Starting phenix.real_space_refine on Sat Mar 7 07:39:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raw_4785/03_2026/6raw_4785.map" } resolution = 3.7 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= 0.002 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 54 5.49 5 S 233 5.16 5 C 24842 2.51 5 N 6960 2.21 5 O 7621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 254 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39710 Number of models: 1 Model: "" Number of chains: 18 Chain: "2" Number of atoms: 4769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4769 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4551 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 21, 'TRANS': 563} Chain breaks: 8 Chain: "4" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4863 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 26, 'TRANS': 581} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4532 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 551} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4777 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 583} Chain breaks: 4 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: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4923 Classifications: {'peptide': 631} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 606} Unresolved chain links: 4 Chain breaks: 3 Unresolved chain link angles: 16 Unresolved chain link dihedrals: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4362 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 14, 'TRANS': 527} Chain breaks: 2 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: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1395 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 14, 'TRANS': 156} Chain: "M" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1349 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "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: 7.86, per 1000 atoms: 0.20 Number of scatterers: 39710 At special positions: 0 Unit cell: (208.44, 183.6, 141.48, 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 233 16.00 P 54 15.00 O 7621 8.00 N 6960 7.00 C 24842 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=2.03 Simple disulfide: pdb=" SG CYS 6 152 " - pdb=" SG CYS 6 179 " distance=2.03 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 Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9258 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 35 sheets defined 36.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain '2' and resid 175 through 177 No H-bonds generated for 'chain '2' and resid 175 through 177' Processing helix chain '2' and resid 178 through 186 removed outlier: 3.644A pdb=" N ASN 2 182 " --> pdb=" O THR 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 3.788A pdb=" N ASP 2 202 " --> pdb=" O TYR 2 198 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN 2 210 " --> pdb=" O ARG 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 226 removed outlier: 3.535A pdb=" N LEU 2 222 " --> pdb=" O SER 2 218 " (cutoff:3.500A) Processing helix chain '2' and resid 236 through 256 removed outlier: 4.095A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 260 removed outlier: 3.638A pdb=" N GLU 2 260 " --> pdb=" O PRO 2 257 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 257 through 260' Processing helix chain '2' and resid 283 through 287 Processing helix chain '2' and resid 448 through 453 removed outlier: 3.816A pdb=" N LEU 2 452 " --> pdb=" O THR 2 448 " (cutoff:3.500A) Processing helix chain '2' and resid 456 through 463 removed outlier: 3.584A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 486 removed outlier: 3.562A pdb=" N LYS 2 477 " --> pdb=" O HIS 2 473 " (cutoff:3.500A) Processing helix chain '2' and resid 516 through 525 removed outlier: 4.194A pdb=" N TYR 2 520 " --> pdb=" O GLN 2 516 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR 2 521 " --> pdb=" O PHE 2 517 " (cutoff:3.500A) Processing helix chain '2' and resid 560 through 564 Processing helix chain '2' and resid 573 through 577 removed outlier: 3.564A pdb=" N MET 2 577 " --> pdb=" O PHE 2 574 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 583 removed outlier: 3.594A pdb=" N ARG 2 582 " --> pdb=" O ASN 2 578 " (cutoff:3.500A) Processing helix chain '2' and resid 587 through 592 removed outlier: 3.789A pdb=" N GLN 2 591 " --> pdb=" O GLU 2 587 " (cutoff:3.500A) Processing helix chain '2' and resid 635 through 640 removed outlier: 3.651A pdb=" N LEU 2 639 " --> pdb=" O SER 2 635 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER 2 640 " --> pdb=" O GLU 2 636 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 635 through 640' Processing helix chain '2' and resid 653 through 668 removed outlier: 3.527A pdb=" N ASP 2 657 " --> pdb=" O ASP 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 693 through 707 removed outlier: 4.514A pdb=" N LEU 2 697 " --> pdb=" O PRO 2 693 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN 2 699 " --> pdb=" O ASP 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 718 through 731 removed outlier: 3.569A pdb=" N LYS 2 722 " --> pdb=" O ASP 2 718 " (cutoff:3.500A) Processing helix chain '2' and resid 741 through 744 Processing helix chain '2' and resid 745 through 758 Processing helix chain '2' and resid 764 through 782 removed outlier: 4.100A pdb=" N VAL 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 795 Processing helix chain '3' and resid 7 through 18 removed outlier: 3.733A pdb=" N ASP 3 11 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 53 removed outlier: 3.565A 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 removed outlier: 3.792A pdb=" N THR 3 83 " --> pdb=" O GLU 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 89 Processing helix chain '3' and resid 109 through 113 removed outlier: 3.870A pdb=" N LEU 3 113 " --> pdb=" O PRO 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 201 through 205 removed outlier: 4.057A pdb=" N LYS 3 204 " --> pdb=" O MET 3 201 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 223 removed outlier: 3.559A pdb=" N LEU 3 222 " --> pdb=" O ASP 3 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL 3 223 " --> pdb=" O ASP 3 220 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 219 through 223' Processing helix chain '3' and resid 276 through 285 Processing helix chain '3' and resid 290 through 299 removed outlier: 4.381A pdb=" N ALA 3 299 " --> pdb=" O SER 3 295 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 316 removed outlier: 4.122A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 355 removed outlier: 3.730A pdb=" N LEU 3 354 " --> pdb=" O LEU 3 350 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN 3 355 " --> pdb=" O ARG 3 351 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 350 through 355' Processing helix chain '3' and resid 393 through 397 Processing helix chain '3' and resid 413 through 423 Processing helix chain '3' and resid 469 through 474 Processing helix chain '3' and resid 488 through 500 Processing helix chain '3' and resid 559 through 565 Processing helix chain '3' and resid 566 through 572 Processing helix chain '3' and resid 580 through 595 Processing helix chain '3' and resid 610 through 623 Processing helix chain '3' and resid 632 through 641 Processing helix chain '4' and resid 160 through 174 removed outlier: 3.671A pdb=" N CYS 4 164 " --> pdb=" O VAL 4 160 " (cutoff:3.500A) 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 Processing helix chain '4' and resid 223 through 231 Processing helix chain '4' and resid 232 through 252 removed outlier: 3.700A pdb=" N ILE 4 237 " --> pdb=" O PRO 4 233 " (cutoff:3.500A) Proline residue: 4 238 - end of helix removed outlier: 3.608A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 382 Processing helix chain '4' and resid 445 through 456 removed outlier: 3.900A pdb=" N GLU 4 449 " --> pdb=" O PRO 4 445 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU 4 450 " --> pdb=" O GLU 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 459 through 468 removed outlier: 3.687A pdb=" N LEU 4 464 " --> pdb=" O ILE 4 460 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA 4 465 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) Processing helix chain '4' and resid 475 through 487 removed outlier: 4.374A pdb=" N LYS 4 479 " --> pdb=" O ASN 4 475 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS 4 480 " --> pdb=" O ASP 4 476 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY 4 481 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN 4 485 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 527 Processing helix chain '4' and resid 564 through 569 removed outlier: 3.702A pdb=" N ASP 4 569 " --> pdb=" O VAL 4 566 " (cutoff:3.500A) Processing helix chain '4' and resid 588 through 596 Processing helix chain '4' and resid 657 through 659 No H-bonds generated for 'chain '4' and resid 657 through 659' Processing helix chain '4' and resid 660 through 675 removed outlier: 3.754A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL 4 669 " --> pdb=" O ALA 4 665 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR 4 672 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 695 removed outlier: 3.830A pdb=" N ASP 4 691 " --> pdb=" O SER 4 687 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 4 693 " --> pdb=" O LEU 4 689 " (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 709 through 720 removed outlier: 6.375A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 734 through 749 removed outlier: 3.717A pdb=" N SER 4 738 " --> pdb=" O ARG 4 734 " (cutoff:3.500A) Processing helix chain '4' and resid 757 through 769 removed outlier: 4.260A pdb=" N GLU 4 761 " --> pdb=" O LEU 4 757 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU 4 762 " --> pdb=" O LEU 4 758 " (cutoff:3.500A) Processing helix chain '5' and resid 26 through 32 removed outlier: 4.084A pdb=" N VAL 5 30 " --> pdb=" O ASN 5 26 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS 5 32 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 41 removed outlier: 3.718A pdb=" N ILE 5 38 " --> pdb=" O TYR 5 34 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG 5 39 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 59 Processing helix chain '5' and resid 71 through 75 Processing helix chain '5' and resid 78 through 84 Processing helix chain '5' and resid 86 through 107 removed outlier: 3.510A pdb=" N HIS 5 90 " --> pdb=" O GLN 5 86 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.194A 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 324 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: 3.882A pdb=" N PHE 5 355 " --> pdb=" O THR 5 351 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.940A pdb=" N LEU 5 387 " --> pdb=" O ALA 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 448 through 451 removed outlier: 3.763A pdb=" N ASP 5 451 " --> pdb=" O ARG 5 448 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 448 through 451' Processing helix chain '5' and resid 452 through 462 removed outlier: 3.788A pdb=" N MET 5 459 " --> pdb=" O ILE 5 455 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN 5 461 " --> pdb=" O GLU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 496 removed outlier: 4.535A pdb=" N ASP 5 494 " --> pdb=" O GLY 5 490 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 5 496 " --> pdb=" O TRP 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 537 removed outlier: 3.627A pdb=" N ILE 5 533 " --> pdb=" O LEU 5 529 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN 5 535 " --> pdb=" O LYS 5 531 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL 5 536 " --> pdb=" O HIS 5 532 " (cutoff:3.500A) Processing helix chain '5' and resid 554 through 566 removed outlier: 3.516A pdb=" N PHE 5 558 " --> pdb=" O SER 5 554 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 598 removed outlier: 4.216A pdb=" N GLU 5 579 " --> pdb=" O GLU 5 575 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) Processing helix chain '5' and resid 608 through 627 removed outlier: 4.132A pdb=" N LEU 5 612 " --> pdb=" O THR 5 608 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG 5 617 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 5 618 " --> pdb=" O ALA 5 614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 5 619 " --> pdb=" O VAL 5 615 " (cutoff:3.500A) Processing helix chain '5' and resid 636 through 650 removed outlier: 3.842A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 31 removed outlier: 3.734A pdb=" N GLU 6 31 " --> pdb=" O ASP 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 48 Processing helix chain '6' and resid 59 through 65 Processing helix chain '6' and resid 69 through 74 Processing helix chain '6' and resid 76 through 93 Proline residue: 6 82 - end of helix removed outlier: 3.705A pdb=" N CYS 6 85 " --> pdb=" O TYR 6 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN 6 86 " --> pdb=" O PRO 6 82 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 333 removed outlier: 5.026A pdb=" N GLU 6 331 " --> pdb=" O HIS 6 327 " (cutoff:3.500A) Processing helix chain '6' and resid 337 through 344 Processing helix chain '6' and resid 360 through 365 removed outlier: 3.919A pdb=" N GLN 6 364 " --> pdb=" O ILE 6 360 " (cutoff:3.500A) Processing helix chain '6' and resid 395 through 400 removed outlier: 3.979A 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 440 through 444 Processing helix chain '6' and resid 460 through 469 removed outlier: 3.987A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET 6 469 " --> pdb=" O ILE 6 465 " (cutoff:3.500A) Processing helix chain '6' and resid 507 through 513 Processing helix chain '6' and resid 517 through 522 removed outlier: 4.440A pdb=" N ARG 6 521 " --> pdb=" O PRO 6 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE 6 522 " --> pdb=" O ILE 6 518 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 517 through 522' Processing helix chain '6' and resid 533 through 545 removed outlier: 3.743A pdb=" N ASP 6 537 " --> pdb=" O ASN 6 533 " (cutoff:3.500A) Processing helix chain '6' and resid 560 through 572 removed outlier: 3.849A pdb=" N ARG 6 572 " --> pdb=" O VAL 6 568 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 597 removed outlier: 5.777A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 6 589 " --> pdb=" O MET 6 585 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 626 removed outlier: 3.542A pdb=" N ILE 6 617 " --> pdb=" O LEU 6 613 " (cutoff:3.500A) Processing helix chain '6' and resid 635 through 652 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: 3.897A pdb=" N LEU 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN 7 59 " --> pdb=" O LEU 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 70 removed outlier: 4.298A pdb=" N ASP 7 68 " --> pdb=" O GLU 7 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 72 through 83 removed outlier: 3.786A pdb=" N GLU 7 83 " --> pdb=" O ASP 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 108 Processing helix chain '7' and resid 223 through 227 removed outlier: 3.762A pdb=" N GLY 7 226 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing helix chain '7' and resid 320 through 328 removed outlier: 4.344A pdb=" N GLU 7 325 " --> pdb=" O PRO 7 321 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 333 through 338 Processing helix chain '7' and resid 347 through 360 removed outlier: 3.602A pdb=" N LYS 7 351 " --> pdb=" O HIS 7 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS 7 352 " --> pdb=" O LEU 7 348 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) Processing helix chain '7' and resid 365 through 369 removed outlier: 3.666A pdb=" N GLY 7 368 " --> pdb=" O ARG 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.786A pdb=" N LEU 7 390 " --> pdb=" O ALA 7 386 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU 7 391 " --> pdb=" O LYS 7 387 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG 7 396 " --> pdb=" O GLY 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 415 Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 453 through 460 removed outlier: 3.542A pdb=" N ALA 7 457 " --> pdb=" O GLN 7 453 " (cutoff:3.500A) Processing helix chain '7' and resid 508 through 514 Processing helix chain '7' and resid 528 through 538 removed outlier: 3.886A pdb=" N ARG 7 532 " --> pdb=" O ASP 7 528 " (cutoff:3.500A) Processing helix chain '7' and resid 538 through 543 removed outlier: 3.599A pdb=" N SER 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 538 through 543' Processing helix chain '7' and resid 555 through 567 removed outlier: 3.709A pdb=" N ARG 7 561 " --> pdb=" O ASN 7 557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN 7 564 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS 7 566 " --> pdb=" O TYR 7 562 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS 7 567 " --> pdb=" O ILE 7 563 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 592 removed outlier: 3.697A pdb=" N ASP 7 579 " --> pdb=" O ASP 7 575 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR 7 580 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA 7 592 " --> pdb=" O LEU 7 588 " (cutoff:3.500A) Processing helix chain '7' and resid 604 through 619 removed outlier: 3.804A pdb=" N LEU 7 610 " --> pdb=" O LEU 7 606 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG 7 611 " --> pdb=" O LEU 7 607 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR 7 614 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 628 through 641 removed outlier: 3.833A pdb=" N GLU 7 632 " --> pdb=" O ASP 7 628 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG 7 635 " --> pdb=" O ALA 7 631 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 7 641 " --> pdb=" O LEU 7 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 41 removed outlier: 3.668A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 4.306A 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 183 through 201 removed outlier: 3.809A pdb=" N GLN A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.917A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 4.355A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.740A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.655A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 4.368A pdb=" N GLU A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.900A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 358 " --> pdb=" O PHE A 354 " (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 414 removed outlier: 3.796A pdb=" N ASP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 448 removed outlier: 3.956A pdb=" N SER A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 removed outlier: 3.707A pdb=" N PHE A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.893A 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 34 through 40 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 44 through 49 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 98 removed outlier: 3.715A pdb=" N LEU H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN H 68 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 4.045A pdb=" N PHE H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 11 Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.693A pdb=" N LYS L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 80 removed outlier: 5.236A pdb=" N LYS L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 101 removed outlier: 4.084A pdb=" N VAL L 95 " --> pdb=" O HIS L 91 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L 96 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 106 removed outlier: 3.583A pdb=" N ASP L 105 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 131 removed outlier: 3.984A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 131 " --> pdb=" O LYS L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 156 Processing helix chain 'L' and resid 159 through 169 removed outlier: 4.388A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 62 removed outlier: 3.801A pdb=" N GLU M 61 " --> pdb=" O TYR M 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU M 62 " --> pdb=" O ILE M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 88 removed outlier: 3.709A 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: 3.777A pdb=" N ILE M 120 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 171 removed outlier: 3.624A pdb=" N LEU M 156 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 51 removed outlier: 4.048A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS N 51 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 3.641A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 3.905A 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 126 removed outlier: 3.720A pdb=" N GLN N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 153 removed outlier: 3.594A pdb=" N THR N 138 " --> pdb=" O SER N 134 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP N 149 " --> pdb=" O ALA N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 223 Processing sheet with id=AA1, first strand: chain '2' and resid 215 through 217 Processing sheet with id=AA2, first strand: chain '2' and resid 296 through 297 removed outlier: 3.695A pdb=" N ARG 2 356 " --> pdb=" O GLN 2 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 296 through 297 removed outlier: 3.830A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 2 383 " --> pdb=" O GLN 2 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 568 through 571 Processing sheet with id=AA5, first strand: chain '2' and resid 593 through 595 removed outlier: 3.894A pdb=" N LEU 2 605 " --> pdb=" O ILE 2 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 134 through 136 removed outlier: 3.516A pdb=" N ARG 3 135 " --> pdb=" O HIS 3 193 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 216 through 218 removed outlier: 4.337A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 362 through 363 Processing sheet with id=AA9, first strand: chain '4' and resid 285 through 286 removed outlier: 3.809A pdb=" N GLY 4 395 " --> pdb=" O ILE 4 286 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG 4 425 " --> pdb=" O THR 4 392 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 285 through 286 removed outlier: 3.809A pdb=" N GLY 4 395 " --> pdb=" O ILE 4 286 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU 4 402 " --> pdb=" O VAL 4 414 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL 4 414 " --> pdb=" O LEU 4 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '4' and resid 304 through 306 removed outlier: 3.586A pdb=" N ALA 4 305 " --> pdb=" O VAL 4 318 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL 4 318 " --> pdb=" O ALA 4 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '4' and resid 355 through 357 Processing sheet with id=AB4, first strand: chain '4' and resid 510 through 511 removed outlier: 4.088A pdb=" N CYS 4 511 " --> pdb=" O PHE 4 650 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '4' and resid 532 through 534 removed outlier: 6.275A pdb=" N GLN 4 533 " --> pdb=" O CYS 4 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 548 through 552 removed outlier: 4.116A pdb=" N THR 4 562 " --> pdb=" O TYR 4 548 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR 4 550 " --> pdb=" O LEU 4 560 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU 4 560 " --> pdb=" O THR 4 550 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP 4 552 " --> pdb=" O LEU 4 558 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU 4 558 " --> pdb=" O ASP 4 552 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 599 through 601 Processing sheet with id=AB8, first strand: chain '5' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain '5' and resid 146 through 149 removed outlier: 3.733A pdb=" N ILE 5 260 " --> pdb=" O ILE 5 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '5' and resid 223 through 225 Processing sheet with id=AC2, first strand: chain '5' and resid 262 through 264 removed outlier: 3.766A pdb=" N ILE 5 263 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG 5 291 " --> pdb=" O ILE 5 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '5' and resid 377 through 378 removed outlier: 6.787A pdb=" N LEU 5 377 " --> pdb=" O VAL 5 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 398 through 401 removed outlier: 6.333A pdb=" N VAL 5 399 " --> pdb=" O CYS 5 440 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '6' and resid 135 through 136 removed outlier: 3.650A pdb=" N VAL 6 136 " --> pdb=" O ARG 6 201 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG 6 201 " --> pdb=" O VAL 6 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 47 through 48 Processing sheet with id=AC7, first strand: chain '7' and resid 162 through 164 removed outlier: 6.421A pdb=" N VAL 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE 7 303 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU 7 278 " --> pdb=" O PHE 7 297 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE 7 297 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '7' and resid 166 through 168 Processing sheet with id=AC9, first strand: chain '7' and resid 174 through 176 Processing sheet with id=AD1, first strand: chain '7' and resid 179 through 180 Processing sheet with id=AD2, first strand: chain '7' and resid 376 through 377 removed outlier: 3.983A pdb=" N CYS 7 442 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 417 through 418 Processing sheet with id=AD4, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.330A pdb=" N ILE A 19 " --> pdb=" O VAL A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.960A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 504 through 505 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 1038 hydrogen bonds defined for protein. 2934 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: 6.62 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10412 1.33 - 1.46: 8327 1.46 - 1.58: 21255 1.58 - 1.70: 104 1.70 - 1.83: 368 Bond restraints: 40466 Sorted by residual: bond pdb=" C4 ATP 2 902 " pdb=" C5 ATP 2 902 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 ATP 3 901 " pdb=" C5 ATP 3 901 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C5 ATP 3 901 " pdb=" C6 ATP 3 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 ATP 2 902 " pdb=" C6 ATP 2 902 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.51e+01 ... (remaining 40461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 54292 4.93 - 9.86: 461 9.86 - 14.79: 52 14.79 - 19.72: 12 19.72 - 24.65: 5 Bond angle restraints: 54822 Sorted by residual: angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 115.22 24.65 1.00e+00 1.00e+00 6.08e+02 angle pdb=" PA ATP 2 902 " pdb=" O3A ATP 2 902 " pdb=" PB ATP 2 902 " ideal model delta sigma weight residual 136.83 112.42 24.41 1.00e+00 1.00e+00 5.96e+02 angle pdb=" PB ATP 2 902 " pdb=" O3B ATP 2 902 " pdb=" PG ATP 2 902 " ideal model delta sigma weight residual 139.87 116.50 23.37 1.00e+00 1.00e+00 5.46e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 115.56 21.27 1.00e+00 1.00e+00 4.52e+02 angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 119.39 20.48 1.00e+00 1.00e+00 4.19e+02 ... (remaining 54817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 22799 26.68 - 53.35: 1722 53.35 - 80.03: 204 80.03 - 106.71: 44 106.71 - 133.38: 4 Dihedral angle restraints: 24773 sinusoidal: 10523 harmonic: 14250 Sorted by residual: dihedral pdb=" CD ARG 4 734 " pdb=" NE ARG 4 734 " pdb=" CZ ARG 4 734 " pdb=" NH1 ARG 4 734 " ideal model delta sinusoidal sigma weight residual 0.00 110.84 -110.84 1 1.00e+01 1.00e-02 1.30e+02 dihedral pdb=" CA THR 6 609 " pdb=" C THR 6 609 " pdb=" N VAL 6 610 " pdb=" CA VAL 6 610 " ideal model delta harmonic sigma weight residual -180.00 -126.77 -53.23 0 5.00e+00 4.00e-02 1.13e+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 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 24770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.428: 6159 0.428 - 0.856: 9 0.856 - 1.284: 0 1.284 - 1.712: 15 1.712 - 2.140: 10 Chirality restraints: 6193 Sorted by residual: chirality pdb=" CB THR 6 609 " pdb=" CA THR 6 609 " pdb=" OG1 THR 6 609 " pdb=" CG2 THR 6 609 " both_signs ideal model delta sigma weight residual False 2.55 0.41 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" CB ILE 3 484 " pdb=" CA ILE 3 484 " pdb=" CG1 ILE 3 484 " pdb=" CG2 ILE 3 484 " both_signs ideal model delta sigma weight residual False 2.64 0.72 1.93 2.00e-01 2.50e+01 9.28e+01 chirality pdb=" CG LEU 5 529 " pdb=" CB LEU 5 529 " pdb=" CD1 LEU 5 529 " pdb=" CD2 LEU 5 529 " both_signs ideal model delta sigma weight residual False -2.59 -0.67 -1.92 2.00e-01 2.50e+01 9.22e+01 ... (remaining 6190 not shown) Planarity restraints: 6950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 604 " -0.381 9.50e-02 1.11e+02 1.98e-01 1.42e+02 pdb=" NE ARG 7 604 " 0.092 2.00e-02 2.50e+03 pdb=" CZ ARG 7 604 " -0.188 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 604 " 0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 604 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 734 " -0.530 9.50e-02 1.11e+02 2.55e-01 1.41e+02 pdb=" NE ARG 4 734 " 0.098 2.00e-02 2.50e+03 pdb=" CZ ARG 4 734 " -0.172 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 734 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 734 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 641 " 0.319 9.50e-02 1.11e+02 1.72e-01 1.29e+02 pdb=" NE ARG 2 641 " -0.086 2.00e-02 2.50e+03 pdb=" CZ ARG 2 641 " 0.183 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 641 " -0.064 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 641 " -0.046 2.00e-02 2.50e+03 ... (remaining 6947 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 5 1.94 - 2.68: 1641 2.68 - 3.42: 58276 3.42 - 4.16: 90467 4.16 - 4.90: 152149 Nonbonded interactions: 302538 Sorted by model distance: nonbonded pdb=" O HIS 6 466 " pdb=" NH2 ARG 6 521 " model vdw 1.198 3.120 nonbonded pdb=" OD2 ASP 7 382 " pdb=" CE LYS 7 387 " model vdw 1.537 3.440 nonbonded pdb=" OD2 ASP 7 382 " pdb=" NZ LYS 7 387 " model vdw 1.621 3.120 nonbonded pdb=" CG ASP 7 382 " pdb=" CE LYS 7 387 " model vdw 1.829 3.670 nonbonded pdb=" CD1 LEU 2 541 " pdb=" CA ALA 6 479 " model vdw 1.931 3.890 ... (remaining 302533 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: 3.890 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.940 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4826 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 : 0.008 0.852 40475 Z= 0.553 Angle : 1.287 24.651 54828 Z= 0.719 Chirality : 0.126 2.140 6193 Planarity : 0.010 0.385 6950 Dihedral : 18.381 133.383 15506 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 18.92 % Favored : 80.77 % Rotamer: Outliers : 6.37 % Allowed : 12.88 % Favored : 80.74 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.80 % 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: -5.55 (0.09), residues: 4789 helix: -3.21 (0.09), residues: 1515 sheet: -4.49 (0.17), residues: 370 loop : -4.07 (0.10), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.193 0.003 ARG 7 604 TYR 0.055 0.003 TYR 3 454 PHE 0.082 0.004 PHE 5 41 TRP 0.034 0.003 TRP M 170 HIS 0.037 0.003 HIS M 98 Details of bonding type rmsd covalent geometry : bond 0.00668 (40466) covalent geometry : angle 1.28732 (54822) SS BOND : bond 0.00131 ( 3) SS BOND : angle 1.66003 ( 6) hydrogen bonds : bond 0.19059 ( 1028) hydrogen bonds : angle 8.19270 ( 2934) Misc. bond : bond 0.37008 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 1055 time to evaluate : 1.534 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 TARDY: cannot create tardy model for: "MET 7 108 " (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 TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7210 (t0) cc_final: 0.6646 (t0) REVERT: 2 271 SER cc_start: 0.6369 (OUTLIER) cc_final: 0.5884 (m) REVERT: 2 281 THR cc_start: 0.6576 (p) cc_final: 0.6202 (m) REVERT: 2 314 CYS cc_start: -0.2554 (OUTLIER) cc_final: -0.3421 (t) REVERT: 2 350 MET cc_start: 0.3764 (mmt) cc_final: 0.2237 (ptp) REVERT: 2 355 TYR cc_start: 0.6305 (m-80) cc_final: 0.5782 (m-80) REVERT: 2 643 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5522 (m-30) REVERT: 2 657 ASP cc_start: 0.6133 (m-30) cc_final: 0.5815 (m-30) REVERT: 2 723 MET cc_start: 0.3865 (mmt) cc_final: 0.3215 (mmp) REVERT: 2 761 GLU cc_start: 0.6628 (tt0) cc_final: 0.6351 (tm-30) REVERT: 3 8 PHE cc_start: 0.5864 (p90) cc_final: 0.5166 (m-80) REVERT: 3 13 GLN cc_start: 0.7535 (mt0) cc_final: 0.7334 (mt0) REVERT: 3 118 LEU cc_start: 0.6565 (tp) cc_final: 0.6273 (tp) REVERT: 3 124 VAL cc_start: 0.5017 (OUTLIER) cc_final: 0.4768 (m) REVERT: 3 214 VAL cc_start: 0.1192 (OUTLIER) cc_final: 0.0638 (m) REVERT: 3 234 ILE cc_start: 0.6395 (tp) cc_final: 0.6062 (tp) REVERT: 3 278 ILE cc_start: 0.6712 (tt) cc_final: 0.6414 (mt) REVERT: 3 402 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5666 (p) REVERT: 3 461 MET cc_start: 0.6914 (tpp) cc_final: 0.6631 (tpt) REVERT: 3 462 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: 3 610 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6180 (mtt180) REVERT: 4 200 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.2997 (mt) REVERT: 4 201 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7566 (mt-10) REVERT: 4 242 MET cc_start: 0.3188 (tpp) cc_final: 0.2241 (ptt) REVERT: 4 483 LEU cc_start: 0.6828 (mp) cc_final: 0.6531 (mp) REVERT: 4 551 LYS cc_start: 0.5421 (tptp) cc_final: 0.4171 (mtpt) REVERT: 4 653 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4335 (tt) REVERT: 4 693 ILE cc_start: 0.8224 (mt) cc_final: 0.7034 (mt) REVERT: 5 120 GLN cc_start: 0.4728 (pt0) cc_final: 0.4381 (tt0) REVERT: 5 435 ASP cc_start: 0.6414 (p0) cc_final: 0.6144 (p0) REVERT: 5 620 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5390 (mm-30) REVERT: 6 55 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4941 (tt) REVERT: 6 80 ILE cc_start: 0.6650 (mt) cc_final: 0.6267 (mt) REVERT: 6 113 THR cc_start: 0.6189 (m) cc_final: 0.5877 (m) REVERT: 6 114 ARG cc_start: 0.5892 (mpt-90) cc_final: 0.5241 (tmt170) REVERT: 6 151 MET cc_start: 0.1530 (ppp) cc_final: 0.0495 (tmm) REVERT: 6 194 PHE cc_start: 0.5209 (OUTLIER) cc_final: 0.3923 (m-80) REVERT: 6 332 MET cc_start: 0.7283 (mtt) cc_final: 0.7072 (mtp) REVERT: 6 365 PHE cc_start: 0.5565 (OUTLIER) cc_final: 0.5309 (t80) REVERT: 6 519 MET cc_start: 0.4377 (ptt) cc_final: 0.3997 (ptp) REVERT: 6 533 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6701 (p0) REVERT: 6 632 VAL cc_start: 0.1905 (OUTLIER) cc_final: 0.1591 (m) REVERT: 7 160 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6340 (tp) REVERT: 7 302 ARG cc_start: 0.5511 (tpp-160) cc_final: 0.5142 (tpp-160) REVERT: 7 308 LYS cc_start: 0.2352 (OUTLIER) cc_final: 0.1829 (mttm) REVERT: 7 365 ARG cc_start: 0.5236 (mmm-85) cc_final: 0.2576 (ptp90) REVERT: 7 402 GLN cc_start: 0.5018 (mm110) cc_final: 0.4501 (mt0) REVERT: 7 450 MET cc_start: 0.5583 (tpt) cc_final: 0.5309 (tpt) REVERT: 7 468 SER cc_start: 0.6276 (m) cc_final: 0.5984 (p) REVERT: 7 489 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6505 (p0) REVERT: 7 528 ASP cc_start: 0.6757 (m-30) cc_final: 0.6549 (m-30) REVERT: 7 627 LYS cc_start: 0.6555 (tptp) cc_final: 0.6335 (tttt) REVERT: A 45 MET cc_start: 0.2991 (mpp) cc_final: 0.2171 (mtt) REVERT: A 83 ILE cc_start: 0.4913 (pt) cc_final: 0.4712 (pt) REVERT: A 86 LEU cc_start: 0.7884 (tp) cc_final: 0.7298 (mm) REVERT: A 93 VAL cc_start: 0.6680 (t) cc_final: 0.6428 (m) REVERT: A 166 ASP cc_start: 0.0999 (OUTLIER) cc_final: -0.1309 (t0) REVERT: A 258 LEU cc_start: -0.0448 (OUTLIER) cc_final: -0.0999 (pp) REVERT: A 405 THR cc_start: 0.3852 (OUTLIER) cc_final: 0.3520 (p) REVERT: A 564 THR cc_start: 0.5486 (OUTLIER) cc_final: 0.5281 (m) REVERT: H 40 GLU cc_start: 0.7942 (tt0) cc_final: 0.7612 (mm-30) REVERT: H 76 ARG cc_start: 0.2466 (tpt170) cc_final: 0.0564 (ptm-80) REVERT: H 80 CYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6570 (p) REVERT: H 86 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.4548 (t80) REVERT: H 130 MET cc_start: 0.5076 (mtm) cc_final: 0.4790 (ptp) REVERT: L 8 PHE cc_start: 0.2450 (m-80) cc_final: 0.2118 (m-80) REVERT: L 99 VAL cc_start: 0.3690 (t) cc_final: 0.3429 (t) REVERT: L 109 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6961 (mtp180) REVERT: L 114 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.3582 (mmt90) REVERT: L 154 HIS cc_start: 0.2369 (p90) cc_final: 0.2052 (p90) REVERT: L 171 GLN cc_start: 0.5772 (OUTLIER) cc_final: 0.5570 (mp10) REVERT: M 56 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6589 (tt) REVERT: N 142 GLN cc_start: 0.4592 (mp-120) cc_final: 0.4283 (mm-40) outliers start: 272 outliers final: 73 residues processed: 1274 average time/residue: 0.2502 time to fit residues: 503.6542 Evaluate side-chains 750 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 650 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 THR Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 424 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 603 THR Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 2 residue 742 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 402 CYS Chi-restraints excluded: chain 3 residue 462 GLU Chi-restraints excluded: chain 3 residue 478 PHE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 296 SER Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 411 VAL Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 550 THR Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 613 THR Chi-restraints excluded: chain 4 residue 653 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 505 PRO Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 574 SER Chi-restraints excluded: chain 5 residue 620 GLU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 230 VAL Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 365 PHE Chi-restraints excluded: chain 6 residue 425 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 533 ASN Chi-restraints excluded: chain 6 residue 579 SER Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 632 VAL Chi-restraints excluded: chain 6 residue 644 LEU Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 269 ASP Chi-restraints excluded: chain 7 residue 308 LYS Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 387 LYS Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 466 THR Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 489 ASN Chi-restraints excluded: chain 7 residue 546 GLN Chi-restraints excluded: chain 7 residue 558 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 470 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 289 GLN 2 352 GLN 2 428 HIS 2 534 GLN 2 656 GLN 2 699 GLN 3 13 GLN 3 65 ASN 3 199 GLN 3 233 GLN 3 335 ASN 3 418 HIS 3 448 ASN 3 495 HIS 3 553 HIS 4 182 GLN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS 4 501 ASN 4 557 GLN 4 637 GLN 4 735 GLN 4 746 HIS 5 233 GLN ** 5 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 5 541 ASN 6 353 ASN 6 584 HIS 7 45 GLN 7 105 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 479 ASN 7 496 ASN ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 276 ASN A 453 HIS A 467 HIS H 175 HIS H 181 GLN H 199 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN N 36 GLN N 117 GLN N 153 HIS N 180 HIS N 214 GLN N 224 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.285978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.262851 restraints weight = 62783.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.264312 restraints weight = 54851.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.266064 restraints weight = 41768.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.266538 restraints weight = 33858.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.266928 restraints weight = 30381.636| |-----------------------------------------------------------------------------| r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5135 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40475 Z= 0.177 Angle : 0.869 15.642 54828 Z= 0.440 Chirality : 0.050 0.364 6193 Planarity : 0.006 0.076 6950 Dihedral : 13.602 126.335 6037 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.69 % Favored : 88.29 % Rotamer: Outliers : 4.29 % Allowed : 18.83 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.15 % 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: -4.33 (0.10), residues: 4789 helix: -1.87 (0.12), residues: 1552 sheet: -3.42 (0.19), residues: 495 loop : -3.54 (0.10), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 6 618 TYR 0.023 0.002 TYR 3 454 PHE 0.021 0.002 PHE 5 243 TRP 0.031 0.002 TRP M 170 HIS 0.011 0.001 HIS 2 586 Details of bonding type rmsd covalent geometry : bond 0.00389 (40466) covalent geometry : angle 0.86859 (54822) SS BOND : bond 0.00317 ( 3) SS BOND : angle 1.59313 ( 6) hydrogen bonds : bond 0.04976 ( 1028) hydrogen bonds : angle 6.16296 ( 2934) Misc. bond : bond 0.00487 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 779 time to evaluate : 1.567 Fit side-chains 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: "GLU 7 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 250 ASP cc_start: 0.7288 (t0) cc_final: 0.6841 (t0) REVERT: 2 277 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6194 (pt0) REVERT: 2 350 MET cc_start: 0.3274 (mmt) cc_final: 0.2620 (ptp) REVERT: 2 362 THR cc_start: 0.6323 (p) cc_final: 0.6061 (p) REVERT: 2 454 LYS cc_start: 0.6311 (mtmm) cc_final: 0.6000 (mtmm) REVERT: 2 476 ILE cc_start: 0.8007 (pt) cc_final: 0.7718 (pt) REVERT: 2 723 MET cc_start: 0.3891 (mmt) cc_final: 0.2277 (ptt) REVERT: 3 221 ASP cc_start: 0.6778 (t70) cc_final: 0.6548 (t70) REVERT: 3 278 ILE cc_start: 0.6208 (tt) cc_final: 0.5950 (mp) REVERT: 3 296 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.4958 (ttmt) REVERT: 3 441 CYS cc_start: 0.4415 (p) cc_final: 0.3866 (p) REVERT: 3 480 MET cc_start: 0.2421 (tpp) cc_final: 0.2024 (tpp) REVERT: 3 495 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6705 (t-90) REVERT: 4 173 MET cc_start: 0.6666 (mmm) cc_final: 0.6123 (mmm) REVERT: 4 242 MET cc_start: 0.1883 (tpp) cc_final: 0.0497 (ptt) REVERT: 4 246 GLU cc_start: 0.5521 (mt-10) cc_final: 0.4534 (tp30) REVERT: 4 247 MET cc_start: 0.7090 (ttp) cc_final: 0.5787 (tpt) REVERT: 4 397 TYR cc_start: 0.2702 (OUTLIER) cc_final: 0.1844 (m-80) REVERT: 4 451 LEU cc_start: 0.7144 (mt) cc_final: 0.6932 (tp) REVERT: 4 551 LYS cc_start: 0.6103 (tptp) cc_final: 0.4779 (mtpt) REVERT: 4 580 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7711 (mmtm) REVERT: 4 664 LEU cc_start: 0.6995 (pp) cc_final: 0.6225 (mt) REVERT: 4 675 THR cc_start: 0.1102 (OUTLIER) cc_final: 0.0879 (p) REVERT: 4 771 LEU cc_start: 0.5100 (mt) cc_final: 0.4732 (pp) REVERT: 5 51 ARG cc_start: 0.3896 (mtp85) cc_final: 0.2474 (mtp85) REVERT: 5 65 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5196 (tp) REVERT: 5 120 GLN cc_start: 0.5871 (pt0) cc_final: 0.5649 (pt0) REVERT: 5 508 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7919 (tt) REVERT: 6 151 MET cc_start: 0.0362 (ppp) cc_final: -0.0271 (tmm) REVERT: 6 194 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.4594 (m-80) REVERT: 6 469 MET cc_start: 0.4694 (ppp) cc_final: 0.4328 (ptm) REVERT: 6 519 MET cc_start: 0.4320 (ptt) cc_final: 0.3821 (ptp) REVERT: 6 548 HIS cc_start: 0.3807 (m-70) cc_final: 0.3515 (m90) REVERT: 6 630 ASN cc_start: 0.3459 (OUTLIER) cc_final: 0.3082 (m-40) REVERT: 7 31 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.6212 (m-80) REVERT: 7 106 ARG cc_start: 0.1982 (OUTLIER) cc_final: 0.1308 (mmt180) REVERT: 7 260 GLU cc_start: 0.5867 (mp0) cc_final: 0.5554 (mp0) REVERT: 7 365 ARG cc_start: 0.4570 (mmm-85) cc_final: 0.2170 (ptp90) REVERT: 7 598 MET cc_start: 0.6479 (mmt) cc_final: 0.6033 (mmp) REVERT: A 45 MET cc_start: 0.3079 (mpp) cc_final: 0.2763 (mtt) REVERT: A 303 MET cc_start: 0.7293 (mtt) cc_final: 0.7077 (mtt) REVERT: A 342 TYR cc_start: 0.6170 (t80) cc_final: 0.5766 (t80) REVERT: A 541 LYS cc_start: 0.7958 (tptt) cc_final: 0.7449 (tmtt) REVERT: H 70 ARG cc_start: 0.6950 (tmm160) cc_final: 0.6646 (tmm160) REVERT: H 76 ARG cc_start: 0.3811 (tpt170) cc_final: 0.1945 (ptm-80) REVERT: N 73 MET cc_start: 0.7245 (mmt) cc_final: 0.6965 (mmm) outliers start: 183 outliers final: 91 residues processed: 913 average time/residue: 0.2429 time to fit residues: 358.0450 Evaluate side-chains 726 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 624 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 524 VAL Chi-restraints excluded: chain 2 residue 574 PHE Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 114 THR Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 296 LYS Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 313 LEU Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 421 MET Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 495 HIS Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 448 VAL Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 675 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 507 ILE Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 580 LYS Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 512 ILE Chi-restraints excluded: chain 6 residue 590 TYR Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 31 PHE Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 106 ARG Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 106 VAL 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 255 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 153 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 74 optimal weight: 0.0050 chunk 205 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 399 optimal weight: 0.0570 chunk 203 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 335 ASN 3 418 HIS 3 495 HIS 3 644 GLN 4 223 GLN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN 4 533 GLN 4 735 GLN 4 767 HIS 5 233 GLN 5 373 ASN 6 231 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 592 HIS 6 636 HIS 7 155 GLN ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS A 495 GLN H 145 ASN M 9 ASN N 153 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.285976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.262357 restraints weight = 62441.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.263442 restraints weight = 53778.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.264966 restraints weight = 41510.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.265701 restraints weight = 32741.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.265940 restraints weight = 29958.991| |-----------------------------------------------------------------------------| r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40475 Z= 0.151 Angle : 0.753 11.552 54828 Z= 0.379 Chirality : 0.046 0.253 6193 Planarity : 0.005 0.064 6950 Dihedral : 12.761 129.149 5913 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 4.47 % Allowed : 20.80 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.09 % 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: -3.80 (0.11), residues: 4789 helix: -1.33 (0.12), residues: 1590 sheet: -2.89 (0.20), residues: 521 loop : -3.34 (0.11), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 617 TYR 0.020 0.001 TYR 4 196 PHE 0.028 0.002 PHE 3 253 TRP 0.037 0.002 TRP A 297 HIS 0.029 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00313 (40466) covalent geometry : angle 0.75317 (54822) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.12782 ( 6) hydrogen bonds : bond 0.04252 ( 1028) hydrogen bonds : angle 5.63671 ( 2934) Misc. bond : bond 0.00176 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 716 time to evaluate : 1.297 Fit side-chains 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: "MET 7 108 " (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: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 240 MET cc_start: 0.6320 (mmm) cc_final: 0.6088 (tpp) REVERT: 2 250 ASP cc_start: 0.7367 (t0) cc_final: 0.6945 (t0) REVERT: 2 277 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5812 (pt0) REVERT: 2 350 MET cc_start: 0.3141 (mmt) cc_final: 0.2835 (ptp) REVERT: 2 362 THR cc_start: 0.6690 (p) cc_final: 0.6482 (p) REVERT: 2 458 ILE cc_start: 0.2742 (OUTLIER) cc_final: 0.2379 (pp) REVERT: 2 723 MET cc_start: 0.4253 (mmt) cc_final: 0.3081 (ptt) REVERT: 2 754 HIS cc_start: 0.5088 (m170) cc_final: 0.4051 (m170) REVERT: 3 278 ILE cc_start: 0.6287 (tt) cc_final: 0.6006 (mp) REVERT: 3 608 THR cc_start: 0.4909 (p) cc_final: 0.4702 (t) REVERT: 4 242 MET cc_start: 0.1590 (tpp) cc_final: 0.0248 (ptt) REVERT: 4 247 MET cc_start: 0.7210 (ttp) cc_final: 0.5921 (tpt) REVERT: 4 397 TYR cc_start: 0.2936 (OUTLIER) cc_final: 0.1802 (m-80) REVERT: 4 593 MET cc_start: 0.6363 (mtt) cc_final: 0.5978 (mtt) REVERT: 4 594 GLU cc_start: 0.6270 (mp0) cc_final: 0.6060 (mm-30) REVERT: 4 664 LEU cc_start: 0.7012 (pp) cc_final: 0.6074 (mt) REVERT: 4 697 ARG cc_start: 0.8589 (mmm160) cc_final: 0.8033 (mtt180) REVERT: 4 771 LEU cc_start: 0.5529 (mt) cc_final: 0.5044 (pp) REVERT: 5 49 LYS cc_start: 0.3882 (OUTLIER) cc_final: 0.3606 (mttp) REVERT: 5 51 ARG cc_start: 0.4696 (mtp85) cc_final: 0.3303 (mtp85) REVERT: 5 65 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5366 (tp) REVERT: 5 259 LEU cc_start: 0.7222 (mt) cc_final: 0.7007 (mt) REVERT: 5 508 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8068 (tt) REVERT: 6 194 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4647 (m-80) REVERT: 6 469 MET cc_start: 0.5218 (ppp) cc_final: 0.4409 (ptp) REVERT: 6 519 MET cc_start: 0.4678 (ptt) cc_final: 0.4094 (ptp) REVERT: 6 548 HIS cc_start: 0.3835 (m-70) cc_final: 0.3610 (m90) REVERT: 6 630 ASN cc_start: 0.3621 (OUTLIER) cc_final: 0.3133 (m-40) REVERT: 7 336 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5298 (tt) REVERT: 7 369 MET cc_start: 0.4374 (OUTLIER) cc_final: 0.3983 (mtt) REVERT: 7 419 MET cc_start: 0.3808 (ttt) cc_final: 0.3585 (ttt) REVERT: 7 588 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5797 (tp) REVERT: A 303 MET cc_start: 0.7895 (mtt) cc_final: 0.7478 (mtt) REVERT: A 342 TYR cc_start: 0.6192 (t80) cc_final: 0.5788 (t80) REVERT: A 541 LYS cc_start: 0.7913 (tptt) cc_final: 0.7550 (tmtt) REVERT: H 11 LYS cc_start: 0.5992 (mttm) cc_final: 0.5789 (tttm) REVERT: H 76 ARG cc_start: 0.3706 (tpt170) cc_final: 0.1966 (ptm-80) REVERT: L 114 ARG cc_start: 0.6327 (tmt170) cc_final: 0.5045 (mmm-85) REVERT: L 171 GLN cc_start: 0.4480 (OUTLIER) cc_final: 0.3923 (tp-100) REVERT: M 131 HIS cc_start: 0.5953 (t70) cc_final: 0.5642 (t70) REVERT: N 142 GLN cc_start: 0.4465 (OUTLIER) cc_final: 0.4232 (mm-40) outliers start: 191 outliers final: 104 residues processed: 852 average time/residue: 0.2389 time to fit residues: 329.5536 Evaluate side-chains 720 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 603 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 458 ILE Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 3 residue 160 THR Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 4 residue 191 VAL Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER 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 424 PHE Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 5 residue 49 LYS Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 622 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 339 TYR Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 398 LEU Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 508 LEU Chi-restraints excluded: chain 6 residue 618 ARG Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 21 CYS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 191 THR Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 401 SER Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 588 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain N residue 30 MET Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 142 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 446 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 370 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 chunk 239 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 339 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 433 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 185 GLN 2 364 GLN 2 415 GLN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 591 GLN 2 694 GLN ** 2 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 467 GLN 3 644 GLN 4 193 GLN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 GLN 5 239 HIS ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN 6 353 ASN 6 400 GLN 6 466 HIS 6 472 GLN 6 645 ASN 7 155 GLN 7 347 HIS 7 543 HIS A 101 HIS A 229 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 487 HIS A 540 GLN H 195 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN M 81 HIS ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.274817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.247756 restraints weight = 60990.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.249160 restraints weight = 50986.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.250047 restraints weight = 40709.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.250532 restraints weight = 33856.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.250873 restraints weight = 31744.579| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 40475 Z= 0.207 Angle : 0.839 16.922 54828 Z= 0.425 Chirality : 0.050 0.301 6193 Planarity : 0.007 0.180 6950 Dihedral : 12.484 132.024 5905 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.16 % Favored : 86.82 % Rotamer: Outliers : 5.76 % Allowed : 21.78 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.11 % 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: -3.67 (0.11), residues: 4789 helix: -1.20 (0.12), residues: 1588 sheet: -2.79 (0.19), residues: 583 loop : -3.27 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 709 TYR 0.023 0.002 TYR N 104 PHE 0.029 0.002 PHE 3 253 TRP 0.062 0.003 TRP A 297 HIS 0.031 0.002 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00460 (40466) covalent geometry : angle 0.83864 (54822) SS BOND : bond 0.00881 ( 3) SS BOND : angle 1.39148 ( 6) hydrogen bonds : bond 0.04475 ( 1028) hydrogen bonds : angle 5.78568 ( 2934) Misc. bond : bond 0.00186 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 726 time to evaluate : 1.337 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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: "ILE H 201 " (corrupted residue). Skipping it. 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: 2 250 ASP cc_start: 0.7665 (t0) cc_final: 0.7116 (t0) REVERT: 2 277 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6964 (pt0) REVERT: 2 723 MET cc_start: 0.4972 (mmt) cc_final: 0.3500 (ptt) REVERT: 3 73 PHE cc_start: 0.6670 (m-80) cc_final: 0.6343 (m-80) REVERT: 3 277 ASP cc_start: 0.7509 (m-30) cc_final: 0.7229 (m-30) REVERT: 3 296 LYS cc_start: 0.6736 (ttmt) cc_final: 0.6362 (ttpp) REVERT: 3 355 ASN cc_start: 0.7773 (p0) cc_final: 0.7391 (m110) REVERT: 3 464 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7514 (mt) REVERT: 4 242 MET cc_start: 0.2002 (tpp) cc_final: 0.0729 (ptt) REVERT: 4 247 MET cc_start: 0.7721 (ttp) cc_final: 0.6311 (tpt) REVERT: 4 397 TYR cc_start: 0.3223 (OUTLIER) cc_final: 0.1785 (m-80) REVERT: 4 697 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8104 (mtt180) REVERT: 5 65 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6479 (tp) REVERT: 5 220 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7224 (tp40) REVERT: 5 344 ARG cc_start: 0.7437 (mtm180) cc_final: 0.7119 (ptp-170) REVERT: 5 508 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8420 (tt) REVERT: 6 95 ARG cc_start: 0.1422 (mtm-85) cc_final: 0.0998 (mtm180) REVERT: 6 151 MET cc_start: 0.0260 (ppp) cc_final: -0.0398 (tmm) REVERT: 6 194 PHE cc_start: 0.6381 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: 6 382 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7895 (pt) REVERT: 6 469 MET cc_start: 0.6159 (ppp) cc_final: 0.5191 (ptp) REVERT: 6 519 MET cc_start: 0.5720 (ptt) cc_final: 0.5115 (ptp) REVERT: 6 630 ASN cc_start: 0.4458 (OUTLIER) cc_final: 0.4248 (m110) REVERT: 7 31 PHE cc_start: 0.6295 (m-80) cc_final: 0.5763 (m-80) REVERT: 7 48 ILE cc_start: 0.5201 (OUTLIER) cc_final: 0.4607 (pt) REVERT: 7 72 ARG cc_start: 0.3034 (OUTLIER) cc_final: 0.2026 (ttm170) REVERT: 7 369 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.3923 (mtt) REVERT: 7 419 MET cc_start: 0.4043 (ttt) cc_final: 0.3612 (ttt) REVERT: 7 562 TYR cc_start: 0.3828 (m-80) cc_final: 0.3158 (m-80) REVERT: A 86 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7341 (tp) REVERT: A 101 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5574 (p-80) REVERT: A 303 MET cc_start: 0.8087 (mtt) cc_final: 0.7726 (mtt) REVERT: A 312 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.5981 (mp10) REVERT: A 342 TYR cc_start: 0.6529 (t80) cc_final: 0.6302 (t80) REVERT: A 522 VAL cc_start: 0.7305 (p) cc_final: 0.7040 (t) REVERT: A 541 LYS cc_start: 0.7965 (tptt) cc_final: 0.7586 (tmtt) REVERT: H 76 ARG cc_start: 0.4332 (tpt170) cc_final: 0.2834 (ptm-80) REVERT: L 27 HIS cc_start: 0.4105 (OUTLIER) cc_final: 0.3681 (t70) REVERT: L 114 ARG cc_start: 0.6427 (tmt170) cc_final: 0.5407 (mmm-85) REVERT: L 171 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.5251 (tp-100) REVERT: M 108 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6941 (tt) REVERT: N 73 MET cc_start: 0.7513 (mmm) cc_final: 0.7289 (mmm) REVERT: N 94 LEU cc_start: 0.5666 (tt) cc_final: 0.5447 (tt) outliers start: 246 outliers final: 130 residues processed: 909 average time/residue: 0.2363 time to fit residues: 349.5610 Evaluate side-chains 777 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 629 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 531 THR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 450 VAL Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 448 VAL Chi-restraints excluded: chain 4 residue 626 TRP Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 736 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 433 LEU Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 200 ILE Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 508 LEU Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 618 ARG Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 21 CYS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 224 THR Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 591 GLU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 27 HIS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 406 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 193 optimal weight: 0.0020 chunk 146 optimal weight: 0.8980 chunk 422 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 486 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 491 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 GLN 2 729 GLN 2 754 HIS 2 758 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 GLN 5 241 GLN 6 198 GLN 6 203 GLN ** 6 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN 6 341 ASN ** 6 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 229 ASN A 325 HIS A 421 HIS H 120 ASN L 91 HIS ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** 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 = 0.5052 r_free = 0.5052 target = 0.275842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.248233 restraints weight = 60450.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.249369 restraints weight = 49755.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.250312 restraints weight = 38121.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.251194 restraints weight = 33829.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.251573 restraints weight = 30277.683| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40475 Z= 0.144 Angle : 0.745 17.408 54828 Z= 0.372 Chirality : 0.046 0.200 6193 Planarity : 0.005 0.080 6950 Dihedral : 11.916 127.019 5896 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 5.22 % Allowed : 23.49 % Favored : 71.28 % 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: -3.35 (0.11), residues: 4789 helix: -0.94 (0.13), residues: 1598 sheet: -2.48 (0.20), residues: 568 loop : -3.12 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 590 TYR 0.017 0.001 TYR 5 48 PHE 0.035 0.002 PHE A 440 TRP 0.054 0.002 TRP A 297 HIS 0.022 0.001 HIS 7 347 Details of bonding type rmsd covalent geometry : bond 0.00327 (40466) covalent geometry : angle 0.74464 (54822) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.89906 ( 6) hydrogen bonds : bond 0.03837 ( 1028) hydrogen bonds : angle 5.50853 ( 2934) Misc. bond : bond 0.00115 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 698 time to evaluate : 1.466 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7521 (t0) cc_final: 0.7074 (t0) REVERT: 2 253 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6472 (mp) REVERT: 2 723 MET cc_start: 0.5035 (mmt) cc_final: 0.4181 (ptt) REVERT: 2 792 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7092 (ttt180) REVERT: 3 73 PHE cc_start: 0.6764 (m-80) cc_final: 0.6426 (m-80) REVERT: 3 203 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: 3 464 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7626 (mt) REVERT: 4 221 PHE cc_start: 0.4613 (OUTLIER) cc_final: 0.3952 (t80) REVERT: 4 242 MET cc_start: 0.1489 (tpp) cc_final: 0.0577 (ptt) REVERT: 4 247 MET cc_start: 0.7846 (ttp) cc_final: 0.7493 (ttt) REVERT: 4 397 TYR cc_start: 0.3036 (OUTLIER) cc_final: 0.1701 (m-10) REVERT: 4 462 ASP cc_start: 0.7867 (t0) cc_final: 0.7604 (t0) REVERT: 4 663 ARG cc_start: 0.6025 (ptp90) cc_final: 0.5797 (mtm-85) REVERT: 5 65 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6468 (tp) REVERT: 5 220 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: 5 340 ILE cc_start: 0.6934 (mp) cc_final: 0.6502 (mt) REVERT: 5 589 ARG cc_start: 0.4877 (OUTLIER) cc_final: 0.4398 (ptt180) REVERT: 6 151 MET cc_start: 0.0952 (ppp) cc_final: -0.0541 (tmm) REVERT: 6 167 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5389 (ttpt) REVERT: 6 194 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5059 (m-80) REVERT: 6 382 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7940 (pt) REVERT: 6 469 MET cc_start: 0.5720 (ppp) cc_final: 0.5278 (ptp) REVERT: 6 519 MET cc_start: 0.5988 (ptt) cc_final: 0.5392 (ptp) REVERT: 6 621 GLU cc_start: 0.3621 (pp20) cc_final: 0.3301 (pt0) REVERT: 6 630 ASN cc_start: 0.4408 (OUTLIER) cc_final: 0.4194 (m110) REVERT: 7 31 PHE cc_start: 0.6562 (m-80) cc_final: 0.6133 (m-80) REVERT: 7 48 ILE cc_start: 0.5087 (OUTLIER) cc_final: 0.4533 (pt) REVERT: 7 72 ARG cc_start: 0.3089 (OUTLIER) cc_final: 0.2014 (ttm170) REVERT: 7 281 MET cc_start: 0.6173 (tmm) cc_final: 0.5800 (mtt) REVERT: 7 369 MET cc_start: 0.4580 (OUTLIER) cc_final: 0.4125 (mtt) REVERT: A 6 LEU cc_start: 0.3848 (OUTLIER) cc_final: 0.2805 (pp) REVERT: A 86 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7360 (tp) REVERT: A 284 THR cc_start: 0.8566 (t) cc_final: 0.8111 (p) REVERT: A 303 MET cc_start: 0.8090 (mtt) cc_final: 0.7731 (mtt) REVERT: A 312 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5884 (mp10) REVERT: A 339 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7563 (mtt-85) REVERT: A 522 VAL cc_start: 0.6985 (p) cc_final: 0.6752 (t) REVERT: A 541 LYS cc_start: 0.7953 (tptt) cc_final: 0.7611 (tmtt) REVERT: H 70 ARG cc_start: 0.7036 (tmm160) cc_final: 0.6697 (tmm160) REVERT: H 76 ARG cc_start: 0.4516 (tpt170) cc_final: 0.3136 (ptm-80) REVERT: L 114 ARG cc_start: 0.6357 (tmt170) cc_final: 0.5327 (mmm-85) REVERT: L 170 TYR cc_start: 0.3664 (t80) cc_final: 0.3392 (t80) REVERT: L 171 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5395 (tp-100) REVERT: M 33 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.6647 (mtt180) REVERT: N 73 MET cc_start: 0.7576 (mmm) cc_final: 0.7260 (mmt) REVERT: N 176 ASN cc_start: 0.7589 (t0) cc_final: 0.7285 (t0) outliers start: 223 outliers final: 130 residues processed: 854 average time/residue: 0.2339 time to fit residues: 324.4455 Evaluate side-chains 785 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 636 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 350 MET Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 391 CYS 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 452 LEU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 491 ASN Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 750 MET Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 46 VAL Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 223 VAL Chi-restraints excluded: chain 3 residue 253 PHE 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 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 443 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 488 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 424 PHE Chi-restraints excluded: chain 4 residue 448 VAL Chi-restraints excluded: chain 4 residue 573 CYS Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 241 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 568 HIS Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 508 LEU Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 618 ARG Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL 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 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 210 optimal weight: 1.9990 chunk 290 optimal weight: 0.0570 chunk 75 optimal weight: 0.0030 chunk 163 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 379 optimal weight: 0.6980 chunk 238 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 211 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS ** 2 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 335 ASN 3 637 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 6 134 GLN 6 260 ASN 6 353 ASN 7 155 GLN 7 546 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN N 153 HIS N 226 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.278170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.250625 restraints weight = 60498.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.252253 restraints weight = 47690.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.252826 restraints weight = 36396.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.253820 restraints weight = 31987.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.254324 restraints weight = 28961.050| |-----------------------------------------------------------------------------| r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40475 Z= 0.125 Angle : 0.714 18.349 54828 Z= 0.354 Chirality : 0.045 0.283 6193 Planarity : 0.005 0.073 6950 Dihedral : 11.531 123.745 5892 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 4.38 % Allowed : 24.78 % Favored : 70.84 % 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: -3.09 (0.11), residues: 4789 helix: -0.68 (0.13), residues: 1608 sheet: -2.30 (0.20), residues: 563 loop : -3.01 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 709 TYR 0.041 0.001 TYR 6 236 PHE 0.030 0.001 PHE 6 185 TRP 0.031 0.002 TRP 6 326 HIS 0.037 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00278 (40466) covalent geometry : angle 0.71450 (54822) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.58218 ( 6) hydrogen bonds : bond 0.03540 ( 1028) hydrogen bonds : angle 5.24261 ( 2934) Misc. bond : bond 0.00127 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 692 time to evaluate : 1.488 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7466 (t0) cc_final: 0.6993 (t0) REVERT: 2 415 GLN cc_start: 0.4002 (mt0) cc_final: 0.3142 (mp10) REVERT: 2 723 MET cc_start: 0.5113 (mmt) cc_final: 0.4265 (ptt) REVERT: 3 73 PHE cc_start: 0.6748 (m-80) cc_final: 0.6500 (m-80) REVERT: 3 464 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7744 (mt) REVERT: 4 242 MET cc_start: 0.1231 (tpp) cc_final: 0.0345 (ptt) REVERT: 4 247 MET cc_start: 0.8006 (ttp) cc_final: 0.7692 (ttt) REVERT: 4 397 TYR cc_start: 0.3045 (OUTLIER) cc_final: 0.1734 (m-10) REVERT: 4 532 SER cc_start: 0.8011 (t) cc_final: 0.7800 (p) REVERT: 4 772 LYS cc_start: 0.0756 (tptt) cc_final: 0.0078 (tppt) REVERT: 5 220 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7400 (tp40) REVERT: 5 340 ILE cc_start: 0.6906 (mp) cc_final: 0.6437 (mt) REVERT: 5 384 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7383 (mtmt) REVERT: 5 448 ARG cc_start: 0.6968 (mmm-85) cc_final: 0.6604 (mmm160) REVERT: 5 589 ARG cc_start: 0.4933 (OUTLIER) cc_final: 0.4371 (ptt180) REVERT: 5 612 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6015 (mt) REVERT: 6 95 ARG cc_start: 0.1529 (mtm-85) cc_final: 0.0334 (mtm180) REVERT: 6 151 MET cc_start: 0.0875 (ppp) cc_final: -0.0408 (tmm) REVERT: 6 167 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5340 (ttpt) REVERT: 6 194 PHE cc_start: 0.6010 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: 6 519 MET cc_start: 0.6123 (ptt) cc_final: 0.5521 (ptp) REVERT: 6 621 GLU cc_start: 0.3765 (pp20) cc_final: 0.3356 (pt0) REVERT: 6 630 ASN cc_start: 0.4166 (OUTLIER) cc_final: 0.3903 (m110) REVERT: 7 31 PHE cc_start: 0.6582 (m-80) cc_final: 0.6229 (m-80) REVERT: 7 48 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4443 (pt) REVERT: 7 281 MET cc_start: 0.6283 (tmm) cc_final: 0.5750 (mtt) REVERT: 7 282 ARG cc_start: 0.6649 (tpp80) cc_final: 0.6259 (tpp80) REVERT: 7 299 GLN cc_start: 0.6677 (tp-100) cc_final: 0.5714 (tp-100) REVERT: 7 369 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4204 (mtt) REVERT: 7 601 THR cc_start: 0.6357 (m) cc_final: 0.5917 (p) REVERT: A 6 LEU cc_start: 0.3906 (OUTLIER) cc_final: 0.3074 (pp) REVERT: A 86 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 101 HIS cc_start: 0.6128 (OUTLIER) cc_final: 0.4757 (p90) REVERT: A 113 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7438 (tpp-160) REVERT: A 284 THR cc_start: 0.8514 (t) cc_final: 0.8114 (p) REVERT: A 303 MET cc_start: 0.7914 (mtt) cc_final: 0.7457 (mtt) REVERT: A 306 SER cc_start: 0.7417 (OUTLIER) cc_final: 0.7201 (p) REVERT: A 312 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: A 541 LYS cc_start: 0.7894 (tptt) cc_final: 0.7616 (tmtt) REVERT: H 70 ARG cc_start: 0.7340 (tmm160) cc_final: 0.6672 (tmm160) REVERT: H 76 ARG cc_start: 0.4453 (tpt170) cc_final: 0.3368 (ptm-80) REVERT: H 198 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6653 (tt) REVERT: L 114 ARG cc_start: 0.6250 (tmt170) cc_final: 0.5482 (mmm-85) REVERT: L 169 ARG cc_start: 0.2894 (ptm-80) cc_final: 0.2483 (ptm-80) REVERT: L 171 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.5189 (tp40) REVERT: N 80 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7749 (pp) REVERT: N 176 ASN cc_start: 0.7485 (t0) cc_final: 0.7275 (t0) outliers start: 187 outliers final: 119 residues processed: 822 average time/residue: 0.2280 time to fit residues: 304.9671 Evaluate side-chains 771 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 633 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS Chi-restraints excluded: chain 2 residue 391 CYS 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 452 LEU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 491 ASN Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 750 MET Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 46 VAL Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 223 VAL Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 293 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 443 VAL Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 488 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 154 VAL Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER 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 641 THR Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 693 ILE Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 568 HIS Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 612 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 PHE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 141 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 403 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 49 ASN 3 92 HIS 3 233 GLN 3 310 GLN 3 622 HIS ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 523 GLN 4 527 ASN 5 84 ASN 5 462 GLN ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 203 GLN 6 353 ASN 6 446 ASN 6 486 ASN 6 589 ASN ** 7 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 270 ASN A 444 GLN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 142 GLN N 226 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.261723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.232372 restraints weight = 59689.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.231807 restraints weight = 46972.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.232597 restraints weight = 38480.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.233199 restraints weight = 35204.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.233507 restraints weight = 31775.331| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.9054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 40475 Z= 0.252 Angle : 0.936 17.146 54828 Z= 0.477 Chirality : 0.053 0.261 6193 Planarity : 0.007 0.090 6950 Dihedral : 12.157 113.153 5889 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 6.30 % Allowed : 23.94 % Favored : 69.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.09 % 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: -3.53 (0.11), residues: 4789 helix: -1.15 (0.12), residues: 1590 sheet: -2.40 (0.21), residues: 536 loop : -3.22 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 5 56 TYR 0.044 0.003 TYR 6 236 PHE 0.032 0.003 PHE 6 108 TRP 0.061 0.003 TRP A 297 HIS 0.015 0.002 HIS N 180 Details of bonding type rmsd covalent geometry : bond 0.00576 (40466) covalent geometry : angle 0.93562 (54822) SS BOND : bond 0.00189 ( 3) SS BOND : angle 1.63633 ( 6) hydrogen bonds : bond 0.05267 ( 1028) hydrogen bonds : angle 6.03119 ( 2934) Misc. bond : bond 0.00278 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 722 time to evaluate : 1.602 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. 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. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7767 (t0) cc_final: 0.7386 (t0) REVERT: 2 251 MET cc_start: 0.7128 (mmm) cc_final: 0.6415 (mtp) REVERT: 2 253 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7059 (mp) REVERT: 2 293 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8233 (p) REVERT: 2 351 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5663 (mt-10) REVERT: 2 415 GLN cc_start: 0.4093 (mt0) cc_final: 0.3632 (mt0) REVERT: 2 452 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6901 (pp) REVERT: 2 454 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8060 (mtmm) REVERT: 2 460 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6491 (pt0) REVERT: 2 592 GLN cc_start: 0.6740 (mm-40) cc_final: 0.6535 (mm-40) REVERT: 2 723 MET cc_start: 0.6044 (mmt) cc_final: 0.5604 (mmp) REVERT: 2 788 MET cc_start: 0.6989 (pmm) cc_final: 0.6624 (ppp) REVERT: 3 19 PHE cc_start: 0.6315 (t80) cc_final: 0.5812 (t80) REVERT: 3 203 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6648 (pt0) REVERT: 3 499 MET cc_start: 0.6201 (mmm) cc_final: 0.5679 (mmp) REVERT: 3 590 ARG cc_start: 0.6374 (tpm170) cc_final: 0.6155 (tpp-160) REVERT: 4 200 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7072 (mp) REVERT: 4 221 PHE cc_start: 0.4419 (OUTLIER) cc_final: 0.3787 (t80) REVERT: 4 242 MET cc_start: 0.1236 (tpp) cc_final: 0.0294 (ptt) REVERT: 4 247 MET cc_start: 0.8125 (ttp) cc_final: 0.7802 (ttt) REVERT: 4 248 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5958 (m-10) REVERT: 4 297 ASN cc_start: 0.7268 (p0) cc_final: 0.6933 (p0) REVERT: 4 695 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.7013 (t80) REVERT: 5 65 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7380 (tp) REVERT: 5 259 LEU cc_start: 0.8360 (mt) cc_final: 0.8067 (mt) REVERT: 5 290 MET cc_start: 0.6061 (tpp) cc_final: 0.5835 (tpp) REVERT: 5 308 TYR cc_start: 0.3165 (OUTLIER) cc_final: 0.2309 (m-10) REVERT: 5 340 ILE cc_start: 0.7398 (mp) cc_final: 0.7054 (mt) REVERT: 5 384 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7450 (mtmt) REVERT: 5 462 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.7083 (mt0) REVERT: 5 581 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7119 (mp) REVERT: 5 589 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.4481 (ptt180) REVERT: 5 612 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6664 (mt) REVERT: 6 68 ASN cc_start: 0.6806 (m110) cc_final: 0.6603 (m110) REVERT: 6 90 ASN cc_start: 0.7356 (t0) cc_final: 0.7110 (t0) REVERT: 6 167 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5395 (ttpt) REVERT: 6 194 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: 6 519 MET cc_start: 0.7128 (ptt) cc_final: 0.6510 (ptp) REVERT: 6 617 ILE cc_start: 0.6729 (pt) cc_final: 0.6392 (pt) REVERT: 6 621 GLU cc_start: 0.4137 (pp20) cc_final: 0.3813 (pt0) REVERT: 7 48 ILE cc_start: 0.4902 (OUTLIER) cc_final: 0.4409 (pt) REVERT: 7 260 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5375 (pm20) REVERT: 7 369 MET cc_start: 0.4668 (OUTLIER) cc_final: 0.4285 (mmm) REVERT: 7 623 ASP cc_start: 0.2835 (t0) cc_final: 0.2615 (t0) REVERT: A 6 LEU cc_start: 0.3696 (OUTLIER) cc_final: 0.2660 (pp) REVERT: A 25 TYR cc_start: 0.5743 (m-80) cc_final: 0.4953 (t80) REVERT: A 86 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7397 (tp) REVERT: A 101 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5188 (p90) REVERT: A 230 MET cc_start: 0.6311 (mmm) cc_final: 0.5778 (mtt) REVERT: A 303 MET cc_start: 0.8340 (mtt) cc_final: 0.8083 (mtt) REVERT: A 304 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5559 (ttp80) REVERT: A 306 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 312 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6775 (mp10) REVERT: A 329 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8262 (tp) REVERT: A 389 TYR cc_start: 0.6535 (m-80) cc_final: 0.6101 (m-80) REVERT: A 400 VAL cc_start: 0.0376 (OUTLIER) cc_final: 0.0158 (t) REVERT: A 541 LYS cc_start: 0.7877 (tptt) cc_final: 0.7418 (tmtt) REVERT: H 70 ARG cc_start: 0.7833 (tmm160) cc_final: 0.7205 (tmm160) REVERT: H 76 ARG cc_start: 0.5339 (tpt170) cc_final: 0.3903 (ptm-80) REVERT: H 86 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.5421 (t80) REVERT: H 198 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6640 (tt) REVERT: L 27 HIS cc_start: 0.4726 (OUTLIER) cc_final: 0.4332 (t70) REVERT: L 114 ARG cc_start: 0.6849 (tmt170) cc_final: 0.5750 (mmm-85) REVERT: M 57 TRP cc_start: 0.7635 (p-90) cc_final: 0.7372 (p-90) REVERT: M 102 TYR cc_start: 0.5567 (m-10) cc_final: 0.5096 (m-80) REVERT: N 62 MET cc_start: 0.7361 (ptm) cc_final: 0.7087 (ptt) REVERT: N 66 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7280 (mmp) REVERT: N 80 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8266 (pp) outliers start: 269 outliers final: 159 residues processed: 928 average time/residue: 0.2323 time to fit residues: 350.7707 Evaluate side-chains 824 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 630 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS 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 402 ILE Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 497 LYS Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 586 HIS Chi-restraints excluded: chain 2 residue 601 ILE Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 118 LEU Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 223 VAL Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE 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 326 ASN Chi-restraints excluded: chain 3 residue 356 THR Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 3 residue 450 VAL Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 3 residue 608 THR Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 298 VAL Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 350 THR Chi-restraints excluded: chain 4 residue 374 LEU 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 448 VAL Chi-restraints excluded: chain 4 residue 536 SER Chi-restraints excluded: chain 4 residue 626 TRP Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 TYR Chi-restraints excluded: chain 4 residue 689 LEU Chi-restraints excluded: chain 4 residue 693 ILE Chi-restraints excluded: chain 4 residue 695 TYR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 130 THR Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 219 PHE Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 260 ILE Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 394 VAL Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 433 LEU Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 462 GLN Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 581 LEU Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 612 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 245 VAL Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 508 LEU Chi-restraints excluded: chain 6 residue 529 VAL Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 21 CYS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 76 ILE Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 195 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 260 GLU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 394 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 27 HIS Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 85 CYS Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 152 PHE Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 234 optimal weight: 1.9990 chunk 384 optimal weight: 0.0870 chunk 185 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 148 optimal weight: 0.0770 chunk 120 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 270 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 491 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS 3 199 GLN 3 335 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 627 ASN 5 26 ASN ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN ** 5 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 628 GLN ** 6 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 ASN 6 592 HIS 7 155 GLN ** 7 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 HIS N 118 HIS N 224 GLN N 226 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.270615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.240552 restraints weight = 60297.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.242250 restraints weight = 46900.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.243907 restraints weight = 36006.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.245172 restraints weight = 28264.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.245350 restraints weight = 26104.364| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.9284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40475 Z= 0.141 Angle : 0.775 15.823 54828 Z= 0.385 Chirality : 0.047 0.460 6193 Planarity : 0.005 0.076 6950 Dihedral : 11.551 104.396 5889 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 3.82 % Allowed : 27.20 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -3.10 (0.11), residues: 4789 helix: -0.69 (0.13), residues: 1582 sheet: -2.27 (0.21), residues: 559 loop : -3.01 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 5 56 TYR 0.052 0.002 TYR 6 236 PHE 0.056 0.002 PHE H 8 TRP 0.043 0.002 TRP A 297 HIS 0.013 0.001 HIS 2 754 Details of bonding type rmsd covalent geometry : bond 0.00315 (40466) covalent geometry : angle 0.77537 (54822) SS BOND : bond 0.00165 ( 3) SS BOND : angle 0.69765 ( 6) hydrogen bonds : bond 0.03857 ( 1028) hydrogen bonds : angle 5.45467 ( 2934) Misc. bond : bond 0.00360 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 667 time to evaluate : 1.320 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 214 SER cc_start: 0.8268 (m) cc_final: 0.7504 (p) REVERT: 2 250 ASP cc_start: 0.7523 (t0) cc_final: 0.7206 (t0) REVERT: 2 253 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6704 (mp) REVERT: 2 351 GLU cc_start: 0.5448 (pm20) cc_final: 0.5171 (mt-10) REVERT: 2 626 MET cc_start: 0.4152 (tpp) cc_final: 0.3691 (ttm) REVERT: 2 723 MET cc_start: 0.5568 (mmt) cc_final: 0.4665 (ppp) REVERT: 2 728 ARG cc_start: 0.5818 (ttt180) cc_final: 0.5616 (ttt180) REVERT: 3 19 PHE cc_start: 0.6094 (t80) cc_final: 0.5721 (t80) REVERT: 3 499 MET cc_start: 0.5472 (mmm) cc_final: 0.5186 (mmp) REVERT: 4 200 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7048 (mp) REVERT: 4 221 PHE cc_start: 0.4715 (OUTLIER) cc_final: 0.3840 (t80) REVERT: 4 242 MET cc_start: 0.1323 (tpp) cc_final: 0.0594 (ptt) REVERT: 4 247 MET cc_start: 0.8357 (ttp) cc_final: 0.8034 (ttt) REVERT: 4 248 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6251 (m-10) REVERT: 4 772 LYS cc_start: 0.0711 (tptt) cc_final: 0.0088 (tppt) REVERT: 5 65 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6898 (tp) REVERT: 5 259 LEU cc_start: 0.7837 (mt) cc_final: 0.7590 (mt) REVERT: 5 290 MET cc_start: 0.6036 (tpp) cc_final: 0.5786 (tpp) REVERT: 5 321 ARG cc_start: 0.6240 (tpt170) cc_final: 0.5708 (tpm170) REVERT: 5 340 ILE cc_start: 0.7298 (mp) cc_final: 0.6991 (mt) REVERT: 5 384 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7393 (mtmt) REVERT: 5 564 TYR cc_start: 0.7509 (t80) cc_final: 0.7303 (t80) REVERT: 5 589 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4331 (ptt180) REVERT: 5 612 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6527 (mt) REVERT: 6 90 ASN cc_start: 0.7504 (t0) cc_final: 0.7134 (t0) REVERT: 6 95 ARG cc_start: 0.2457 (mtm-85) cc_final: 0.1471 (mtm180) REVERT: 6 151 MET cc_start: 0.0327 (ppp) cc_final: -0.0750 (ttp) REVERT: 6 167 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5448 (ttpt) REVERT: 6 194 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5800 (m-80) REVERT: 6 321 MET cc_start: 0.4266 (tpp) cc_final: 0.2379 (mtt) REVERT: 6 621 GLU cc_start: 0.4158 (pp20) cc_final: 0.3766 (pt0) REVERT: 7 48 ILE cc_start: 0.4699 (OUTLIER) cc_final: 0.4140 (pt) REVERT: 7 281 MET cc_start: 0.6672 (tmm) cc_final: 0.5737 (mtt) REVERT: 7 299 GLN cc_start: 0.6793 (tp-100) cc_final: 0.5900 (tp-100) REVERT: 7 369 MET cc_start: 0.4906 (OUTLIER) cc_final: 0.4625 (mmm) REVERT: 7 380 MET cc_start: 0.7072 (ttm) cc_final: 0.6861 (ttm) REVERT: 7 623 ASP cc_start: 0.2422 (t0) cc_final: 0.2183 (t0) REVERT: A 6 LEU cc_start: 0.3880 (OUTLIER) cc_final: 0.3070 (pp) REVERT: A 86 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7433 (tp) REVERT: A 101 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.4956 (p90) REVERT: A 284 THR cc_start: 0.8596 (t) cc_final: 0.8280 (p) REVERT: A 303 MET cc_start: 0.8202 (mtt) cc_final: 0.7889 (mtt) REVERT: A 479 LEU cc_start: 0.7866 (mt) cc_final: 0.7050 (tp) REVERT: A 513 MET cc_start: 0.6858 (ppp) cc_final: 0.3078 (mmm) REVERT: A 541 LYS cc_start: 0.7886 (tptt) cc_final: 0.7467 (tmtt) REVERT: H 76 ARG cc_start: 0.4693 (tpt170) cc_final: 0.3733 (ptm-80) REVERT: H 86 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5251 (t80) REVERT: H 198 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7034 (tt) REVERT: L 114 ARG cc_start: 0.6671 (tmt170) cc_final: 0.5730 (mmm-85) REVERT: N 80 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7983 (pp) outliers start: 163 outliers final: 107 residues processed: 780 average time/residue: 0.2281 time to fit residues: 291.9018 Evaluate side-chains 755 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 630 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS 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 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 491 ASN Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 601 ILE Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 309 LYS Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 479 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 221 PHE Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 374 LEU Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 TYR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 219 PHE Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 612 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 PHE Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 174 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 7 residue 21 CYS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 591 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 296 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 chunk 338 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 464 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 400 optimal weight: 0.2980 chunk 479 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 288 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 754 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 754 GLN ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 589 ASN ** 7 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 153 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.271301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.241406 restraints weight = 60970.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.243081 restraints weight = 46552.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.244303 restraints weight = 35634.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.245301 restraints weight = 29584.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.245712 restraints weight = 26776.856| |-----------------------------------------------------------------------------| r_work (final): 0.4782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.9471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40475 Z= 0.133 Angle : 0.752 15.910 54828 Z= 0.372 Chirality : 0.045 0.323 6193 Planarity : 0.005 0.083 6950 Dihedral : 11.328 97.477 5889 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 3.65 % Allowed : 27.92 % Favored : 68.42 % 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: -2.99 (0.11), residues: 4789 helix: -0.60 (0.13), residues: 1594 sheet: -2.17 (0.21), residues: 572 loop : -2.96 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 5 56 TYR 0.048 0.001 TYR 6 236 PHE 0.045 0.002 PHE H 8 TRP 0.045 0.002 TRP A 297 HIS 0.014 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00301 (40466) covalent geometry : angle 0.75210 (54822) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.48088 ( 6) hydrogen bonds : bond 0.03697 ( 1028) hydrogen bonds : angle 5.33311 ( 2934) Misc. bond : bond 0.00314 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 648 time to evaluate : 1.255 Fit side-chains 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: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 214 SER cc_start: 0.8210 (m) cc_final: 0.7385 (p) REVERT: 2 250 ASP cc_start: 0.7468 (t0) cc_final: 0.7133 (t0) REVERT: 2 253 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6774 (mp) REVERT: 2 351 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5369 (mt-10) REVERT: 2 452 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6729 (pp) REVERT: 2 626 MET cc_start: 0.4265 (tpp) cc_final: 0.3835 (ttm) REVERT: 2 723 MET cc_start: 0.5633 (mmt) cc_final: 0.4796 (tmm) REVERT: 3 19 PHE cc_start: 0.6119 (t80) cc_final: 0.5717 (t80) REVERT: 3 109 THR cc_start: 0.7248 (p) cc_final: 0.7031 (p) REVERT: 3 203 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: 3 499 MET cc_start: 0.5483 (mmm) cc_final: 0.5211 (mmp) REVERT: 4 200 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6772 (mp) REVERT: 4 242 MET cc_start: 0.1307 (tpp) cc_final: 0.0523 (ptt) REVERT: 4 247 MET cc_start: 0.8359 (ttp) cc_final: 0.8004 (ttt) REVERT: 4 353 GLN cc_start: 0.6895 (tm-30) cc_final: 0.6690 (tm-30) REVERT: 4 772 LYS cc_start: 0.1361 (tptt) cc_final: 0.0716 (tppt) REVERT: 5 116 MET cc_start: 0.7339 (mmm) cc_final: 0.7091 (mmm) REVERT: 5 259 LEU cc_start: 0.7845 (mt) cc_final: 0.7567 (mt) REVERT: 5 290 MET cc_start: 0.5979 (tpp) cc_final: 0.5733 (tpp) REVERT: 5 308 TYR cc_start: 0.3465 (OUTLIER) cc_final: 0.2390 (m-10) REVERT: 5 321 ARG cc_start: 0.6453 (tpt170) cc_final: 0.5849 (tpm170) REVERT: 5 340 ILE cc_start: 0.7288 (mp) cc_final: 0.6912 (mt) REVERT: 5 508 LEU cc_start: 0.8741 (tt) cc_final: 0.8532 (tt) REVERT: 5 581 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6993 (mp) REVERT: 5 589 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.4321 (ptt180) REVERT: 5 612 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6630 (mt) REVERT: 6 90 ASN cc_start: 0.7482 (t0) cc_final: 0.7120 (t0) REVERT: 6 95 ARG cc_start: 0.2464 (mtm-85) cc_final: 0.1523 (mtm180) REVERT: 6 151 MET cc_start: 0.0240 (ppp) cc_final: -0.0820 (ttp) REVERT: 6 167 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5476 (ttpt) REVERT: 6 194 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: 6 321 MET cc_start: 0.3986 (tpp) cc_final: 0.2610 (mtt) REVERT: 6 461 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.5750 (t0) REVERT: 6 478 ARG cc_start: 0.4708 (OUTLIER) cc_final: 0.4002 (ptp90) REVERT: 6 519 MET cc_start: 0.6867 (ptt) cc_final: 0.6369 (ttp) REVERT: 6 621 GLU cc_start: 0.4528 (pp20) cc_final: 0.4000 (pt0) REVERT: 7 48 ILE cc_start: 0.4680 (OUTLIER) cc_final: 0.4233 (pt) REVERT: 7 281 MET cc_start: 0.6684 (tmm) cc_final: 0.5777 (mtt) REVERT: 7 299 GLN cc_start: 0.6833 (tp-100) cc_final: 0.5930 (tp-100) REVERT: 7 365 ARG cc_start: 0.5307 (OUTLIER) cc_final: 0.3153 (tpt-90) REVERT: 7 369 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.4475 (mtt) REVERT: A 6 LEU cc_start: 0.3705 (OUTLIER) cc_final: 0.3094 (pp) REVERT: A 86 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 101 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.4896 (p90) REVERT: A 230 MET cc_start: 0.6123 (mmm) cc_final: 0.5671 (mtt) REVERT: A 284 THR cc_start: 0.8557 (t) cc_final: 0.8194 (p) REVERT: A 303 MET cc_start: 0.8164 (mtt) cc_final: 0.7922 (mtt) REVERT: A 479 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 513 MET cc_start: 0.7072 (ppp) cc_final: 0.3305 (mmm) REVERT: A 541 LYS cc_start: 0.7802 (tptt) cc_final: 0.7463 (tmtt) REVERT: H 76 ARG cc_start: 0.4595 (tpt170) cc_final: 0.3793 (ptm-80) REVERT: H 86 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5149 (t80) REVERT: H 198 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7205 (tt) REVERT: L 48 MET cc_start: 0.7450 (ttp) cc_final: 0.7179 (ttp) REVERT: L 114 ARG cc_start: 0.6331 (tmt170) cc_final: 0.5736 (mmm-85) REVERT: M 34 MET cc_start: 0.4707 (mmp) cc_final: 0.4464 (mmp) REVERT: N 80 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7894 (pp) outliers start: 156 outliers final: 111 residues processed: 756 average time/residue: 0.2244 time to fit residues: 279.5905 Evaluate side-chains 752 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 618 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS 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 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 572 ASP Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 309 LYS Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 374 LEU Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 672 TYR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 219 PHE Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 581 LEU Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 612 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 174 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 461 ASP Chi-restraints excluded: chain 6 residue 478 ARG Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 MET Chi-restraints excluded: chain 7 residue 143 THR Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 365 ARG Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 591 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain H residue 11 LYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 411 optimal weight: 4.9990 chunk 412 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 295 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 445 optimal weight: 0.6980 chunk 416 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 245 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 288 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 233 GLN 3 288 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 592 HIS 7 155 GLN ** 7 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 248 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 153 HIS N 224 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.269272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.238841 restraints weight = 60450.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.240582 restraints weight = 48590.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.241591 restraints weight = 36370.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.242560 restraints weight = 30463.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.242861 restraints weight = 27612.551| |-----------------------------------------------------------------------------| r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.9756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40475 Z= 0.145 Angle : 0.767 15.754 54828 Z= 0.380 Chirality : 0.046 0.316 6193 Planarity : 0.005 0.088 6950 Dihedral : 11.315 90.904 5888 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 3.68 % Allowed : 27.64 % Favored : 68.68 % 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: -2.96 (0.11), residues: 4789 helix: -0.58 (0.13), residues: 1591 sheet: -2.21 (0.21), residues: 569 loop : -2.92 (0.11), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 5 56 TYR 0.051 0.002 TYR 6 236 PHE 0.041 0.002 PHE H 8 TRP 0.052 0.002 TRP A 297 HIS 0.033 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00335 (40466) covalent geometry : angle 0.76724 (54822) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.61925 ( 6) hydrogen bonds : bond 0.03806 ( 1028) hydrogen bonds : angle 5.37674 ( 2934) Misc. bond : bond 0.00251 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 642 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (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: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 214 SER cc_start: 0.8295 (m) cc_final: 0.7483 (p) REVERT: 2 250 ASP cc_start: 0.7502 (t0) cc_final: 0.7251 (t0) REVERT: 2 253 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6815 (mp) REVERT: 2 351 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5675 (mt-10) REVERT: 2 723 MET cc_start: 0.5620 (mmt) cc_final: 0.4775 (tmm) REVERT: 2 744 ILE cc_start: 0.8257 (pt) cc_final: 0.7881 (mm) REVERT: 3 19 PHE cc_start: 0.6207 (t80) cc_final: 0.5943 (t80) REVERT: 3 109 THR cc_start: 0.7217 (p) cc_final: 0.6993 (p) REVERT: 3 203 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6219 (pm20) REVERT: 3 254 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7587 (ptp-170) REVERT: 3 499 MET cc_start: 0.5416 (mmm) cc_final: 0.5170 (mmp) REVERT: 4 200 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6981 (mp) REVERT: 4 242 MET cc_start: 0.1168 (tpp) cc_final: 0.0496 (ptt) REVERT: 4 247 MET cc_start: 0.8364 (ttp) cc_final: 0.8089 (ttt) REVERT: 4 510 LEU cc_start: 0.7768 (pt) cc_final: 0.7537 (pt) REVERT: 4 594 GLU cc_start: 0.7048 (mp0) cc_final: 0.6751 (mp0) REVERT: 4 648 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5558 (pt) REVERT: 4 716 TYR cc_start: 0.5033 (m-80) cc_final: 0.4813 (m-80) REVERT: 4 740 ILE cc_start: 0.7564 (pt) cc_final: 0.6754 (mp) REVERT: 4 772 LYS cc_start: 0.1447 (tptt) cc_final: 0.0888 (tppt) REVERT: 5 116 MET cc_start: 0.7363 (mmm) cc_final: 0.7124 (mmm) REVERT: 5 259 LEU cc_start: 0.7997 (mt) cc_final: 0.7741 (mt) REVERT: 5 290 MET cc_start: 0.6039 (tpp) cc_final: 0.5759 (tpp) REVERT: 5 308 TYR cc_start: 0.3167 (OUTLIER) cc_final: 0.2025 (m-10) REVERT: 5 321 ARG cc_start: 0.6385 (tpt170) cc_final: 0.5781 (tpm170) REVERT: 5 384 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7150 (mtmt) REVERT: 5 508 LEU cc_start: 0.8773 (tt) cc_final: 0.8568 (tt) REVERT: 5 581 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7141 (mp) REVERT: 5 589 ARG cc_start: 0.5020 (OUTLIER) cc_final: 0.4320 (ptt180) REVERT: 5 612 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6449 (mt) REVERT: 6 90 ASN cc_start: 0.7554 (t0) cc_final: 0.7221 (t0) REVERT: 6 95 ARG cc_start: 0.2635 (mtm-85) cc_final: 0.1860 (mtm180) REVERT: 6 167 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5372 (ttpt) REVERT: 6 194 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: 6 321 MET cc_start: 0.4634 (tpp) cc_final: 0.2775 (mtt) REVERT: 6 461 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5710 (t0) REVERT: 6 478 ARG cc_start: 0.4819 (OUTLIER) cc_final: 0.4087 (ptp90) REVERT: 6 519 MET cc_start: 0.6967 (ptt) cc_final: 0.6440 (ttp) REVERT: 6 621 GLU cc_start: 0.4449 (pp20) cc_final: 0.3878 (pt0) REVERT: 7 48 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4259 (pt) REVERT: 7 76 ILE cc_start: 0.6194 (tt) cc_final: 0.5795 (tp) REVERT: 7 281 MET cc_start: 0.6547 (tmm) cc_final: 0.5715 (mtt) REVERT: 7 299 GLN cc_start: 0.6862 (tp-100) cc_final: 0.5965 (tp-100) REVERT: 7 365 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.3213 (tpt-90) REVERT: 7 369 MET cc_start: 0.5117 (OUTLIER) cc_final: 0.4644 (mtt) REVERT: 7 557 ASN cc_start: 0.7942 (p0) cc_final: 0.7059 (t0) REVERT: 7 623 ASP cc_start: 0.2652 (t0) cc_final: 0.2393 (t0) REVERT: A 6 LEU cc_start: 0.3727 (OUTLIER) cc_final: 0.3095 (pp) REVERT: A 86 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7567 (tp) REVERT: A 101 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.5004 (p90) REVERT: A 230 MET cc_start: 0.6147 (mmm) cc_final: 0.5113 (mtt) REVERT: A 284 THR cc_start: 0.8576 (t) cc_final: 0.8203 (p) REVERT: A 303 MET cc_start: 0.8308 (mtt) cc_final: 0.8012 (mtt) REVERT: A 479 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7128 (tp) REVERT: A 513 MET cc_start: 0.6726 (ppp) cc_final: 0.4160 (mmm) REVERT: A 541 LYS cc_start: 0.7895 (tptt) cc_final: 0.7423 (tmtt) REVERT: H 76 ARG cc_start: 0.4624 (tpt170) cc_final: 0.3831 (ptm-80) REVERT: H 86 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.5238 (t80) REVERT: H 198 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7375 (tt) REVERT: L 73 GLU cc_start: 0.5268 (mm-30) cc_final: 0.4958 (mm-30) REVERT: L 114 ARG cc_start: 0.6479 (tmt170) cc_final: 0.5782 (mmm-85) REVERT: M 119 ARG cc_start: 0.6427 (mpt180) cc_final: 0.6127 (mpt180) REVERT: N 80 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7949 (pp) outliers start: 157 outliers final: 119 residues processed: 753 average time/residue: 0.2268 time to fit residues: 281.4745 Evaluate side-chains 761 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 618 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 253 LEU Chi-restraints excluded: chain 2 residue 277 GLU Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 351 GLU Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 379 LYS 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 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 601 ILE Chi-restraints excluded: chain 2 residue 785 PHE Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 122 VAL Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 238 TYR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 309 LYS Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 371 VAL Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 4 residue 200 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 248 PHE Chi-restraints excluded: chain 4 residue 277 LEU Chi-restraints excluded: chain 4 residue 302 MET Chi-restraints excluded: chain 4 residue 338 HIS Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 374 LEU Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 672 TYR Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 4 residue 764 TRP Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 219 PHE Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 311 ILE Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 384 LYS Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 444 PHE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 581 LEU Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 612 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 56 GLU Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 174 CYS Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 313 THR Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 461 ASP Chi-restraints excluded: chain 6 residue 478 ARG Chi-restraints excluded: chain 6 residue 531 GLU Chi-restraints excluded: chain 6 residue 592 HIS Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 48 ILE Chi-restraints excluded: chain 7 residue 109 MET Chi-restraints excluded: chain 7 residue 143 THR Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 155 GLN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 329 GLN Chi-restraints excluded: chain 7 residue 365 ARG Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 591 GLU Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 135 PHE Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 154 optimal weight: 0.1980 chunk 370 optimal weight: 0.0010 chunk 113 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 339 optimal weight: 0.0030 chunk 420 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 288 ASN 2 491 ASN ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 288 ASN 4 337 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN 6 592 HIS 7 155 GLN ** 7 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 248 HIS A 243 GLN A 487 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 153 HIS N 224 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.272046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.243024 restraints weight = 60975.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.244511 restraints weight = 46733.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.245574 restraints weight = 34868.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.246552 restraints weight = 30456.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.246843 restraints weight = 27109.669| |-----------------------------------------------------------------------------| r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.9904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 40475 Z= 0.130 Angle : 0.752 15.866 54828 Z= 0.369 Chirality : 0.045 0.246 6193 Planarity : 0.005 0.081 6950 Dihedral : 11.156 88.281 5888 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.35 % Allowed : 28.32 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.84 (0.12), residues: 4789 helix: -0.46 (0.13), residues: 1593 sheet: -2.01 (0.21), residues: 594 loop : -2.89 (0.11), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 5 56 TYR 0.038 0.001 TYR 6 236 PHE 0.040 0.001 PHE H 8 TRP 0.039 0.002 TRP 2 554 HIS 0.024 0.001 HIS N 153 Details of bonding type rmsd covalent geometry : bond 0.00293 (40466) covalent geometry : angle 0.75205 (54822) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.36608 ( 6) hydrogen bonds : bond 0.03617 ( 1028) hydrogen bonds : angle 5.27248 ( 2934) Misc. bond : bond 0.00217 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7935.68 seconds wall clock time: 137 minutes 27.76 seconds (8247.76 seconds total)