TYR 2 520 " --> pdb=" O GLN 2 516 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR 2 521 " --> pdb=" O PHE 2 517 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU 2 522 " --> pdb=" O LEU 2 518 " (cutoff:3.500A) Processing helix chain '2' and resid 550 through 554 removed outlier: 3.906A pdb=" N TRP 2 554 " --> pdb=" O SER 2 551 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 583 removed outlier: 3.606A pdb=" N ARG 2 582 " --> pdb=" O ASN 2 578 " (cutoff:3.500A) Processing helix chain '2' and resid 635 through 639 removed outlier: 3.739A pdb=" N ILE 2 638 " --> pdb=" O SER 2 635 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 668 Processing helix chain '2' and resid 693 through 707 removed outlier: 4.163A pdb=" N LEU 2 697 " --> pdb=" O PRO 2 693 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN 2 699 " --> pdb=" O ASP 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 718 through 731 removed outlier: 3.697A pdb=" N LYS 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) Processing helix chain '2' and resid 742 through 759 removed outlier: 3.728A pdb=" N ILE 2 748 " --> pdb=" O ILE 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 782 removed outlier: 4.551A pdb=" N VAL 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 795 Processing helix chain '3' and resid 7 through 18 removed outlier: 3.707A pdb=" N ASP 3 11 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 53 removed outlier: 3.963A pdb=" N LEU 3 51 " --> pdb=" O ASN 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 60 Processing helix chain '3' and resid 68 through 85 Processing helix chain '3' and resid 86 through 89 Processing helix chain '3' and resid 109 through 113 removed outlier: 4.173A pdb=" N LEU 3 113 " --> pdb=" O PRO 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 201 through 205 removed outlier: 4.436A pdb=" N LYS 3 204 " --> pdb=" O MET 3 201 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 223 removed outlier: 3.915A pdb=" N VAL 3 223 " --> pdb=" O ASP 3 220 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 4.189A pdb=" N LYS 3 286 " --> pdb=" O LYS 3 282 " (cutoff:3.500A) Processing helix chain '3' and resid 290 through 299 removed outlier: 4.062A pdb=" N LEU 3 298 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA 3 299 " --> pdb=" O SER 3 295 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 317 removed outlier: 4.792A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 345 through 349 removed outlier: 3.618A pdb=" N GLN 3 348 " --> pdb=" O ALA 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 393 through 397 Processing helix chain '3' and resid 412 through 424 removed outlier: 3.839A pdb=" N ALA 3 416 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) Processing helix chain '3' and resid 469 through 474 removed outlier: 3.684A pdb=" N ARG 3 473 " --> pdb=" O SER 3 469 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 502 removed outlier: 4.373A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 559 through 565 Processing helix chain '3' and resid 579 through 595 removed outlier: 3.842A pdb=" N ALA 3 583 " --> pdb=" O GLN 3 579 " (cutoff:3.500A) Processing helix chain '3' and resid 600 through 604 Processing helix chain '3' and resid 610 through 626 removed outlier: 3.554A pdb=" N THR 3 614 " --> pdb=" O ARG 3 610 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG 3 626 " --> pdb=" O HIS 3 622 " (cutoff:3.500A) Processing helix chain '3' and resid 632 through 646 removed outlier: 4.225A pdb=" N LEU 3 642 " --> pdb=" O ALA 3 638 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL 3 643 " --> pdb=" O ALA 3 639 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 174 Processing helix chain '4' and resid 177 through 182 Processing helix chain '4' and resid 194 through 205 Processing helix chain '4' and resid 216 through 220 removed outlier: 3.600A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR 4 220 " --> pdb=" O HIS 4 217 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 216 through 220' Processing helix chain '4' and resid 223 through 231 Processing helix chain '4' and resid 232 through 252 Proline residue: 4 238 - end of helix removed outlier: 3.647A pdb=" N ASP 4 241 " --> pdb=" O ILE 4 237 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 382 removed outlier: 3.607A pdb=" N VAL 4 382 " --> pdb=" O ASN 4 379 " (cutoff:3.500A) Processing helix chain '4' and resid 438 through 442 removed outlier: 3.987A pdb=" N HIS 4 441 " --> pdb=" O GLY 4 438 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE 4 442 " --> pdb=" O LYS 4 439 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 438 through 442' Processing helix chain '4' and resid 444 through 456 removed outlier: 3.617A pdb=" N LEU 4 450 " --> pdb=" O GLU 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 467 removed outlier: 3.901A pdb=" N LEU 4 464 " --> pdb=" O ILE 4 460 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA 4 465 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) Processing helix chain '4' and resid 475 through 477 No H-bonds generated for 'chain '4' and resid 475 through 477' Processing helix chain '4' and resid 478 through 487 removed outlier: 3.586A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN 4 485 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 527 removed outlier: 3.641A pdb=" N ASN 4 527 " --> pdb=" O GLN 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 564 through 568 Processing helix chain '4' and resid 588 through 596 Processing helix chain '4' and resid 641 through 646 removed outlier: 4.088A pdb=" N PHE 4 646 " --> pdb=" O LEU 4 642 " (cutoff:3.500A) Processing helix chain '4' and resid 660 through 675 removed outlier: 4.133A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL 4 669 " --> pdb=" O ALA 4 665 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR 4 672 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 695 removed outlier: 4.210A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 696 through 698 No H-bonds generated for 'chain '4' and resid 696 through 698' Processing helix chain '4' and resid 711 through 720 removed outlier: 6.787A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 734 through 749 Processing helix chain '4' and resid 757 through 769 removed outlier: 4.000A pdb=" N GLU 4 761 " --> pdb=" O LEU 4 757 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 32 removed outlier: 3.854A pdb=" N LYS 5 32 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 41 removed outlier: 4.316A pdb=" N ILE 5 38 " --> pdb=" O TYR 5 34 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG 5 39 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 60 removed outlier: 4.001A pdb=" N ASN 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 76 Processing helix chain '5' and resid 79 through 84 Processing helix chain '5' and resid 86 through 107 removed outlier: 4.229A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE 5 105 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 135 Processing helix chain '5' and resid 312 through 325 Processing helix chain '5' and resid 328 through 333 Processing helix chain '5' and resid 343 through 348 Processing helix chain '5' and resid 351 through 356 removed outlier: 3.824A pdb=" N PHE 5 355 " --> pdb=" O THR 5 351 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY 5 356 " --> pdb=" O CYS 5 352 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 351 through 356' Processing helix chain '5' and resid 383 through 394 removed outlier: 3.661A pdb=" N LEU 5 387 " --> pdb=" O ALA 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 462 removed outlier: 3.862A pdb=" N MET 5 459 " --> pdb=" O ILE 5 455 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN 5 461 " --> pdb=" O GLU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 489 through 496 removed outlier: 3.594A pdb=" N ASP 5 493 " --> pdb=" O PHE 5 489 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP 5 494 " --> pdb=" O GLY 5 490 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 535 Processing helix chain '5' and resid 554 through 566 Processing helix chain '5' and resid 574 through 598 removed outlier: 3.704A pdb=" N GLY 5 578 " --> pdb=" O SER 5 574 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 5 579 " --> pdb=" O GLU 5 575 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) Processing helix chain '5' and resid 608 through 627 removed outlier: 4.184A pdb=" N LEU 5 612 " --> pdb=" O THR 5 608 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG 5 617 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) Processing helix chain '5' and resid 632 through 650 removed outlier: 3.502A pdb=" N VAL 5 636 " --> pdb=" O THR 5 632 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU 5 638 " --> pdb=" O GLU 5 634 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA 5 639 " --> pdb=" O HIS 5 635 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 31 removed outlier: 3.599A pdb=" N GLU 6 31 " --> pdb=" O ASP 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 49 removed outlier: 4.325A pdb=" N SER 6 49 " --> pdb=" O ALA 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 66 removed outlier: 3.869A pdb=" N GLU 6 63 " --> pdb=" O PHE 6 59 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 74 Processing helix chain '6' and resid 76 through 94 Proline residue: 6 82 - end of helix removed outlier: 3.701A pdb=" N CYS 6 85 " --> pdb=" O TYR 6 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 6 94 " --> pdb=" O ASN 6 90 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 330 Processing helix chain '6' and resid 331 through 334 Processing helix chain '6' and resid 337 through 344 Processing helix chain '6' and resid 355 through 365 removed outlier: 5.381A pdb=" N LEU 6 361 " --> pdb=" O LYS 6 357 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU 6 362 " --> pdb=" O ARG 6 358 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN 6 363 " --> pdb=" O GLY 6 359 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN 6 364 " --> pdb=" O ILE 6 360 " (cutoff:3.500A) Processing helix chain '6' and resid 394 through 400 removed outlier: 4.115A pdb=" N LEU 6 398 " --> pdb=" O LYS 6 394 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN 6 400 " --> pdb=" O GLN 6 396 " (cutoff:3.500A) Processing helix chain '6' and resid 400 through 405 Processing helix chain '6' and resid 460 through 469 removed outlier: 4.037A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 507 through 512 Processing helix chain '6' and resid 516 through 522 Processing helix chain '6' and resid 533 through 545 removed outlier: 3.613A pdb=" N ASP 6 537 " --> pdb=" O ASN 6 533 " (cutoff:3.500A) Processing helix chain '6' and resid 560 through 571 Processing helix chain '6' and resid 580 through 585 Processing helix chain '6' and resid 585 through 597 Processing helix chain '6' and resid 610 through 626 Processing helix chain '6' and resid 633 through 652 removed outlier: 3.690A pdb=" N VAL 6 637 " --> pdb=" O LEU 6 633 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 19 Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 51 through 59 removed outlier: 3.722A pdb=" N LEU 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 65 through 70 removed outlier: 4.330A pdb=" N ASN 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 82 Processing helix chain '7' and resid 97 through 108 Processing helix chain '7' and resid 224 through 227 Processing helix chain '7' and resid 319 through 328 removed outlier: 4.196A pdb=" N GLU 7 325 " --> pdb=" O PRO 7 321 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 333 through 339 removed outlier: 3.733A pdb=" N ALA 7 337 " --> pdb=" O TYR 7 333 " (cutoff:3.500A) Processing helix chain '7' and resid 349 through 360 removed outlier: 4.588A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 7 358 " --> pdb=" O LEU 7 354 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 365 through 369 removed outlier: 3.713A pdb=" N GLY 7 368 " --> pdb=" O ARG 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.578A pdb=" N ARG 7 396 " --> pdb=" O GLY 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 414 removed outlier: 3.895A pdb=" N LEU 7 414 " --> pdb=" O GLY 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 453 through 460 removed outlier: 3.504A pdb=" N GLU 7 460 " --> pdb=" O THR 7 456 " (cutoff:3.500A) Processing helix chain '7' and resid 461 through 463 No H-bonds generated for 'chain '7' and resid 461 through 463' Processing helix chain '7' and resid 508 through 514 Processing helix chain '7' and resid 528 through 543 removed outlier: 3.896A pdb=" N LYS 7 535 " --> pdb=" O LEU 7 531 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS 7 536 " --> pdb=" O ARG 7 532 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR 7 539 " --> pdb=" O LYS 7 535 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 568 removed outlier: 3.635A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 7 568 " --> pdb=" O ASN 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 591 removed outlier: 4.375A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) Processing helix chain '7' and resid 604 through 621 removed outlier: 3.905A pdb=" N LEU 7 610 " --> pdb=" O LEU 7 606 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG 7 611 " --> pdb=" O LEU 7 607 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR 7 614 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 removed outlier: 3.632A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG 7 635 " --> pdb=" O ALA 7 631 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 7 641 " --> pdb=" O LEU 7 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 26 through 41 removed outlier: 3.550A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 126 through 130 removed outlier: 4.325A pdb=" N PHE A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.696A pdb=" N GLN A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 229 through 243 removed outlier: 4.533A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.715A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.923A pdb=" N SER A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.688A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 4.082A pdb=" N GLU A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.513A pdb=" N GLN A 340 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 4.038A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 422 through 449 removed outlier: 3.848A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.963A pdb=" N LEU A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.812A pdb=" N ALA A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 17 through 20 Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.851A pdb=" N PHE H 45 " --> pdb=" O ILE H 41 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 63 through 96 removed outlier: 3.951A pdb=" N ASN H 68 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 Processing helix chain 'L' and resid 6 through 11 Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.613A pdb=" N LYS L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 81 removed outlier: 5.156A pdb=" N LYS L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 101 removed outlier: 3.980A pdb=" N GLN L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 106 Processing helix chain 'L' and resid 111 through 131 removed outlier: 3.892A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 135 Processing helix chain 'L' and resid 149 through 154 removed outlier: 4.170A pdb=" N ILE L 153 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 149 through 154' Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.192A pdb=" N TYR L 162 " --> pdb=" O PRO L 158 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 174 through 177 removed outlier: 3.718A pdb=" N SER L 177 " --> pdb=" O ALA L 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 174 through 177' Processing helix chain 'M' and resid 57 through 62 removed outlier: 3.849A pdb=" N GLU M 61 " --> pdb=" O TYR M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 88 removed outlier: 4.090A pdb=" N LYS M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 Processing helix chain 'M' and resid 110 through 112 No H-bonds generated for 'chain 'M' and resid 110 through 112' Processing helix chain 'M' and resid 116 through 132 removed outlier: 3.889A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 171 removed outlier: 3.858A pdb=" N LEU M 156 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 4.435A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS N 51 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 4.043A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU N 80 " --> pdb=" O GLN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 115 Processing helix chain 'N' and resid 118 through 127 removed outlier: 3.627A pdb=" N GLN N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 153 Processing helix chain 'N' and resid 218 through 223 Processing sheet with id=AA1, first strand: chain '2' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain '2' and resid 296 through 298 removed outlier: 4.474A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 296 through 298 removed outlier: 4.474A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 2 379 " --> pdb=" O LEU 2 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 310 through 312 removed outlier: 4.077A pdb=" N ILE 2 310 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR 2 312 " --> pdb=" O GLY 2 322 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY 2 322 " --> pdb=" O TYR 2 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 397 through 399 Processing sheet with id=AA6, first strand: chain '2' and resid 505 through 506 removed outlier: 6.503A pdb=" N LEU 2 505 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3' and resid 135 through 136 removed outlier: 4.069A pdb=" N ARG 3 135 " --> pdb=" O HIS 3 193 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA 3 259 " --> pdb=" O VAL 3 217 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN 3 260 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL 3 235 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE 3 262 " --> pdb=" O GLN 3 233 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN 3 233 " --> pdb=" O ILE 3 262 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU 3 264 " --> pdb=" O ARG 3 231 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG 3 231 " --> pdb=" O LEU 3 264 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 140 through 142 Processing sheet with id=AA9, first strand: chain '3' and resid 322 through 323 removed outlier: 4.717A pdb=" N LYS 3 322 " --> pdb=" O LEU 3 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 317 through 319 removed outlier: 4.065A pdb=" N VAL 4 318 " --> pdb=" O ALA 4 305 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 305 " --> pdb=" O VAL 4 318 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG 4 341 " --> pdb=" O SER 4 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 355 through 357 Processing sheet with id=AB3, first strand: chain '4' and resid 391 through 394 removed outlier: 3.563A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 397 through 400 Processing sheet with id=AB5, first strand: chain '4' and resid 411 through 412 Processing sheet with id=AB6, first strand: chain '4' and resid 532 through 534 removed outlier: 6.396A pdb=" N GLN 4 533 " --> pdb=" O CYS 4 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 550 through 552 removed outlier: 4.174A pdb=" N THR 4 550 " --> pdb=" O VAL 4 559 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 4 559 " --> pdb=" O THR 4 550 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 600 through 601 Processing sheet with id=AB9, first strand: chain '5' and resid 64 through 65 removed outlier: 3.737A pdb=" N LEU 5 65 " --> pdb=" O GLN 5 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '5' and resid 164 through 165 removed outlier: 4.295A pdb=" N SER 5 164 " --> pdb=" O MET 5 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '5' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain '5' and resid 262 through 264 Processing sheet with id=AC4, first strand: chain '5' and resid 481 through 485 removed outlier: 4.208A pdb=" N GLY 5 378 " --> pdb=" O ALA 5 485 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET 5 513 " --> pdb=" O ASN 5 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 572 through 573 removed outlier: 7.588A pdb=" N ARG 5 572 " --> pdb=" O ALA 5 631 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '6' and resid 198 through 202 removed outlier: 3.846A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '6' and resid 241 through 242 removed outlier: 3.767A pdb=" N THR 6 241 " --> pdb=" O LEU 6 291 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 6 291 " --> pdb=" O THR 6 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '6' and resid 387 through 388 removed outlier: 6.656A pdb=" N VAL 6 387 " --> pdb=" O LEU 6 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '7' and resid 162 through 168 removed outlier: 9.378A pdb=" N LEU 7 298 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR 7 254 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA 7 300 " --> pdb=" O THR 7 254 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET 7 256 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ARG 7 302 " --> pdb=" O MET 7 256 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE 7 303 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '7' and resid 175 through 177 Processing sheet with id=AD2, first strand: chain '7' and resid 193 through 194 removed outlier: 3.593A pdb=" N ALA 7 180 " --> pdb=" O GLN 7 193 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 376 through 377 removed outlier: 3.660A pdb=" N CYS 7 442 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 417 through 418 Processing sheet with id=AD5, first strand: chain 'A' and resid 49 through 50 removed outlier: 9.693A pdb=" N VAL A 50 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU A 20 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 501 through 505 removed outlier: 3.707A pdb=" N ALA A 503 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 516 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 556 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 14 through 17 Processing sheet with id=AD8, first strand: chain 'N' and resid 183 through 184 1092 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.95 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13140 1.34 - 1.46: 9190 1.46 - 1.59: 18943 1.59 - 1.71: 83 1.71 - 1.84: 377 Bond restraints: 41733 Sorted by residual: bond pdb=" C4 ATP 3 901 " pdb=" C5 ATP 3 901 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP 5 801 " pdb=" C5 ATP 5 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP 5 801 " pdb=" C6 ATP 5 801 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.11e+01 bond pdb=" C5 ATP 2 901 " pdb=" C6 ATP 2 901 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 41728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 55991 5.50 - 10.99: 461 10.99 - 16.49: 38 16.49 - 21.98: 9 21.98 - 27.48: 3 Bond angle restraints: 56502 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 117.79 22.08 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP 5 801 " pdb=" O3B ATP 5 801 " pdb=" PG ATP 5 801 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 117.36 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP 5 801 " pdb=" O3A ATP 5 801 " pdb=" PB ATP 5 801 " ideal model delta sigma weight residual 136.83 117.38 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 ... (remaining 56497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 24623 34.93 - 69.86: 910 69.86 - 104.79: 75 104.79 - 139.72: 3 139.72 - 174.65: 1 Dihedral angle restraints: 25612 sinusoidal: 10807 harmonic: 14805 Sorted by residual: dihedral pdb=" CA ASP 7 382 " pdb=" C ASP 7 382 " pdb=" N PRO 7 383 " pdb=" CA PRO 7 383 " ideal model delta harmonic sigma weight residual -180.00 -119.40 -60.60 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA ILE 4 615 " pdb=" C ILE 4 615 " pdb=" N LEU 4 616 " pdb=" CA LEU 4 616 " ideal model delta harmonic sigma weight residual 180.00 136.47 43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 25609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6338 0.584 - 1.169: 3 1.169 - 1.753: 17 1.753 - 2.338: 3 2.338 - 2.922: 1 Chirality restraints: 6362 Sorted by residual: chirality pdb=" CB VAL 5 432 " pdb=" CA VAL 5 432 " pdb=" CG1 VAL 5 432 " pdb=" CG2 VAL 5 432 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.14e+02 chirality pdb=" CB ILE 2 585 " pdb=" CA ILE 2 585 " pdb=" CG1 ILE 2 585 " pdb=" CG2 ILE 2 585 " both_signs ideal model delta sigma weight residual False 2.64 0.66 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" CB VAL 2 463 " pdb=" CA VAL 2 463 " pdb=" CG1 VAL 2 463 " pdb=" CG2 VAL 2 463 " both_signs ideal model delta sigma weight residual False -2.63 -0.68 -1.95 2.00e-01 2.50e+01 9.50e+01 ... (remaining 6359 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 521 " -0.425 9.50e-02 1.11e+02 2.21e-01 1.78e+02 pdb=" NE ARG 6 521 " 0.105 2.00e-02 2.50e+03 pdb=" CZ ARG 6 521 " -0.210 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 521 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 521 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 5 199 " -0.100 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO 5 200 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO 5 200 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO 5 200 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 513 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO 4 514 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO 4 514 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO 4 514 " -0.066 5.00e-02 4.00e+02 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 8 2.03 - 2.74: 6121 2.74 - 3.46: 64089 3.46 - 4.18: 98377 4.18 - 4.90: 160140 Nonbonded interactions: 328735 Sorted by model distance: nonbonded pdb=" OG SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.308 3.040 nonbonded pdb=" CB SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.373 3.440 nonbonded pdb=" O ILE A 237 " pdb=" OG1 THR A 241 " model vdw 1.971 3.040 nonbonded pdb=" O GLU 2 278 " pdb=" OG1 THR 2 281 " model vdw 1.998 3.040 nonbonded pdb=" O GLU L 90 " pdb=" OG1 THR L 149 " model vdw 2.002 3.040 ... (remaining 328730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 37.900 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 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 : 0.012 0.891 41741 Z= 0.667 Angle : 1.462 27.476 56508 Z= 0.799 Chirality : 0.127 2.922 6362 Planarity : 0.009 0.221 7230 Dihedral : 18.186 174.646 15993 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 19.24 % Favored : 80.28 % Rotamer: Outliers : 6.70 % Allowed : 15.27 % Favored : 78.03 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.61 (0.09), residues: 5000 helix: -3.27 (0.09), residues: 1545 sheet: -4.59 (0.15), residues: 465 loop : -4.03 (0.10), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.215 0.003 ARG 6 521 TYR 0.063 0.004 TYR N 104 PHE 0.041 0.005 PHE M 17 TRP 0.029 0.005 TRP M 170 HIS 0.020 0.004 HIS M 115 Details of bonding type rmsd covalent geometry : bond 0.01135 (41733) covalent geometry : angle 1.45836 (56502) SS BOND : bond 0.01666 ( 3) SS BOND : angle 9.79356 ( 6) hydrogen bonds : bond 0.21269 ( 1089) hydrogen bonds : angle 8.98989 ( 3105) Misc. bond : bond 0.39829 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 961 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 212 MET cc_start: 0.7591 (mmp) cc_final: 0.5610 (ttp) REVERT: 2 271 SER cc_start: 0.5576 (OUTLIER) cc_final: 0.5199 (t) REVERT: 2 284 LYS cc_start: 0.6311 (pptt) cc_final: 0.5987 (tttm) REVERT: 2 553 GLU cc_start: 0.6522 (mp0) cc_final: 0.5208 (tp30) REVERT: 2 568 VAL cc_start: 0.4054 (OUTLIER) cc_final: 0.3693 (p) REVERT: 2 626 MET cc_start: -0.0253 (ttt) cc_final: -0.0504 (mtt) REVERT: 2 666 HIS cc_start: 0.8439 (t70) cc_final: 0.8231 (t70) REVERT: 2 722 LYS cc_start: 0.6548 (mptt) cc_final: 0.6282 (ptmm) REVERT: 2 752 GLU cc_start: 0.6432 (pt0) cc_final: 0.5847 (pt0) REVERT: 3 85 ASP cc_start: 0.8161 (t0) cc_final: 0.7773 (t0) REVERT: 3 221 ASP cc_start: 0.6922 (m-30) cc_final: 0.6636 (t0) REVERT: 3 226 CYS cc_start: 0.3352 (t) cc_final: 0.3119 (t) REVERT: 3 265 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7022 (pp) REVERT: 3 296 LYS cc_start: 0.6419 (mttt) cc_final: 0.5854 (pttt) REVERT: 3 348 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4223 (tp40) REVERT: 3 458 LYS cc_start: 0.6945 (tmmt) cc_final: 0.5784 (mmmt) REVERT: 3 470 LEU cc_start: 0.5901 (mp) cc_final: 0.5260 (pp) REVERT: 3 525 PHE cc_start: 0.5387 (m-10) cc_final: 0.5039 (m-80) REVERT: 3 572 MET cc_start: 0.7074 (mmp) cc_final: 0.6653 (mmp) REVERT: 3 641 GLU cc_start: 0.5762 (mt-10) cc_final: 0.5012 (tp30) REVERT: 4 188 ASN cc_start: 0.6025 (m-40) cc_final: 0.5664 (p0) REVERT: 4 193 GLN cc_start: 0.5552 (tt0) cc_final: 0.5059 (tm-30) REVERT: 4 278 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: 4 424 PHE cc_start: 0.6929 (m-80) cc_final: 0.6704 (m-80) REVERT: 4 558 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5592 (mm) REVERT: 4 590 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.4064 (m170) REVERT: 4 595 GLN cc_start: 0.8242 (mt0) cc_final: 0.7129 (mm-40) REVERT: 4 645 ARG cc_start: 0.2379 (OUTLIER) cc_final: 0.2095 (tmt-80) REVERT: 4 647 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: 4 653 LEU cc_start: 0.4993 (pt) cc_final: 0.4384 (tp) REVERT: 4 676 ARG cc_start: 0.3033 (pmt-80) cc_final: 0.1451 (ppt170) REVERT: 4 680 GLU cc_start: 0.1557 (pm20) cc_final: 0.0396 (mt-10) REVERT: 5 68 GLU cc_start: 0.5551 (pt0) cc_final: 0.5121 (pt0) REVERT: 5 71 ASP cc_start: 0.7275 (p0) cc_final: 0.6868 (p0) REVERT: 5 216 CYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6295 (p) REVERT: 5 239 HIS cc_start: 0.7775 (p90) cc_final: 0.7571 (p-80) REVERT: 5 241 GLN cc_start: 0.4793 (pt0) cc_final: 0.4508 (mm-40) REVERT: 5 257 ARG cc_start: 0.6559 (mtm180) cc_final: 0.6068 (ptp-110) REVERT: 5 307 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5137 (pmt170) REVERT: 5 360 LYS cc_start: 0.3016 (mmtt) cc_final: 0.2658 (mmtp) REVERT: 5 379 ASP cc_start: 0.7075 (t0) cc_final: 0.6691 (t0) REVERT: 5 402 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6696 (t) REVERT: 5 417 LYS cc_start: 0.7944 (pttt) cc_final: 0.7023 (mppt) REVERT: 5 443 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: 5 514 ILE cc_start: 0.4010 (mp) cc_final: 0.3768 (mp) REVERT: 5 588 MET cc_start: 0.6800 (tpp) cc_final: 0.5673 (tpp) REVERT: 5 641 ARG cc_start: 0.6202 (mmt180) cc_final: 0.5980 (mmm160) REVERT: 6 16 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6158 (tp30) REVERT: 6 55 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5032 (pt) REVERT: 6 90 ASN cc_start: 0.7782 (m110) cc_final: 0.7528 (m-40) REVERT: 6 116 LYS cc_start: 0.5981 (mmtt) cc_final: 0.5597 (ttmm) REVERT: 6 220 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6477 (mm) REVERT: 6 284 LEU cc_start: 0.2619 (OUTLIER) cc_final: 0.2226 (pp) REVERT: 6 296 GLN cc_start: 0.7603 (tp-100) cc_final: 0.6713 (tt0) REVERT: 6 309 MET cc_start: 0.2657 (mtp) cc_final: 0.1376 (tmm) REVERT: 6 325 GLU cc_start: 0.6290 (mp0) cc_final: 0.5212 (mp0) REVERT: 6 332 MET cc_start: 0.4115 (mpp) cc_final: 0.2237 (tpt) REVERT: 6 410 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.3111 (t80) REVERT: 6 537 ASP cc_start: 0.7255 (m-30) cc_final: 0.6939 (m-30) REVERT: 6 612 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: 6 639 GLU cc_start: 0.4315 (tt0) cc_final: 0.4033 (mt-10) REVERT: 7 57 GLU cc_start: 0.6852 (tt0) cc_final: 0.6315 (mp0) REVERT: 7 83 GLU cc_start: 0.5046 (mm-30) cc_final: 0.3981 (tp30) REVERT: 7 131 MET cc_start: 0.6273 (ptm) cc_final: 0.5900 (tmm) REVERT: 7 223 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8443 (tp-100) REVERT: 7 281 MET cc_start: 0.7784 (mtm) cc_final: 0.7117 (mtp) REVERT: 7 282 ARG cc_start: 0.6986 (tmt-80) cc_final: 0.5896 (ttm-80) REVERT: 7 419 MET cc_start: -0.4666 (ttp) cc_final: -0.5332 (mmt) REVERT: 7 494 ARG cc_start: 0.3790 (ptm-80) cc_final: 0.2558 (ttm170) REVERT: 7 527 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6026 (mmt180) REVERT: 7 536 HIS cc_start: 0.5355 (m90) cc_final: 0.5081 (m-70) REVERT: 7 556 MET cc_start: 0.2602 (ptm) cc_final: 0.1666 (tmm) REVERT: 7 589 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6991 (mtp85) REVERT: 7 634 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5874 (mt) REVERT: 7 635 ARG cc_start: 0.6370 (ptm-80) cc_final: 0.6074 (tpp-160) REVERT: A 53 MET cc_start: 0.4975 (mpp) cc_final: 0.4127 (ttp) REVERT: A 65 HIS cc_start: 0.8701 (m90) cc_final: 0.8426 (m170) REVERT: A 223 TRP cc_start: 0.6285 (t60) cc_final: 0.5816 (t60) REVERT: A 460 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 567 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5597 (tt) REVERT: H 16 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2668 (mp) REVERT: H 70 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7324 (tmm160) REVERT: H 88 ARG cc_start: 0.6762 (mmt180) cc_final: 0.5624 (mmt180) REVERT: L 119 ASP cc_start: 0.7719 (t70) cc_final: 0.7510 (t0) REVERT: N 60 THR cc_start: 0.7518 (p) cc_final: 0.7059 (m) REVERT: N 107 CYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4463 (m) REVERT: N 151 TYR cc_start: 0.4065 (t80) cc_final: 0.3626 (t80) outliers start: 297 outliers final: 120 residues processed: 1214 average time/residue: 0.2709 time to fit residues: 523.3979 Evaluate side-chains 785 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 642 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 307 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 381 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 442 THR Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 518 LEU Chi-restraints excluded: chain 2 residue 531 THR Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 565 ASP Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 605 LEU Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 743 HIS Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 256 VAL Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 301 SER Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 374 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 4 residue 237 ILE Chi-restraints excluded: chain 4 residue 276 SER Chi-restraints excluded: chain 4 residue 278 ASN Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 558 LEU Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 638 LEU Chi-restraints excluded: chain 4 residue 645 ARG Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 740 ILE Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 137 SER Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 313 SER Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 387 LEU Chi-restraints excluded: chain 5 residue 402 SER Chi-restraints excluded: chain 5 residue 441 ILE Chi-restraints excluded: chain 5 residue 443 GLU Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 464 ILE Chi-restraints excluded: chain 5 residue 502 ASP Chi-restraints excluded: chain 5 residue 536 VAL Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 398 LEU Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 451 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 612 GLN Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 269 ASP Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 356 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 634 LEU Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 CYS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 CYS Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 267 HIS 2 306 GLN 2 352 GLN 2 390 GLN 2 412 ASN 2 534 GLN 2 548 ASN 2 592 GLN 2 631 ASN 2 659 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 699 GLN 2 762 ASN 3 13 GLN 3 57 GLN 3 143 HIS 3 348 GLN 3 434 HIS 3 448 ASN 3 495 HIS 3 504 ASN 4 182 GLN 4 214 ASN 4 223 GLN 4 234 GLN 4 260 GLN 4 267 ASN 4 344 HIS 4 378 HIS 4 485 GLN 4 533 GLN 4 627 ASN 4 735 GLN 5 21 GLN 5 120 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN 5 373 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 462 GLN 5 486 ASN ** 5 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 134 GLN 6 383 ASN 6 533 ASN 6 612 GLN 7 42 HIS 7 193 GLN 7 214 ASN 7 347 HIS ** 7 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 645 ASN A 154 HIS A 229 ASN A 273 ASN A 312 GLN A 421 HIS A 467 HIS ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN H 48 ASN H 68 ASN H 109 GLN H 120 ASN H 121 ASN H 145 ASN L 55 GLN L 91 HIS L 147 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN N 153 HIS N 164 GLN N 214 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.274952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.262440 restraints weight = 74131.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.262389 restraints weight = 86668.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.261450 restraints weight = 60128.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.261371 restraints weight = 57893.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.261587 restraints weight = 51416.795| |-----------------------------------------------------------------------------| r_work (final): 0.5067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41741 Z= 0.170 Angle : 0.862 12.281 56508 Z= 0.441 Chirality : 0.050 0.287 6362 Planarity : 0.006 0.089 7230 Dihedral : 13.332 138.679 6220 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.66 % Favored : 87.32 % Rotamer: Outliers : 5.23 % Allowed : 18.84 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.10), residues: 5000 helix: -2.00 (0.11), residues: 1595 sheet: -3.77 (0.17), residues: 576 loop : -3.57 (0.10), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 521 TYR 0.041 0.002 TYR 3 16 PHE 0.031 0.002 PHE 7 229 TRP 0.027 0.003 TRP A 193 HIS 0.011 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00371 (41733) covalent geometry : angle 0.86220 (56502) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.56318 ( 6) hydrogen bonds : bond 0.05363 ( 1089) hydrogen bonds : angle 6.68663 ( 3105) Misc. bond : bond 0.00231 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 802 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 214 SER cc_start: 0.8150 (m) cc_final: 0.7827 (p) REVERT: 2 271 SER cc_start: 0.6376 (OUTLIER) cc_final: 0.5888 (t) REVERT: 2 389 ASP cc_start: 0.6084 (t70) cc_final: 0.5776 (t0) REVERT: 2 488 GLU cc_start: 0.4685 (mm-30) cc_final: 0.3935 (mm-30) REVERT: 2 605 LEU cc_start: 0.6729 (tp) cc_final: 0.6128 (tp) REVERT: 2 722 LYS cc_start: 0.6302 (mptt) cc_final: 0.6066 (mttp) REVERT: 2 752 GLU cc_start: 0.5239 (pt0) cc_final: 0.4558 (pt0) REVERT: 3 90 LYS cc_start: 0.6632 (mmtt) cc_final: 0.6046 (mmtt) REVERT: 3 91 MET cc_start: 0.6211 (mpp) cc_final: 0.5710 (tpt) REVERT: 3 190 TYR cc_start: 0.4753 (p90) cc_final: 0.4208 (p90) REVERT: 3 214 VAL cc_start: 0.2267 (OUTLIER) cc_final: 0.2015 (m) REVERT: 3 253 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5646 (t80) REVERT: 3 348 GLN cc_start: 0.5770 (OUTLIER) cc_final: 0.5337 (tp40) REVERT: 3 364 THR cc_start: 0.6068 (p) cc_final: 0.5565 (p) REVERT: 3 458 LYS cc_start: 0.6203 (tmmt) cc_final: 0.5388 (mmmt) REVERT: 3 459 THR cc_start: 0.5968 (OUTLIER) cc_final: 0.5658 (p) REVERT: 3 462 GLU cc_start: 0.6770 (tp30) cc_final: 0.6402 (tp30) REVERT: 4 211 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5524 (tp) REVERT: 4 247 MET cc_start: 0.3876 (tpp) cc_final: 0.2116 (tpp) REVERT: 4 250 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6299 (tt0) REVERT: 4 513 ASP cc_start: 0.6783 (m-30) cc_final: 0.6358 (p0) REVERT: 4 524 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.5237 (m-80) REVERT: 4 668 LEU cc_start: 0.7306 (mt) cc_final: 0.6797 (mt) REVERT: 4 680 GLU cc_start: 0.1819 (pm20) cc_final: 0.0789 (mt-10) REVERT: 5 40 THR cc_start: 0.7081 (m) cc_final: 0.6818 (t) REVERT: 5 71 ASP cc_start: 0.7312 (p0) cc_final: 0.7053 (p0) REVERT: 5 216 CYS cc_start: 0.5449 (OUTLIER) cc_final: 0.5228 (p) REVERT: 5 377 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7165 (pp) REVERT: 5 379 ASP cc_start: 0.7305 (t0) cc_final: 0.7064 (t0) REVERT: 5 513 MET cc_start: 0.2486 (mpp) cc_final: 0.1911 (pmm) REVERT: 6 80 ILE cc_start: 0.6490 (mt) cc_final: 0.5280 (mt) REVERT: 6 151 MET cc_start: 0.2428 (tmm) cc_final: 0.1939 (ttp) REVERT: 6 183 LYS cc_start: 0.5894 (mptt) cc_final: 0.4225 (tppt) REVERT: 6 284 LEU cc_start: 0.3662 (OUTLIER) cc_final: 0.2967 (pp) REVERT: 6 309 MET cc_start: 0.2188 (mtp) cc_final: 0.0365 (tmm) REVERT: 6 332 MET cc_start: 0.3729 (mpp) cc_final: 0.3325 (tpt) REVERT: 6 410 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3583 (t80) REVERT: 7 150 ARG cc_start: 0.6779 (ptm-80) cc_final: 0.6458 (ptm-80) REVERT: 7 167 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8139 (t) REVERT: 7 210 ASP cc_start: 0.4687 (t0) cc_final: 0.3423 (m-30) REVERT: 7 281 MET cc_start: 0.6239 (mtm) cc_final: 0.5918 (mtp) REVERT: 7 419 MET cc_start: -0.1369 (ttp) cc_final: -0.4160 (mmt) REVERT: 7 494 ARG cc_start: 0.4128 (ptm-80) cc_final: 0.2861 (ttm170) REVERT: 7 644 LEU cc_start: 0.4066 (pt) cc_final: 0.3477 (pp) REVERT: A 18 ARG cc_start: 0.6205 (ptp90) cc_final: 0.5474 (ptp-170) REVERT: A 53 MET cc_start: 0.4410 (mpp) cc_final: 0.3705 (mtm) REVERT: A 304 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7412 (ttp80) REVERT: A 422 LYS cc_start: 0.4306 (mmtt) cc_final: 0.3963 (mmmt) REVERT: H 78 LYS cc_start: 0.4799 (tptt) cc_final: 0.4483 (tptt) REVERT: H 113 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6197 (tp30) REVERT: H 198 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6212 (tt) REVERT: L 120 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7287 (mm) REVERT: L 151 LEU cc_start: 0.7067 (mp) cc_final: 0.6862 (tp) REVERT: M 46 LEU cc_start: 0.2625 (tt) cc_final: 0.2415 (mp) REVERT: M 113 ARG cc_start: 0.3616 (mmp-170) cc_final: 0.2673 (ttt180) REVERT: N 82 LYS cc_start: 0.5542 (mppt) cc_final: 0.4799 (pttm) REVERT: N 193 ILE cc_start: 0.4567 (OUTLIER) cc_final: 0.4343 (pt) outliers start: 232 outliers final: 96 residues processed: 976 average time/residue: 0.2658 time to fit residues: 414.8156 Evaluate side-chains 730 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 618 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 506 ILE Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 328 THR Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 459 THR Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 528 SER Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 508 LEU Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 281 MET Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 7 residue 5 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 130 optimal weight: 0.2980 chunk 191 optimal weight: 0.7980 chunk 340 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 418 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 467 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 444 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 267 HIS 2 436 GLN 2 659 GLN 2 666 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 694 GLN 3 233 GLN 3 438 ASN 4 620 ASN 4 656 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS 7 248 HIS 7 376 ASN 7 439 GLN ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN H 109 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN M 172 GLN N 117 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5187 r_free = 0.5187 target = 0.276018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.263700 restraints weight = 73888.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.263863 restraints weight = 83261.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.263929 restraints weight = 58477.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.263787 restraints weight = 50378.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.263818 restraints weight = 48098.639| |-----------------------------------------------------------------------------| r_work (final): 0.5085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41741 Z= 0.145 Angle : 0.774 11.916 56508 Z= 0.393 Chirality : 0.047 0.207 6362 Planarity : 0.006 0.075 7230 Dihedral : 12.274 143.901 6058 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.78 % Favored : 87.20 % Rotamer: Outliers : 4.99 % Allowed : 21.77 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.11), residues: 5000 helix: -1.47 (0.12), residues: 1652 sheet: -3.49 (0.18), residues: 554 loop : -3.37 (0.10), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 99 TYR 0.026 0.002 TYR 7 562 PHE 0.025 0.002 PHE 4 424 TRP 0.022 0.002 TRP M 170 HIS 0.008 0.001 HIS 5 117 Details of bonding type rmsd covalent geometry : bond 0.00313 (41733) covalent geometry : angle 0.77382 (56502) SS BOND : bond 0.00172 ( 3) SS BOND : angle 0.94495 ( 6) hydrogen bonds : bond 0.04590 ( 1089) hydrogen bonds : angle 6.06912 ( 3105) Misc. bond : bond 0.00134 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 693 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 214 SER cc_start: 0.7941 (m) cc_final: 0.7603 (p) REVERT: 2 232 PHE cc_start: 0.3664 (m-80) cc_final: 0.3024 (m-80) REVERT: 2 271 SER cc_start: 0.6264 (OUTLIER) cc_final: 0.5874 (t) REVERT: 2 389 ASP cc_start: 0.5833 (t70) cc_final: 0.5556 (t0) REVERT: 2 461 ARG cc_start: 0.6912 (ttm110) cc_final: 0.6258 (ttm170) REVERT: 2 488 GLU cc_start: 0.4905 (mm-30) cc_final: 0.4302 (mm-30) REVERT: 2 605 LEU cc_start: 0.6698 (tp) cc_final: 0.6089 (tp) REVERT: 2 670 LYS cc_start: 0.3888 (pttp) cc_final: 0.3654 (mttp) REVERT: 2 752 GLU cc_start: 0.5219 (pt0) cc_final: 0.4627 (pt0) REVERT: 3 233 GLN cc_start: 0.5581 (OUTLIER) cc_final: 0.5200 (mp10) REVERT: 3 253 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.5711 (t80) REVERT: 3 286 LYS cc_start: 0.4240 (tptt) cc_final: 0.3950 (tptp) REVERT: 3 348 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5113 (tp40) REVERT: 3 462 GLU cc_start: 0.6759 (tp30) cc_final: 0.6378 (tp30) REVERT: 4 211 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5532 (tp) REVERT: 4 513 ASP cc_start: 0.6836 (m-30) cc_final: 0.6618 (p0) REVERT: 4 524 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.5055 (m-80) REVERT: 4 680 GLU cc_start: 0.1679 (pm20) cc_final: 0.0745 (mt-10) REVERT: 5 40 THR cc_start: 0.7319 (m) cc_final: 0.6839 (t) REVERT: 5 417 LYS cc_start: 0.7946 (mppt) cc_final: 0.7590 (mptt) REVERT: 5 558 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5774 (t80) REVERT: 5 587 LEU cc_start: 0.7786 (pp) cc_final: 0.7583 (pp) REVERT: 6 151 MET cc_start: 0.1902 (OUTLIER) cc_final: 0.1288 (ttt) REVERT: 6 284 LEU cc_start: 0.3735 (OUTLIER) cc_final: 0.2954 (pp) REVERT: 6 288 MET cc_start: 0.7651 (tmm) cc_final: 0.7218 (tmm) REVERT: 6 309 MET cc_start: 0.2660 (mtp) cc_final: 0.2410 (tmm) REVERT: 6 410 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.3433 (t80) REVERT: 7 215 LYS cc_start: 0.1679 (OUTLIER) cc_final: 0.1057 (tttp) REVERT: 7 255 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6364 (pt) REVERT: 7 281 MET cc_start: 0.6308 (mtm) cc_final: 0.5980 (mtp) REVERT: 7 419 MET cc_start: -0.1251 (ttp) cc_final: -0.4022 (mmt) REVERT: 7 494 ARG cc_start: 0.4313 (ptm-80) cc_final: 0.3116 (ttm170) REVERT: A 53 MET cc_start: 0.4696 (mpp) cc_final: 0.4045 (mtm) REVERT: A 304 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6433 (tmm-80) REVERT: A 398 GLU cc_start: 0.5364 (tt0) cc_final: 0.5099 (tt0) REVERT: A 417 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6049 (mt) REVERT: A 422 LYS cc_start: 0.4372 (mmtt) cc_final: 0.3943 (mmmt) REVERT: A 434 LEU cc_start: 0.8202 (pp) cc_final: 0.7984 (tt) REVERT: A 507 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5460 (mt) REVERT: L 120 ILE cc_start: 0.8094 (tp) cc_final: 0.7085 (mm) REVERT: M 173 MET cc_start: 0.6320 (pmm) cc_final: 0.5874 (pmm) outliers start: 221 outliers final: 119 residues processed: 856 average time/residue: 0.2606 time to fit residues: 360.0574 Evaluate side-chains 732 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 598 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 210 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 788 MET Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 233 GLN Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 215 CYS Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 255 ILE Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 350 VAL Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 513 SER Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 164 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 237 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 158 optimal weight: 0.3980 chunk 201 optimal weight: 3.9990 chunk 188 optimal weight: 0.0030 chunk 272 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 chunk 423 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 233 GLN 4 386 GLN 4 677 HIS 5 115 HIS 5 256 ASN 5 334 GLN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 376 ASN 7 504 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN L 166 HIS ** M 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5199 r_free = 0.5199 target = 0.277659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.264995 restraints weight = 73549.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.265163 restraints weight = 82689.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.264409 restraints weight = 56404.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.264278 restraints weight = 55949.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.264384 restraints weight = 50991.932| |-----------------------------------------------------------------------------| r_work (final): 0.5084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41741 Z= 0.132 Angle : 0.742 12.944 56508 Z= 0.373 Chirality : 0.046 0.374 6362 Planarity : 0.005 0.067 7230 Dihedral : 11.846 154.003 6043 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.64 % Favored : 88.34 % Rotamer: Outliers : 4.62 % Allowed : 22.81 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.11), residues: 5000 helix: -1.15 (0.12), residues: 1665 sheet: -3.17 (0.19), residues: 564 loop : -3.29 (0.10), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 7 514 TYR 0.042 0.001 TYR 3 16 PHE 0.020 0.002 PHE M 17 TRP 0.016 0.002 TRP M 170 HIS 0.012 0.001 HIS 6 79 Details of bonding type rmsd covalent geometry : bond 0.00289 (41733) covalent geometry : angle 0.74215 (56502) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.72767 ( 6) hydrogen bonds : bond 0.04227 ( 1089) hydrogen bonds : angle 5.73867 ( 3105) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 674 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.6187 (mmt) cc_final: 0.5543 (mtp) REVERT: 2 232 PHE cc_start: 0.3507 (m-80) cc_final: 0.2779 (m-80) REVERT: 2 461 ARG cc_start: 0.6842 (ttm110) cc_final: 0.6191 (ttm170) REVERT: 2 488 GLU cc_start: 0.4817 (mm-30) cc_final: 0.4314 (mm-30) REVERT: 2 660 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7397 (tt) REVERT: 2 752 GLU cc_start: 0.5178 (pt0) cc_final: 0.4513 (pt0) REVERT: 3 121 MET cc_start: 0.5922 (mpp) cc_final: 0.4568 (ttt) REVERT: 3 201 MET cc_start: 0.5567 (mmm) cc_final: 0.5208 (mpp) REVERT: 3 233 GLN cc_start: 0.5907 (OUTLIER) cc_final: 0.5645 (mp10) REVERT: 3 241 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5795 (mp) REVERT: 3 253 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5608 (t80) REVERT: 3 348 GLN cc_start: 0.5793 (OUTLIER) cc_final: 0.4914 (tp40) REVERT: 3 364 THR cc_start: 0.4825 (OUTLIER) cc_final: 0.4439 (p) REVERT: 3 462 GLU cc_start: 0.6748 (tp30) cc_final: 0.6425 (tp30) REVERT: 3 564 LYS cc_start: 0.7390 (ttpt) cc_final: 0.6998 (tttt) REVERT: 3 572 MET cc_start: 0.3725 (mmp) cc_final: 0.2763 (mmp) REVERT: 4 513 ASP cc_start: 0.7040 (m-30) cc_final: 0.6724 (p0) REVERT: 4 524 TYR cc_start: 0.5401 (OUTLIER) cc_final: 0.5040 (m-80) REVERT: 4 680 GLU cc_start: 0.1566 (pm20) cc_final: 0.0611 (mt-10) REVERT: 5 51 ARG cc_start: 0.4151 (mtp85) cc_final: 0.3310 (mtp85) REVERT: 5 416 MET cc_start: 0.8123 (ppp) cc_final: 0.7880 (ppp) REVERT: 5 558 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5660 (t80) REVERT: 6 151 MET cc_start: 0.1680 (OUTLIER) cc_final: 0.0885 (ttt) REVERT: 6 161 ASN cc_start: 0.5251 (p0) cc_final: 0.5004 (p0) REVERT: 6 284 LEU cc_start: 0.3672 (OUTLIER) cc_final: 0.2947 (pp) REVERT: 6 410 TYR cc_start: 0.5108 (OUTLIER) cc_final: 0.3493 (t80) REVERT: 7 109 MET cc_start: 0.3733 (mtp) cc_final: 0.2619 (ttm) REVERT: 7 215 LYS cc_start: 0.1570 (OUTLIER) cc_final: 0.0837 (tttp) REVERT: 7 281 MET cc_start: 0.6310 (mtm) cc_final: 0.5980 (mtp) REVERT: 7 299 GLN cc_start: 0.6936 (tp40) cc_final: 0.6626 (tt0) REVERT: 7 494 ARG cc_start: 0.4282 (ptm-80) cc_final: 0.3037 (ptp-170) REVERT: 7 527 ARG cc_start: 0.6105 (mmt180) cc_final: 0.5580 (ttp80) REVERT: A 45 MET cc_start: 0.5179 (mpp) cc_final: 0.4655 (ptp) REVERT: A 53 MET cc_start: 0.4756 (mpp) cc_final: 0.4005 (mtm) REVERT: A 304 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6939 (tmm-80) REVERT: A 398 GLU cc_start: 0.5534 (tt0) cc_final: 0.5283 (tt0) REVERT: A 417 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6079 (mt) REVERT: A 507 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5446 (mp) REVERT: H 7 MET cc_start: 0.3821 (mtp) cc_final: 0.3447 (mmp) REVERT: H 113 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6877 (tp30) REVERT: L 120 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7576 (mm) REVERT: M 84 VAL cc_start: 0.6625 (m) cc_final: 0.6339 (p) REVERT: N 73 MET cc_start: 0.6452 (mmm) cc_final: 0.6210 (mmm) outliers start: 205 outliers final: 126 residues processed: 829 average time/residue: 0.2660 time to fit residues: 356.8439 Evaluate side-chains 741 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 599 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 577 MET Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 233 GLN Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 164 CYS Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 215 CYS Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 282 MET Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 5 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 513 SER Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 607 LEU Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 276 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 430 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 666 HIS 3 194 GLN 3 288 ASN 4 368 GLN 4 735 GLN 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 486 ASN 6 79 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 396 GLN 7 42 HIS ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 229 ASN A 444 GLN H 109 GLN L 166 HIS ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.273641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.260466 restraints weight = 73883.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.259509 restraints weight = 89971.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.260510 restraints weight = 81934.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.260157 restraints weight = 61977.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.260490 restraints weight = 60440.211| |-----------------------------------------------------------------------------| r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41741 Z= 0.141 Angle : 0.729 11.543 56508 Z= 0.368 Chirality : 0.046 0.208 6362 Planarity : 0.005 0.067 7230 Dihedral : 11.666 160.514 6033 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.58 % Favored : 87.40 % Rotamer: Outliers : 5.01 % Allowed : 23.73 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.11), residues: 5000 helix: -0.95 (0.13), residues: 1642 sheet: -3.03 (0.19), residues: 567 loop : -3.18 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 70 TYR 0.033 0.002 TYR 2 200 PHE 0.022 0.002 PHE 5 643 TRP 0.015 0.002 TRP M 170 HIS 0.016 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00315 (41733) covalent geometry : angle 0.72922 (56502) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.80439 ( 6) hydrogen bonds : bond 0.04152 ( 1089) hydrogen bonds : angle 5.62503 ( 3105) Misc. bond : bond 0.00087 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 643 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.6125 (mmt) cc_final: 0.5338 (mtp) REVERT: 2 364 GLN cc_start: 0.5082 (OUTLIER) cc_final: 0.4871 (tt0) REVERT: 2 461 ARG cc_start: 0.6930 (ttm110) cc_final: 0.6208 (ttm170) REVERT: 2 488 GLU cc_start: 0.5030 (mm-30) cc_final: 0.4451 (mm-30) REVERT: 2 605 LEU cc_start: 0.6898 (tp) cc_final: 0.6350 (tp) REVERT: 2 720 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7574 (tt) REVERT: 2 727 LEU cc_start: 0.2963 (tt) cc_final: 0.2425 (mp) REVERT: 2 752 GLU cc_start: 0.5234 (pt0) cc_final: 0.4592 (pt0) REVERT: 3 201 MET cc_start: 0.5544 (mmm) cc_final: 0.5116 (mpp) REVERT: 3 241 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6022 (mp) REVERT: 3 253 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5617 (t80) REVERT: 3 348 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5079 (tp40) REVERT: 3 564 LYS cc_start: 0.7437 (ttpt) cc_final: 0.7152 (tttt) REVERT: 4 173 MET cc_start: 0.5944 (mmm) cc_final: 0.5050 (ptm) REVERT: 4 513 ASP cc_start: 0.7045 (m-30) cc_final: 0.6829 (p0) REVERT: 4 524 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: 4 680 GLU cc_start: 0.1846 (pm20) cc_final: 0.0848 (mt-10) REVERT: 5 220 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: 5 245 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6537 (t0) REVERT: 5 416 MET cc_start: 0.8416 (ppp) cc_final: 0.8029 (ppp) REVERT: 5 468 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7652 (mmmt) REVERT: 5 558 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5002 (t80) REVERT: 5 562 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7628 (mp) REVERT: 6 151 MET cc_start: 0.1717 (OUTLIER) cc_final: 0.0925 (ttt) REVERT: 6 161 ASN cc_start: 0.5021 (p0) cc_final: 0.4688 (p0) REVERT: 6 190 GLU cc_start: 0.7098 (pm20) cc_final: 0.5771 (pt0) REVERT: 6 284 LEU cc_start: 0.3781 (OUTLIER) cc_final: 0.3079 (pp) REVERT: 6 410 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.3808 (t80) REVERT: 7 109 MET cc_start: 0.3777 (mtp) cc_final: 0.2747 (ttm) REVERT: 7 215 LYS cc_start: 0.1832 (OUTLIER) cc_final: 0.1186 (mtpt) REVERT: 7 281 MET cc_start: 0.6323 (mtm) cc_final: 0.5998 (mtp) REVERT: 7 299 GLN cc_start: 0.7117 (tp40) cc_final: 0.6804 (tt0) REVERT: 7 419 MET cc_start: -0.1349 (ttp) cc_final: -0.1825 (ttp) REVERT: 7 494 ARG cc_start: 0.4356 (ptm-80) cc_final: 0.3155 (ptp-170) REVERT: 7 527 ARG cc_start: 0.6066 (mmt180) cc_final: 0.5603 (ttp80) REVERT: A 45 MET cc_start: 0.5440 (mpp) cc_final: 0.5021 (ptp) REVERT: A 53 MET cc_start: 0.4768 (mpp) cc_final: 0.4060 (mtm) REVERT: A 101 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.4923 (m90) REVERT: A 304 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7047 (tmm-80) REVERT: A 507 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5549 (mp) REVERT: L 120 ILE cc_start: 0.8285 (tp) cc_final: 0.7720 (mm) REVERT: M 84 VAL cc_start: 0.6363 (m) cc_final: 0.6150 (p) outliers start: 222 outliers final: 139 residues processed: 813 average time/residue: 0.2561 time to fit residues: 336.9795 Evaluate side-chains 739 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 583 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 364 GLN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 164 CYS Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 19 optimal weight: 0.0170 chunk 402 optimal weight: 1.9990 chunk 485 optimal weight: 1.9990 chunk 436 optimal weight: 0.9980 chunk 494 optimal weight: 1.9990 chunk 459 optimal weight: 1.9990 chunk 468 optimal weight: 0.0050 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 overall best weight: 0.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 288 ASN 2 436 GLN 2 672 HIS 2 783 GLN 3 199 GLN 4 188 ASN ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS 6 134 GLN ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN H 109 GLN M 20 GLN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.272730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.259386 restraints weight = 73931.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.258781 restraints weight = 92103.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.259647 restraints weight = 76464.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.259326 restraints weight = 59729.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.259630 restraints weight = 57889.607| |-----------------------------------------------------------------------------| r_work (final): 0.5043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41741 Z= 0.136 Angle : 0.724 11.766 56508 Z= 0.365 Chirality : 0.045 0.181 6362 Planarity : 0.005 0.065 7230 Dihedral : 11.484 168.385 6022 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.02 % Favored : 87.96 % Rotamer: Outliers : 5.37 % Allowed : 24.27 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.11), residues: 5000 helix: -0.83 (0.13), residues: 1663 sheet: -2.77 (0.20), residues: 531 loop : -3.15 (0.10), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 5 589 TYR 0.028 0.002 TYR 4 252 PHE 0.022 0.002 PHE 5 643 TRP 0.017 0.002 TRP H 64 HIS 0.013 0.001 HIS 7 248 Details of bonding type rmsd covalent geometry : bond 0.00304 (41733) covalent geometry : angle 0.72413 (56502) SS BOND : bond 0.00101 ( 3) SS BOND : angle 0.76711 ( 6) hydrogen bonds : bond 0.04044 ( 1089) hydrogen bonds : angle 5.45553 ( 3105) Misc. bond : bond 0.00095 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 631 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 364 GLN cc_start: 0.5096 (OUTLIER) cc_final: 0.4875 (tt0) REVERT: 2 461 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6300 (ttm170) REVERT: 2 488 GLU cc_start: 0.5275 (mm-30) cc_final: 0.4715 (mm-30) REVERT: 2 605 LEU cc_start: 0.6735 (tp) cc_final: 0.6176 (tp) REVERT: 2 693 PRO cc_start: 0.3907 (Cg_endo) cc_final: 0.3456 (Cg_exo) REVERT: 2 720 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7724 (tt) REVERT: 2 752 GLU cc_start: 0.5154 (pt0) cc_final: 0.4469 (pt0) REVERT: 3 241 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6201 (mp) REVERT: 3 253 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5645 (t80) REVERT: 3 348 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.4887 (tp40) REVERT: 3 364 THR cc_start: 0.4873 (OUTLIER) cc_final: 0.4494 (p) REVERT: 3 604 THR cc_start: 0.3819 (OUTLIER) cc_final: 0.3377 (m) REVERT: 4 524 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.4891 (m-80) REVERT: 4 649 ILE cc_start: 0.4508 (pt) cc_final: 0.4247 (pt) REVERT: 4 676 ARG cc_start: 0.2202 (pmt-80) cc_final: 0.1476 (ptm160) REVERT: 4 680 GLU cc_start: 0.2101 (OUTLIER) cc_final: 0.1021 (mt-10) REVERT: 5 245 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6563 (t0) REVERT: 5 360 LYS cc_start: 0.3900 (mmtt) cc_final: 0.3522 (mmtt) REVERT: 5 558 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5071 (t80) REVERT: 5 562 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7649 (mp) REVERT: 6 151 MET cc_start: 0.1855 (OUTLIER) cc_final: 0.1042 (ttt) REVERT: 6 190 GLU cc_start: 0.7047 (pm20) cc_final: 0.5894 (pt0) REVERT: 6 284 LEU cc_start: 0.3888 (OUTLIER) cc_final: 0.3183 (pp) REVERT: 6 410 TYR cc_start: 0.5383 (OUTLIER) cc_final: 0.3699 (t80) REVERT: 7 109 MET cc_start: 0.3710 (mtp) cc_final: 0.2875 (ttp) REVERT: 7 215 LYS cc_start: 0.1931 (OUTLIER) cc_final: 0.1230 (mtpt) REVERT: 7 281 MET cc_start: 0.6394 (mtm) cc_final: 0.5972 (mtp) REVERT: 7 299 GLN cc_start: 0.7208 (tp40) cc_final: 0.6902 (tt0) REVERT: 7 419 MET cc_start: -0.1334 (ttp) cc_final: -0.1854 (ttp) REVERT: 7 427 MET cc_start: -0.3289 (mmp) cc_final: -0.3583 (mmp) REVERT: 7 438 ASP cc_start: 0.4353 (p0) cc_final: 0.4128 (p0) REVERT: 7 494 ARG cc_start: 0.4511 (ptm-80) cc_final: 0.3479 (ttm170) REVERT: 7 527 ARG cc_start: 0.6009 (mmt180) cc_final: 0.5501 (ttp80) REVERT: A 45 MET cc_start: 0.5600 (mpp) cc_final: 0.5025 (ptp) REVERT: A 53 MET cc_start: 0.5098 (mpp) cc_final: 0.4570 (mtm) REVERT: A 304 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7125 (tmm-80) REVERT: A 442 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6506 (tp40) REVERT: A 507 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5731 (mp) REVERT: L 120 ILE cc_start: 0.8044 (tp) cc_final: 0.7255 (mm) outliers start: 238 outliers final: 161 residues processed: 815 average time/residue: 0.2485 time to fit residues: 330.4191 Evaluate side-chains 768 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 588 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 364 GLN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 570 LEU Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 188 ASN Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 291 MET Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 698 GLU Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 605 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 115 HIS Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 607 LEU Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 333 optimal weight: 7.9990 chunk 436 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 438 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 269 optimal weight: 0.0570 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 210 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN 3 233 GLN 4 188 ASN 4 746 HIS 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 595 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS H 109 GLN H 137 GLN M 32 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.272592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.259220 restraints weight = 73810.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.258807 restraints weight = 90844.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.259123 restraints weight = 72018.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.258513 restraints weight = 64926.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.259071 restraints weight = 59793.987| |-----------------------------------------------------------------------------| r_work (final): 0.5017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41741 Z= 0.133 Angle : 0.719 11.180 56508 Z= 0.361 Chirality : 0.045 0.222 6362 Planarity : 0.005 0.067 7230 Dihedral : 11.345 169.583 6018 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.84 % Favored : 88.14 % Rotamer: Outliers : 4.90 % Allowed : 25.22 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.11), residues: 5000 helix: -0.65 (0.13), residues: 1645 sheet: -2.63 (0.20), residues: 550 loop : -3.09 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 773 TYR 0.023 0.001 TYR 4 252 PHE 0.024 0.002 PHE A 530 TRP 0.016 0.002 TRP H 64 HIS 0.020 0.001 HIS 6 115 Details of bonding type rmsd covalent geometry : bond 0.00299 (41733) covalent geometry : angle 0.71878 (56502) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.77623 ( 6) hydrogen bonds : bond 0.03913 ( 1089) hydrogen bonds : angle 5.36150 ( 3105) Misc. bond : bond 0.00086 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 622 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER L 185 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 461 ARG cc_start: 0.6983 (ttm110) cc_final: 0.6303 (ttm170) REVERT: 2 488 GLU cc_start: 0.5540 (mm-30) cc_final: 0.5125 (mm-30) REVERT: 2 605 LEU cc_start: 0.6869 (tp) cc_final: 0.6270 (tp) REVERT: 2 693 PRO cc_start: 0.4342 (Cg_endo) cc_final: 0.3996 (Cg_exo) REVERT: 2 720 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7691 (tt) REVERT: 2 752 GLU cc_start: 0.5081 (pt0) cc_final: 0.4466 (pt0) REVERT: 3 241 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6773 (mp) REVERT: 3 253 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5721 (t80) REVERT: 3 348 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.4636 (tp40) REVERT: 3 364 THR cc_start: 0.4887 (OUTLIER) cc_final: 0.4492 (p) REVERT: 3 604 THR cc_start: 0.3936 (OUTLIER) cc_final: 0.3586 (m) REVERT: 4 173 MET cc_start: 0.5728 (mmm) cc_final: 0.4939 (ptm) REVERT: 4 524 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.4733 (m-80) REVERT: 4 649 ILE cc_start: 0.4422 (pt) cc_final: 0.4156 (pt) REVERT: 4 676 ARG cc_start: 0.2371 (pmt-80) cc_final: 0.1557 (ptm160) REVERT: 4 680 GLU cc_start: 0.2104 (OUTLIER) cc_final: 0.1055 (mt-10) REVERT: 5 220 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.5040 (tm-30) REVERT: 5 245 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6439 (t0) REVERT: 5 513 MET cc_start: 0.1996 (mmm) cc_final: 0.1374 (mmm) REVERT: 5 531 LYS cc_start: 0.6190 (mmmt) cc_final: 0.5932 (mmtp) REVERT: 5 558 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.5169 (t80) REVERT: 5 562 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7719 (mp) REVERT: 5 643 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6813 (t80) REVERT: 6 151 MET cc_start: 0.2187 (OUTLIER) cc_final: 0.1402 (ttt) REVERT: 6 190 GLU cc_start: 0.7126 (pm20) cc_final: 0.6004 (pt0) REVERT: 6 284 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.3056 (pp) REVERT: 6 410 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.3715 (t80) REVERT: 7 109 MET cc_start: 0.3907 (mtp) cc_final: 0.3136 (ttp) REVERT: 7 185 ASP cc_start: 0.7547 (m-30) cc_final: 0.6766 (m-30) REVERT: 7 215 LYS cc_start: 0.1947 (OUTLIER) cc_final: 0.1171 (mtpt) REVERT: 7 281 MET cc_start: 0.6495 (mtm) cc_final: 0.6062 (mtp) REVERT: 7 299 GLN cc_start: 0.7148 (tp40) cc_final: 0.6825 (tt0) REVERT: 7 419 MET cc_start: -0.1392 (ttp) cc_final: -0.1851 (ttp) REVERT: 7 427 MET cc_start: -0.3345 (mmp) cc_final: -0.3650 (mmp) REVERT: 7 494 ARG cc_start: 0.4596 (ptm-80) cc_final: 0.3518 (ttm170) REVERT: 7 527 ARG cc_start: 0.6150 (mmt180) cc_final: 0.5510 (ttp80) REVERT: A 40 PHE cc_start: 0.6346 (m-10) cc_final: 0.6062 (m-10) REVERT: A 45 MET cc_start: 0.5680 (mpp) cc_final: 0.5168 (ptp) REVERT: A 53 MET cc_start: 0.5117 (mpp) cc_final: 0.4611 (mtm) REVERT: A 101 HIS cc_start: 0.5702 (t70) cc_final: 0.4978 (m90) REVERT: A 304 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7143 (tmm-80) REVERT: A 339 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7551 (mtm-85) REVERT: A 422 LYS cc_start: 0.4575 (mmtt) cc_final: 0.4369 (mmtt) REVERT: A 442 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: A 507 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.5851 (mp) REVERT: L 120 ILE cc_start: 0.8215 (tp) cc_final: 0.7408 (mm) outliers start: 217 outliers final: 156 residues processed: 786 average time/residue: 0.2626 time to fit residues: 335.5326 Evaluate side-chains 768 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 592 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 347 SER Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 570 LEU Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 568 ILE Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 646 PHE Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 698 GLU Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 607 LEU Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 28 optimal weight: 1.9990 chunk 287 optimal weight: 7.9990 chunk 434 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 151 optimal weight: 0.0670 chunk 295 optimal weight: 0.7980 chunk 120 optimal weight: 0.0970 chunk 395 optimal weight: 2.9990 chunk 440 optimal weight: 0.6980 chunk 269 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 436 GLN 2 592 GLN ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 358 GLN 4 372 ASN 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS A 296 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5174 r_free = 0.5174 target = 0.275115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.261695 restraints weight = 73537.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.260937 restraints weight = 92910.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.261911 restraints weight = 77534.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.261845 restraints weight = 55756.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.262134 restraints weight = 52798.002| |-----------------------------------------------------------------------------| r_work (final): 0.5061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5378 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41741 Z= 0.123 Angle : 0.710 11.918 56508 Z= 0.355 Chirality : 0.044 0.213 6362 Planarity : 0.005 0.067 7230 Dihedral : 11.131 168.882 6016 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.94 % Favored : 89.04 % Rotamer: Outliers : 4.49 % Allowed : 26.05 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.11), residues: 5000 helix: -0.51 (0.13), residues: 1650 sheet: -2.54 (0.20), residues: 575 loop : -3.03 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 499 TYR 0.054 0.001 TYR 7 562 PHE 0.021 0.001 PHE 5 643 TRP 0.019 0.001 TRP H 64 HIS 0.014 0.001 HIS 6 115 Details of bonding type rmsd covalent geometry : bond 0.00271 (41733) covalent geometry : angle 0.71016 (56502) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.70307 ( 6) hydrogen bonds : bond 0.03723 ( 1089) hydrogen bonds : angle 5.20388 ( 3105) Misc. bond : bond 0.00072 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 639 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 461 ARG cc_start: 0.6888 (ttm110) cc_final: 0.6241 (ttm170) REVERT: 2 488 GLU cc_start: 0.5170 (mm-30) cc_final: 0.4747 (mm-30) REVERT: 2 494 GLU cc_start: 0.4348 (pp20) cc_final: 0.3993 (pp20) REVERT: 2 590 GLU cc_start: 0.5526 (pm20) cc_final: 0.5317 (pm20) REVERT: 2 605 LEU cc_start: 0.6926 (tp) cc_final: 0.6360 (tp) REVERT: 2 693 PRO cc_start: 0.4475 (Cg_endo) cc_final: 0.4186 (Cg_exo) REVERT: 2 720 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7772 (tt) REVERT: 2 752 GLU cc_start: 0.4881 (pt0) cc_final: 0.4452 (pt0) REVERT: 3 88 TYR cc_start: 0.5558 (OUTLIER) cc_final: 0.4582 (m-10) REVERT: 3 201 MET cc_start: 0.6241 (mmm) cc_final: 0.5770 (mpp) REVERT: 3 241 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6716 (mp) REVERT: 3 253 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5584 (t80) REVERT: 3 348 GLN cc_start: 0.6041 (OUTLIER) cc_final: 0.4476 (tp40) REVERT: 3 364 THR cc_start: 0.4923 (OUTLIER) cc_final: 0.4617 (p) REVERT: 3 462 GLU cc_start: 0.6569 (tp30) cc_final: 0.6321 (tp30) REVERT: 3 466 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6444 (mt) REVERT: 3 604 THR cc_start: 0.3799 (OUTLIER) cc_final: 0.3382 (m) REVERT: 4 173 MET cc_start: 0.5921 (mmm) cc_final: 0.5055 (ptm) REVERT: 4 487 PHE cc_start: 0.3636 (m-10) cc_final: 0.3352 (m-10) REVERT: 4 676 ARG cc_start: 0.2265 (pmt-80) cc_final: 0.1332 (ptt90) REVERT: 4 680 GLU cc_start: 0.2021 (OUTLIER) cc_final: 0.1110 (mt-10) REVERT: 5 220 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.5161 (tm-30) REVERT: 5 245 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6376 (t0) REVERT: 5 368 ARG cc_start: 0.4272 (ttp-170) cc_final: 0.3914 (mmt180) REVERT: 5 417 LYS cc_start: 0.7899 (mptt) cc_final: 0.7505 (mptt) REVERT: 5 468 LYS cc_start: 0.7796 (mmmt) cc_final: 0.6801 (mmmt) REVERT: 5 513 MET cc_start: 0.2152 (mmm) cc_final: 0.1903 (mmm) REVERT: 5 558 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5260 (t80) REVERT: 5 562 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7718 (mp) REVERT: 6 151 MET cc_start: 0.2054 (OUTLIER) cc_final: 0.1306 (ttt) REVERT: 6 284 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3143 (pp) REVERT: 7 109 MET cc_start: 0.3805 (mtp) cc_final: 0.3084 (ttp) REVERT: 7 185 ASP cc_start: 0.7409 (m-30) cc_final: 0.6584 (m-30) REVERT: 7 215 LYS cc_start: 0.2022 (OUTLIER) cc_final: 0.1279 (mtpt) REVERT: 7 281 MET cc_start: 0.6397 (mtm) cc_final: 0.5973 (mtp) REVERT: 7 299 GLN cc_start: 0.7200 (tp40) cc_final: 0.6895 (tt0) REVERT: 7 419 MET cc_start: -0.1012 (ttp) cc_final: -0.1570 (ttp) REVERT: 7 427 MET cc_start: -0.3369 (mmp) cc_final: -0.3577 (mmp) REVERT: 7 494 ARG cc_start: 0.4623 (ptm-80) cc_final: 0.3586 (ttm170) REVERT: 7 527 ARG cc_start: 0.5922 (mmt180) cc_final: 0.5463 (ttp80) REVERT: 7 607 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3776 (tp) REVERT: A 45 MET cc_start: 0.5623 (mpp) cc_final: 0.5093 (ptp) REVERT: A 53 MET cc_start: 0.5286 (mpp) cc_final: 0.4754 (mtm) REVERT: A 304 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7023 (tmm-80) REVERT: A 507 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.5881 (mp) REVERT: H 179 ASN cc_start: 0.4967 (m-40) cc_final: 0.4596 (p0) REVERT: L 120 ILE cc_start: 0.8061 (tp) cc_final: 0.7427 (mm) outliers start: 199 outliers final: 143 residues processed: 776 average time/residue: 0.2595 time to fit residues: 328.3568 Evaluate side-chains 745 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 583 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 347 SER Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 570 LEU Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 152 MET Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 432 LEU Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 115 HIS Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 186 MET Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 7 residue 5 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 556 MET Chi-restraints excluded: chain 7 residue 607 LEU Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 285 optimal weight: 1.9990 chunk 393 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 488 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 211 ASN 2 329 ASN 2 503 ASN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 796 GLN 3 260 ASN 4 337 ASN 4 345 ASN 4 631 ASN 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 GLN 6 231 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS A 296 HIS A 436 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS L 91 HIS M 32 GLN ** M 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS N 36 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.265232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.250466 restraints weight = 73879.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.249602 restraints weight = 107086.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.250484 restraints weight = 94650.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.250660 restraints weight = 71235.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.250845 restraints weight = 62943.762| |-----------------------------------------------------------------------------| r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 41741 Z= 0.185 Angle : 0.818 12.234 56508 Z= 0.412 Chirality : 0.048 0.300 6362 Planarity : 0.006 0.072 7230 Dihedral : 11.427 161.782 6011 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.56 % Favored : 86.42 % Rotamer: Outliers : 4.49 % Allowed : 26.60 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.11), residues: 5000 helix: -0.73 (0.13), residues: 1647 sheet: -2.46 (0.21), residues: 549 loop : -3.17 (0.10), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 162 TYR 0.028 0.002 TYR N 99 PHE 0.026 0.002 PHE 5 643 TRP 0.018 0.002 TRP H 64 HIS 0.013 0.002 HIS 7 536 Details of bonding type rmsd covalent geometry : bond 0.00423 (41733) covalent geometry : angle 0.81826 (56502) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.03975 ( 6) hydrogen bonds : bond 0.04549 ( 1089) hydrogen bonds : angle 5.50655 ( 3105) Misc. bond : bond 0.00156 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 601 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 461 ARG cc_start: 0.7005 (ttm110) cc_final: 0.6338 (ttm170) REVERT: 2 581 ASP cc_start: 0.5853 (m-30) cc_final: 0.5537 (m-30) REVERT: 2 605 LEU cc_start: 0.7027 (tp) cc_final: 0.6445 (tp) REVERT: 2 693 PRO cc_start: 0.4647 (Cg_endo) cc_final: 0.4397 (Cg_exo) REVERT: 2 720 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7819 (tt) REVERT: 2 752 GLU cc_start: 0.5503 (pt0) cc_final: 0.5024 (pt0) REVERT: 3 88 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.4384 (m-10) REVERT: 3 201 MET cc_start: 0.6204 (mmm) cc_final: 0.5850 (mpp) REVERT: 3 241 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7013 (mp) REVERT: 3 253 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6359 (t80) REVERT: 3 604 THR cc_start: 0.3911 (OUTLIER) cc_final: 0.3550 (m) REVERT: 4 173 MET cc_start: 0.6096 (mmm) cc_final: 0.5543 (mmp) REVERT: 4 306 PHE cc_start: 0.5191 (OUTLIER) cc_final: 0.4956 (m-10) REVERT: 4 676 ARG cc_start: 0.2830 (pmt-80) cc_final: 0.1854 (ptt90) REVERT: 4 680 GLU cc_start: 0.2542 (OUTLIER) cc_final: 0.1493 (mt-10) REVERT: 5 69 MET cc_start: 0.7038 (mmm) cc_final: 0.6623 (tpt) REVERT: 5 70 GLU cc_start: 0.5974 (pp20) cc_final: 0.4849 (pp20) REVERT: 5 220 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: 5 245 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6973 (t0) REVERT: 5 417 LYS cc_start: 0.7927 (mptt) cc_final: 0.7508 (mptt) REVERT: 5 468 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7523 (mmmt) REVERT: 5 513 MET cc_start: 0.2044 (mmm) cc_final: 0.1303 (mmm) REVERT: 5 558 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.5098 (t80) REVERT: 5 562 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (mp) REVERT: 6 151 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.1777 (ttp) REVERT: 6 161 ASN cc_start: 0.4555 (p0) cc_final: 0.3779 (m-40) REVERT: 6 284 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3318 (pp) REVERT: 7 109 MET cc_start: 0.4025 (mtp) cc_final: 0.3309 (ttm) REVERT: 7 215 LYS cc_start: 0.2190 (OUTLIER) cc_final: 0.1227 (mtpt) REVERT: 7 281 MET cc_start: 0.6403 (mtm) cc_final: 0.6016 (mtp) REVERT: 7 299 GLN cc_start: 0.7384 (tp40) cc_final: 0.6891 (tt0) REVERT: 7 369 MET cc_start: 0.3519 (OUTLIER) cc_final: 0.3242 (ptt) REVERT: 7 419 MET cc_start: -0.1496 (ttp) cc_final: -0.1980 (ttp) REVERT: 7 427 MET cc_start: -0.3069 (mmp) cc_final: -0.3340 (mmp) REVERT: 7 475 MET cc_start: 0.0801 (pmm) cc_final: 0.0238 (pmm) REVERT: 7 494 ARG cc_start: 0.4831 (ptm-80) cc_final: 0.3772 (ttm170) REVERT: 7 561 ARG cc_start: 0.7061 (mtt-85) cc_final: 0.6787 (mtt-85) REVERT: A 15 VAL cc_start: 0.6747 (t) cc_final: 0.6519 (p) REVERT: A 45 MET cc_start: 0.5836 (mpp) cc_final: 0.5302 (ptp) REVERT: A 304 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7489 (tmm-80) REVERT: A 442 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6733 (tp40) REVERT: A 507 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6070 (mp) REVERT: H 37 VAL cc_start: 0.6284 (OUTLIER) cc_final: 0.6068 (t) REVERT: H 78 LYS cc_start: 0.6883 (mtpp) cc_final: 0.6618 (tptt) REVERT: H 113 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7548 (tp30) outliers start: 199 outliers final: 146 residues processed: 742 average time/residue: 0.2566 time to fit residues: 313.3768 Evaluate side-chains 723 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 558 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 347 SER Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 570 LEU Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 152 MET Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 291 PHE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 186 MET Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 344 ILE Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 556 MET Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 131 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 408 optimal weight: 2.9990 chunk 370 optimal weight: 0.2980 chunk 279 optimal weight: 0.5980 chunk 369 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 431 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5130 r_free = 0.5130 target = 0.269907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.255973 restraints weight = 73066.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.255097 restraints weight = 89527.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.253305 restraints weight = 65950.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.253207 restraints weight = 67008.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.253372 restraints weight = 59787.072| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41741 Z= 0.139 Angle : 0.773 13.520 56508 Z= 0.385 Chirality : 0.046 0.180 6362 Planarity : 0.005 0.071 7230 Dihedral : 11.144 158.853 6007 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.24 % Favored : 88.74 % Rotamer: Outliers : 3.70 % Allowed : 28.11 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.11), residues: 5000 helix: -0.59 (0.13), residues: 1638 sheet: -2.41 (0.20), residues: 555 loop : -3.07 (0.10), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 130 TYR 0.037 0.002 TYR 4 695 PHE 0.025 0.002 PHE 5 643 TRP 0.024 0.002 TRP H 64 HIS 0.012 0.001 HIS 6 115 Details of bonding type rmsd covalent geometry : bond 0.00315 (41733) covalent geometry : angle 0.77289 (56502) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.77993 ( 6) hydrogen bonds : bond 0.04015 ( 1089) hydrogen bonds : angle 5.33795 ( 3105) Misc. bond : bond 0.00086 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 590 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 461 ARG cc_start: 0.6976 (ttm110) cc_final: 0.6309 (ttm170) REVERT: 2 488 GLU cc_start: 0.5231 (mm-30) cc_final: 0.4766 (mm-30) REVERT: 2 496 HIS cc_start: 0.6163 (p-80) cc_final: 0.5612 (p-80) REVERT: 2 581 ASP cc_start: 0.5751 (m-30) cc_final: 0.5286 (m-30) REVERT: 2 605 LEU cc_start: 0.6874 (tp) cc_final: 0.6301 (tp) REVERT: 2 693 PRO cc_start: 0.4595 (Cg_endo) cc_final: 0.4373 (Cg_exo) REVERT: 2 720 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7815 (tt) REVERT: 2 752 GLU cc_start: 0.4987 (pt0) cc_final: 0.4585 (pt0) REVERT: 3 91 MET cc_start: 0.7193 (mpp) cc_final: 0.5925 (tpt) REVERT: 3 201 MET cc_start: 0.6309 (mmm) cc_final: 0.6066 (mpp) REVERT: 3 241 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7055 (mp) REVERT: 3 253 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6051 (t80) REVERT: 3 604 THR cc_start: 0.4008 (OUTLIER) cc_final: 0.3754 (m) REVERT: 4 173 MET cc_start: 0.6316 (mmm) cc_final: 0.5823 (mmp) REVERT: 4 306 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.5347 (m-10) REVERT: 4 676 ARG cc_start: 0.3154 (pmt-80) cc_final: 0.1856 (ptt90) REVERT: 4 680 GLU cc_start: 0.2465 (OUTLIER) cc_final: 0.1354 (mt-10) REVERT: 5 220 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6187 (tm-30) REVERT: 5 245 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6515 (t0) REVERT: 5 360 LYS cc_start: 0.3453 (mmtt) cc_final: 0.3069 (mmtt) REVERT: 5 417 LYS cc_start: 0.7681 (mptt) cc_final: 0.7458 (mptt) REVERT: 5 468 LYS cc_start: 0.7862 (mmmt) cc_final: 0.6991 (mmmt) REVERT: 5 513 MET cc_start: 0.1828 (mmm) cc_final: 0.1313 (mmm) REVERT: 5 558 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.5508 (t80) REVERT: 5 562 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (mp) REVERT: 6 151 MET cc_start: 0.2340 (OUTLIER) cc_final: 0.1706 (ttp) REVERT: 6 161 ASN cc_start: 0.4469 (p0) cc_final: 0.3659 (m-40) REVERT: 6 190 GLU cc_start: 0.7275 (pm20) cc_final: 0.5703 (pt0) REVERT: 6 284 LEU cc_start: 0.3927 (OUTLIER) cc_final: 0.3321 (pp) REVERT: 7 109 MET cc_start: 0.3964 (mtp) cc_final: 0.3374 (ttm) REVERT: 7 185 ASP cc_start: 0.7621 (m-30) cc_final: 0.6822 (m-30) REVERT: 7 215 LYS cc_start: 0.2147 (OUTLIER) cc_final: 0.1208 (mtpt) REVERT: 7 281 MET cc_start: 0.6347 (mtm) cc_final: 0.5952 (mtp) REVERT: 7 299 GLN cc_start: 0.7321 (tp40) cc_final: 0.6810 (tt0) REVERT: 7 369 MET cc_start: 0.3322 (OUTLIER) cc_final: 0.3029 (ptt) REVERT: 7 419 MET cc_start: -0.1755 (ttp) cc_final: -0.2245 (ttp) REVERT: 7 427 MET cc_start: -0.3518 (mmp) cc_final: -0.3773 (mmp) REVERT: 7 475 MET cc_start: 0.0459 (pmm) cc_final: -0.0124 (pmm) REVERT: 7 494 ARG cc_start: 0.4795 (ptm-80) cc_final: 0.3802 (ttm170) REVERT: 7 561 ARG cc_start: 0.7106 (mtt-85) cc_final: 0.6824 (mtt-85) REVERT: A 45 MET cc_start: 0.5859 (mpp) cc_final: 0.5243 (ptp) REVERT: A 101 HIS cc_start: 0.5919 (OUTLIER) cc_final: 0.5238 (m-70) REVERT: A 304 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6870 (tmm-80) REVERT: A 422 LYS cc_start: 0.4689 (mmtt) cc_final: 0.4475 (mmtt) REVERT: A 507 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6035 (mp) REVERT: H 179 ASN cc_start: 0.5028 (m-40) cc_final: 0.4679 (p0) REVERT: L 120 ILE cc_start: 0.8098 (tp) cc_final: 0.7335 (mm) outliers start: 164 outliers final: 132 residues processed: 705 average time/residue: 0.2568 time to fit residues: 297.6993 Evaluate side-chains 716 residues out of total 4447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 567 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 217 VAL Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 347 SER Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 384 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 404 THR Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 720 ILE Chi-restraints excluded: chain 2 residue 787 VAL Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 92 HIS Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 152 MET Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 480 MET Chi-restraints excluded: chain 3 residue 567 HIS Chi-restraints excluded: chain 3 residue 604 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 432 LEU Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 453 VAL Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 69 LEU Chi-restraints excluded: chain 6 residue 84 LEU Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 151 MET Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 179 CYS Chi-restraints excluded: chain 6 residue 186 MET Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 327 HIS Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 131 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 69 optimal weight: 0.0970 chunk 43 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 50 optimal weight: 0.0670 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 348 optimal weight: 0.0000 chunk 95 optimal weight: 4.9990 chunk 432 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 overall best weight: 0.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 606 GLN ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 HIS 4 345 ASN ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN 6 466 HIS ** 7 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 376 ASN ** 7 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 459 HIS A 296 HIS ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.274990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.260247 restraints weight = 73882.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.259171 restraints weight = 98448.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.259945 restraints weight = 80749.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.260382 restraints weight = 63342.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.260465 restraints weight = 58991.463| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41741 Z= 0.127 Angle : 0.748 12.199 56508 Z= 0.369 Chirality : 0.044 0.262 6362 Planarity : 0.005 0.070 7230 Dihedral : 10.807 151.145 6007 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.88 % Favored : 89.10 % Rotamer: Outliers : 3.16 % Allowed : 28.49 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.11), residues: 5000 helix: -0.46 (0.13), residues: 1640 sheet: -2.26 (0.20), residues: 576 loop : -2.97 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 130 TYR 0.034 0.001 TYR 4 695 PHE 0.030 0.001 PHE A 530 TRP 0.038 0.002 TRP A 223 HIS 0.026 0.001 HIS M 131 Details of bonding type rmsd covalent geometry : bond 0.00283 (41733) covalent geometry : angle 0.74842 (56502) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.71474 ( 6) hydrogen bonds : bond 0.03689 ( 1089) hydrogen bonds : angle 5.18086 ( 3105) Misc. bond : bond 0.00062 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7988.05 seconds wall clock time: 139 minutes 4.01 seconds (8344.01 seconds total)