Starting phenix.real_space_refine on Tue Sep 15 13:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6raw_4785/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.map" model { file = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6raw_4785/09_2026/6raw_4785.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 8.36, per 1000 atoms: 0.21 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: 3.60 Conformation dependent library (CDL) restraints added in 1.6 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: 1.03 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: 7.39 Time building geometry restraints manager: 4.65 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: 22756 26.68 - 53.35: 1682 53.35 - 80.03: 195 80.03 - 106.71: 43 106.71 - 133.38: 4 Dihedral angle restraints: 24680 sinusoidal: 10430 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 24677 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 34.010 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4929 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= 0.563 Angle : 1.292 24.651 54828 Z= 0.734 Chirality : 0.126 2.140 6193 Planarity : 0.010 0.385 6950 Dihedral : 18.235 133.383 15413 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/Z covalent geometry : bond 0.00673 / 0.34 (40466) covalent geometry : angle 1.29220 / 0.73 (54822) SS BOND : bond 0.00131 / 0.07 ( 3) SS BOND : angle 1.66003 / 0.65 ( 6) hydrogen bonds : bond 0.19059 / 12.41 ( 1028) hydrogen bonds : angle 8.19270 / 5.49 ( 2934) Misc. bond : bond 0.37008 / 18.61 ( 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 : 1.526 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: 0.2678 time to fit residues: 540.0463 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 : 1.456 ------------------------------------------------------------------------------- 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... 2 286 HIS 2 289 GLN 2 428 HIS 2 534 GLN ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 656 GLN 2 699 GLN 3 13 GLN 3 199 GLN 3 233 GLN 3 310 GLN 3 335 ASN 3 448 ASN 3 495 HIS 4 353 GLN 4 371 HIS 4 378 HIS ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 557 GLN 4 637 GLN 4 710 GLN ** 4 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 746 HIS 5 233 GLN ** 5 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 HIS 5 541 ASN 5 644 GLN 6 353 ASN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 584 HIS ** 7 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 276 ASN A 467 HIS H 175 HIS H 181 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 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 Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.286133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.263921 restraints weight = 63151.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.265208 restraints weight = 51566.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.265973 restraints weight = 43682.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.266758 restraints weight = 35499.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.267026 restraints weight = 32094.412| |-----------------------------------------------------------------------------| r_work (final): 0.4974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40475 Z= 0.196 Angle : 0.940 15.681 54828 Z= 0.478 Chirality : 0.053 0.527 6193 Planarity : 0.007 0.124 6950 Dihedral : 13.401 122.880 5944 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.09 % Favored : 86.89 % Rotamer: Outliers : 4.54 % Allowed : 18.72 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.28 % 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: -4.60 (0.10), residues: 4789 helix: -2.19 (0.11), residues: 1560 sheet: -3.61 (0.19), residues: 483 loop : -3.63 (0.10), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG 2 742 TYR 0.038 0.002 TYR M 100 PHE 0.030 0.002 PHE M 17 TRP 0.033 0.002 TRP M 170 HIS 0.020 0.002 HIS 4 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (40466) covalent geometry : angle 0.94013 / 0.48 (54822) SS BOND : bond 0.01122 / 0.59 ( 3) SS BOND : angle 1.92564 / 1.07 ( 6) hydrogen bonds : bond 0.05691 / 3.76 ( 1028) hydrogen bonds : angle 6.62845 / 4.49 ( 2934) Misc. bond : bond 0.01045 / 0.57 ( 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 931 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 737 time to evaluate : 1.514 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 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 239 GLN cc_start: 0.8040 (mp10) cc_final: 0.6861 (mt0) REVERT: 2 250 ASP cc_start: 0.7253 (t0) cc_final: 0.6812 (t0) REVERT: 2 255 ILE cc_start: 0.5700 (mt) cc_final: 0.5415 (mt) REVERT: 2 277 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5869 (pt0) REVERT: 2 350 MET cc_start: 0.3453 (mmt) cc_final: 0.2501 (ptp) REVERT: 2 353 THR cc_start: 0.3948 (OUTLIER) cc_final: 0.3214 (t) REVERT: 2 362 THR cc_start: 0.6137 (p) cc_final: 0.5834 (p) REVERT: 2 415 GLN cc_start: 0.5313 (mm-40) cc_final: 0.5053 (mm-40) REVERT: 2 454 LYS cc_start: 0.6286 (mtmm) cc_final: 0.5919 (mtmm) REVERT: 2 589 MET cc_start: 0.3170 (mmp) cc_final: 0.2812 (mmp) REVERT: 2 723 MET cc_start: 0.3474 (mmt) cc_final: 0.1872 (ptt) REVERT: 3 221 ASP cc_start: 0.6742 (t70) cc_final: 0.6518 (t70) REVERT: 3 480 MET cc_start: 0.2508 (tpp) cc_final: 0.1870 (tpp) REVERT: 4 242 MET cc_start: 0.2195 (tpp) cc_final: 0.1172 (ptt) REVERT: 4 247 MET cc_start: 0.6996 (ttp) cc_final: 0.5690 (tpt) REVERT: 4 282 MET cc_start: 0.4495 (tpt) cc_final: 0.2994 (mmm) REVERT: 4 551 LYS cc_start: 0.5983 (tptp) cc_final: 0.4488 (mtpt) REVERT: 4 580 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7748 (mmtm) REVERT: 4 664 LEU cc_start: 0.6988 (pp) cc_final: 0.6304 (mt) REVERT: 4 675 THR cc_start: 0.1003 (OUTLIER) cc_final: 0.0786 (p) REVERT: 4 700 LEU cc_start: 0.3834 (mp) cc_final: 0.3606 (mm) REVERT: 5 120 GLN cc_start: 0.5368 (pt0) cc_final: 0.5010 (pt0) REVERT: 6 194 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: 6 519 MET cc_start: 0.3763 (ptt) cc_final: 0.3362 (ptp) REVERT: 6 642 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6522 (ttp80) REVERT: 7 31 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6130 (m-80) REVERT: 7 58 PHE cc_start: 0.5157 (t80) cc_final: 0.4957 (t80) REVERT: 7 176 MET cc_start: 0.2550 (ttp) cc_final: 0.2288 (ttm) REVERT: 7 260 GLU cc_start: 0.5884 (mp0) cc_final: 0.5364 (mp0) REVERT: 7 269 ASP cc_start: 0.5265 (m-30) cc_final: 0.4822 (t0) REVERT: 7 365 ARG cc_start: 0.4640 (mmm-85) cc_final: 0.2296 (ptp90) REVERT: 7 598 MET cc_start: 0.6153 (mmt) cc_final: 0.5794 (mmp) REVERT: A 45 MET cc_start: 0.2896 (mpp) cc_final: 0.2461 (mtt) REVERT: A 268 LEU cc_start: 0.0202 (OUTLIER) cc_final: -0.0039 (pp) REVERT: A 541 LYS cc_start: 0.8097 (tptt) cc_final: 0.7458 (tmtt) REVERT: H 11 LYS cc_start: 0.6015 (mttm) cc_final: 0.5718 (mttm) REVERT: H 76 ARG cc_start: 0.3522 (tpt170) cc_final: 0.1385 (ptm-80) REVERT: L 8 PHE cc_start: 0.2408 (m-80) cc_final: 0.1927 (m-80) REVERT: M 122 PHE cc_start: 0.4510 (t80) cc_final: 0.4076 (t80) outliers start: 194 outliers final: 107 residues processed: 877 average time/residue: 0.2458 time to fit residues: 350.6337 Evaluate side-chains 721 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 608 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 309 VAL Chi-restraints excluded: chain 2 residue 340 CYS Chi-restraints excluded: chain 2 residue 353 THR 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 590 GLU Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 647 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 253 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 347 SER Chi-restraints excluded: chain 3 residue 421 MET Chi-restraints excluded: chain 3 residue 448 ASN 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 396 ILE 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 4 residue 752 SER Chi-restraints excluded: chain 5 residue 37 PHE Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 292 VAL Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 421 THR Chi-restraints excluded: chain 5 residue 507 ILE Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 183 LYS 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 365 PHE Chi-restraints excluded: chain 6 residue 402 SER Chi-restraints excluded: chain 6 residue 512 ILE Chi-restraints excluded: chain 6 residue 530 ASP Chi-restraints excluded: chain 6 residue 590 TYR Chi-restraints excluded: chain 6 residue 609 THR 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 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 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 379 LEU Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 27 ILE 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 213 SER Chi-restraints excluded: chain A residue 221 LEU 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 302 SER 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 107 ILE 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 M residue 64 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 166 GLN Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 74 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 352 GLN 2 591 GLN 3 65 ASN 3 310 GLN 3 418 HIS 3 495 HIS 3 553 HIS 4 345 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS 4 735 GLN 4 767 HIS 5 373 ASN 5 541 ASN 6 231 GLN ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 GLN 7 105 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS N 224 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.282896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.258505 restraints weight = 62095.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.259677 restraints weight = 50981.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.261148 restraints weight = 41672.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.262053 restraints weight = 33344.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.262188 restraints weight = 31516.838| |-----------------------------------------------------------------------------| r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40475 Z= 0.179 Angle : 0.845 13.402 54828 Z= 0.428 Chirality : 0.049 0.364 6193 Planarity : 0.006 0.074 6950 Dihedral : 12.567 124.343 5829 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 5.62 % Allowed : 20.19 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.13 % 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: -4.11 (0.11), residues: 4789 helix: -1.71 (0.12), residues: 1575 sheet: -3.16 (0.19), residues: 551 loop : -3.41 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 7 106 TYR 0.031 0.002 TYR 5 308 PHE 0.043 0.002 PHE L 84 TRP 0.058 0.003 TRP A 297 HIS 0.019 0.001 HIS 7 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (40466) covalent geometry : angle 0.84528 / 0.43 (54822) SS BOND : bond 0.00153 / 0.07 ( 3) SS BOND : angle 1.33781 / 0.65 ( 6) hydrogen bonds : bond 0.04933 / 3.25 ( 1028) hydrogen bonds : angle 6.16026 / 4.17 ( 2934) Misc. bond : bond 0.00632 / 0.41 ( 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 939 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 699 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 239 GLN cc_start: 0.7496 (mp10) cc_final: 0.6727 (mt0) REVERT: 2 250 ASP cc_start: 0.7379 (t0) cc_final: 0.6926 (t0) REVERT: 2 350 MET cc_start: 0.3347 (mmt) cc_final: 0.2813 (ptp) REVERT: 2 362 THR cc_start: 0.6589 (p) cc_final: 0.6376 (p) REVERT: 2 415 GLN cc_start: 0.4920 (mm-40) cc_final: 0.4694 (mt0) REVERT: 2 454 LYS cc_start: 0.6785 (mtmm) cc_final: 0.6385 (mtmm) REVERT: 2 657 ASP cc_start: 0.5289 (m-30) cc_final: 0.5081 (m-30) REVERT: 2 723 MET cc_start: 0.3626 (mmt) cc_final: 0.2048 (ptt) REVERT: 3 123 CYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4897 (t) REVERT: 3 323 ILE cc_start: 0.6633 (mm) cc_final: 0.6194 (mm) REVERT: 4 173 MET cc_start: 0.6738 (mmm) cc_final: 0.6263 (mmm) REVERT: 4 242 MET cc_start: 0.2030 (tpp) cc_final: 0.0637 (ptt) REVERT: 4 247 MET cc_start: 0.7413 (ttp) cc_final: 0.6174 (tpt) REVERT: 4 397 TYR cc_start: 0.2547 (OUTLIER) cc_final: 0.1392 (m-80) REVERT: 4 451 LEU cc_start: 0.7069 (mt) cc_final: 0.6744 (mt) REVERT: 4 675 THR cc_start: 0.1393 (OUTLIER) cc_final: 0.1149 (p) REVERT: 5 49 LYS cc_start: 0.4233 (OUTLIER) cc_final: 0.3861 (mtmm) REVERT: 5 51 ARG cc_start: 0.4171 (mtp85) cc_final: 0.2813 (mtp85) REVERT: 5 65 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.5204 (tp) REVERT: 5 88 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7264 (m) REVERT: 5 500 ASN cc_start: 0.6784 (t0) cc_final: 0.6480 (m-40) REVERT: 5 508 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8186 (tt) REVERT: 5 589 ARG cc_start: 0.4659 (OUTLIER) cc_final: 0.4380 (ptt180) REVERT: 6 14 LYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5988 (tmmt) REVERT: 6 55 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4840 (tt) REVERT: 6 151 MET cc_start: 0.0385 (ppp) cc_final: -0.0049 (tmm) REVERT: 6 167 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5235 (pttt) REVERT: 6 187 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.4514 (pt) REVERT: 6 194 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.4585 (m-80) REVERT: 6 519 MET cc_start: 0.4409 (ptt) cc_final: 0.3954 (ptp) REVERT: 7 31 PHE cc_start: 0.6769 (m-80) cc_final: 0.6466 (m-80) REVERT: 7 72 ARG cc_start: 0.2368 (OUTLIER) cc_final: 0.1765 (ttm170) REVERT: 7 260 GLU cc_start: 0.5986 (mp0) cc_final: 0.5608 (mp0) REVERT: 7 269 ASP cc_start: 0.5602 (m-30) cc_final: 0.4909 (t0) REVERT: 7 354 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7469 (tt) REVERT: 7 365 ARG cc_start: 0.4780 (mmm-85) cc_final: 0.1958 (ptp90) REVERT: 7 369 MET cc_start: 0.4753 (OUTLIER) cc_final: 0.4243 (mtt) REVERT: 7 598 MET cc_start: 0.6439 (mmt) cc_final: 0.6082 (mmp) REVERT: A 45 MET cc_start: 0.3114 (mpp) cc_final: 0.2852 (mtt) REVERT: A 216 LEU cc_start: 0.6614 (mt) cc_final: 0.6374 (mt) REVERT: A 221 LEU cc_start: 0.4850 (OUTLIER) cc_final: 0.4594 (tp) REVERT: A 541 LYS cc_start: 0.8143 (tptt) cc_final: 0.7563 (tmtt) REVERT: H 11 LYS cc_start: 0.6281 (mttm) cc_final: 0.6065 (mttm) REVERT: H 76 ARG cc_start: 0.3927 (tpt170) cc_final: 0.2050 (ptm-80) REVERT: H 86 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4930 (t80) REVERT: L 8 PHE cc_start: 0.2412 (m-80) cc_final: 0.1897 (m-80) REVERT: L 114 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4634 (mmm-85) REVERT: M 91 HIS cc_start: 0.3903 (OUTLIER) cc_final: 0.3498 (m170) outliers start: 240 outliers final: 129 residues processed: 869 average time/residue: 0.2481 time to fit residues: 351.3462 Evaluate side-chains 764 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 615 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 340 CYS Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 363 LEU 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 452 LEU 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 584 SER Chi-restraints excluded: chain 2 residue 610 THR Chi-restraints excluded: chain 2 residue 612 ILE 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 2 residue 750 MET 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 214 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU 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 347 SER Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 417 ILE Chi-restraints excluded: chain 3 residue 448 ASN Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 263 VAL 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 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 585 THR Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 675 THR Chi-restraints excluded: chain 4 residue 693 ILE Chi-restraints excluded: chain 5 residue 49 LYS Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 88 THR Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 332 LEU Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU Chi-restraints excluded: chain 5 residue 508 LEU Chi-restraints excluded: chain 5 residue 529 LEU Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 14 LYS Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 512 ILE Chi-restraints excluded: chain 6 residue 590 TYR Chi-restraints excluded: chain 6 residue 616 MET 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 25 ASP 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 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 257 CYS 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 354 LEU Chi-restraints excluded: chain 7 residue 362 VAL Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 604 ARG Chi-restraints excluded: chain 7 residue 616 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU 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 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU 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 373 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 516 LEU 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 49 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 30 TYR 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 114 ARG Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 152 PHE Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 446 optimal weight: 0.5980 chunk 255 optimal weight: 0.5980 chunk 370 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 344 optimal weight: 0.0370 chunk 126 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 339 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 433 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 714 ASN 3 418 HIS 4 345 ASN ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 485 GLN 4 533 GLN 5 233 GLN 5 521 HIS 6 337 ASN 6 592 HIS 6 636 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 147 ASN N 153 HIS N 224 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.283415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.258795 restraints weight = 62169.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.260936 restraints weight = 52445.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.262311 restraints weight = 39425.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.262697 restraints weight = 33531.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.263093 restraints weight = 28690.700| |-----------------------------------------------------------------------------| r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 40475 Z= 0.151 Angle : 0.780 12.316 54828 Z= 0.392 Chirality : 0.047 0.345 6193 Planarity : 0.006 0.109 6950 Dihedral : 12.091 125.602 5816 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 5.41 % Allowed : 22.49 % Favored : 72.10 % Cbeta Deviations : 0.00 % 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: -3.81 (0.11), residues: 4789 helix: -1.39 (0.12), residues: 1570 sheet: -2.87 (0.20), residues: 543 loop : -3.31 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 3 617 TYR 0.018 0.002 TYR M 100 PHE 0.036 0.002 PHE 3 253 TRP 0.052 0.002 TRP A 297 HIS 0.018 0.001 HIS 7 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (40466) covalent geometry : angle 0.78008 / 0.39 (54822) SS BOND : bond 0.00533 / 0.28 ( 3) SS BOND : angle 1.05220 / 0.48 ( 6) hydrogen bonds : bond 0.04340 / 2.89 ( 1028) hydrogen bonds : angle 5.91672 / 4.00 ( 2934) Misc. bond : bond 0.00434 / 0.25 ( 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 900 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 669 time to evaluate : 1.490 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 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 TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 2 186 SER cc_start: 0.6398 (t) cc_final: 0.6142 (p) REVERT: 2 250 ASP cc_start: 0.7245 (t0) cc_final: 0.6906 (t0) REVERT: 2 350 MET cc_start: 0.3238 (mmt) cc_final: 0.2858 (ptp) REVERT: 2 362 THR cc_start: 0.6689 (p) cc_final: 0.6455 (p) REVERT: 2 374 ARG cc_start: 0.6943 (mmt90) cc_final: 0.6161 (mmt180) REVERT: 2 723 MET cc_start: 0.3543 (mmt) cc_final: 0.2707 (ptt) REVERT: 2 754 HIS cc_start: 0.5313 (m170) cc_final: 0.4684 (m170) REVERT: 2 794 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6388 (m) REVERT: 3 225 ARG cc_start: 0.6059 (mtp85) cc_final: 0.5844 (ttm-80) REVERT: 3 323 ILE cc_start: 0.6742 (mm) cc_final: 0.6409 (mm) REVERT: 4 173 MET cc_start: 0.6660 (mmm) cc_final: 0.6232 (mmm) REVERT: 4 242 MET cc_start: 0.1877 (tpp) cc_final: 0.0550 (ptt) REVERT: 4 247 MET cc_start: 0.7229 (ttp) cc_final: 0.6021 (tpt) REVERT: 4 397 TYR cc_start: 0.2914 (OUTLIER) cc_final: 0.1728 (m-80) REVERT: 4 664 LEU cc_start: 0.5890 (pp) cc_final: 0.5076 (mp) REVERT: 5 51 ARG cc_start: 0.4413 (mtp85) cc_final: 0.2880 (mtp85) REVERT: 5 65 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5420 (tp) REVERT: 5 88 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7282 (m) REVERT: 5 220 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: 5 416 MET cc_start: 0.6180 (ptm) cc_final: 0.5976 (ptp) REVERT: 5 426 MET cc_start: 0.6616 (ttp) cc_final: 0.6412 (ttt) REVERT: 5 500 ASN cc_start: 0.6714 (t0) cc_final: 0.6514 (m-40) REVERT: 5 508 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8098 (tt) REVERT: 6 151 MET cc_start: 0.0141 (ppp) cc_final: -0.0313 (tmm) REVERT: 6 194 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.4700 (m-80) REVERT: 6 519 MET cc_start: 0.4571 (ptt) cc_final: 0.4027 (ptp) REVERT: 6 630 ASN cc_start: 0.4004 (OUTLIER) cc_final: 0.3457 (m110) REVERT: 7 31 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: 7 260 GLU cc_start: 0.5775 (mp0) cc_final: 0.5488 (mp0) REVERT: 7 269 ASP cc_start: 0.5674 (m-30) cc_final: 0.4905 (t0) REVERT: 7 281 MET cc_start: 0.6468 (tmm) cc_final: 0.5309 (mtt) REVERT: 7 369 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.4090 (mtt) REVERT: 7 397 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7022 (mm) REVERT: A 216 LEU cc_start: 0.6668 (mt) cc_final: 0.6380 (mt) REVERT: A 221 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4472 (tp) REVERT: A 342 TYR cc_start: 0.6178 (t80) cc_final: 0.5711 (t80) REVERT: A 541 LYS cc_start: 0.8000 (tptt) cc_final: 0.7551 (tmtt) REVERT: H 11 LYS cc_start: 0.6049 (mttm) cc_final: 0.5823 (mttm) REVERT: H 76 ARG cc_start: 0.3759 (tpt170) cc_final: 0.2065 (ptm160) REVERT: H 80 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6931 (p) REVERT: H 198 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6414 (tt) REVERT: L 114 ARG cc_start: 0.6271 (tmt170) cc_final: 0.4817 (mmm-85) REVERT: L 171 GLN cc_start: 0.4696 (OUTLIER) cc_final: 0.3913 (tp-100) REVERT: M 91 HIS cc_start: 0.4107 (OUTLIER) cc_final: 0.3787 (m170) REVERT: M 131 HIS cc_start: 0.6067 (t70) cc_final: 0.5641 (t70) REVERT: N 176 ASN cc_start: 0.7807 (t0) cc_final: 0.7584 (t0) outliers start: 231 outliers final: 130 residues processed: 821 average time/residue: 0.2467 time to fit residues: 332.0857 Evaluate side-chains 744 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 598 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 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 381 VAL 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 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 521 THR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 794 THR Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 347 SER Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 244 ILE Chi-restraints excluded: chain 4 residue 263 VAL 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 448 VAL Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 693 ILE Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 88 THR Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 144 VAL Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 361 ARG Chi-restraints excluded: chain 5 residue 376 LEU 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 529 LEU Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 619 SER Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 59 PHE 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 356 VAL Chi-restraints excluded: chain 6 residue 362 LEU Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 630 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP 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 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 173 VAL Chi-restraints excluded: chain 7 residue 191 THR 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 369 MET Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 604 ARG 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 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 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR 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 390 VAL Chi-restraints excluded: chain A residue 435 LEU 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 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain H residue 198 LEU 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 142 TYR Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 168 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 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 152 PHE Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 406 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 422 optimal weight: 0.6980 chunk 299 optimal weight: 0.5980 chunk 251 optimal weight: 0.1980 chunk 486 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 364 GLN 3 418 HIS 3 448 ASN 4 198 GLN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 735 GLN 5 239 HIS 6 260 ASN 6 466 HIS 6 645 ASN 7 155 GLN 7 248 HIS ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 487 HIS H 145 ASN H 195 GLN L 91 HIS N 153 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.283033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.257431 restraints weight = 61609.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.258854 restraints weight = 49006.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.260206 restraints weight = 39354.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.261178 restraints weight = 31732.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.261417 restraints weight = 29097.903| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40475 Z= 0.136 Angle : 0.742 12.187 54828 Z= 0.373 Chirality : 0.045 0.186 6193 Planarity : 0.006 0.074 6950 Dihedral : 11.731 127.473 5811 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 5.08 % Allowed : 23.31 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.59 (0.11), residues: 4789 helix: -1.21 (0.12), residues: 1588 sheet: -2.59 (0.21), residues: 544 loop : -3.22 (0.11), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 709 TYR 0.018 0.001 TYR H 86 PHE 0.034 0.002 PHE 6 185 TRP 0.026 0.001 TRP A 297 HIS 0.019 0.001 HIS 7 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (40466) covalent geometry : angle 0.74209 / 0.37 (54822) SS BOND : bond 0.00857 / 0.45 ( 3) SS BOND : angle 0.79615 / 0.37 ( 6) hydrogen bonds : bond 0.04066 / 2.72 ( 1028) hydrogen bonds : angle 5.66891 / 3.84 ( 2934) Misc. bond : bond 0.00115 / 0.07 ( 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 871 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 654 time to evaluate : 1.508 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 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: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 186 SER cc_start: 0.6498 (t) cc_final: 0.6265 (p) REVERT: 2 239 GLN cc_start: 0.7506 (mp10) cc_final: 0.7265 (mp10) REVERT: 2 250 ASP cc_start: 0.7296 (t0) cc_final: 0.6968 (t0) REVERT: 2 350 MET cc_start: 0.3243 (mmt) cc_final: 0.2905 (ptp) REVERT: 2 362 THR cc_start: 0.6823 (p) cc_final: 0.6554 (p) REVERT: 2 374 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6379 (tpp-160) REVERT: 2 723 MET cc_start: 0.3639 (mmt) cc_final: 0.2490 (ptt) REVERT: 2 794 THR cc_start: 0.6770 (m) cc_final: 0.5930 (m) REVERT: 3 46 VAL cc_start: 0.3523 (OUTLIER) cc_final: 0.3058 (t) REVERT: 3 464 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7195 (mt) REVERT: 3 572 MET cc_start: 0.5683 (mmm) cc_final: 0.5014 (ppp) REVERT: 4 242 MET cc_start: 0.1714 (tpp) cc_final: 0.0392 (ptt) REVERT: 4 247 MET cc_start: 0.7553 (ttp) cc_final: 0.6310 (tpt) REVERT: 4 397 TYR cc_start: 0.3096 (OUTLIER) cc_final: 0.1932 (m-80) REVERT: 4 462 ASP cc_start: 0.7449 (t0) cc_final: 0.7226 (t0) REVERT: 4 664 LEU cc_start: 0.6381 (pp) cc_final: 0.5494 (mp) REVERT: 4 697 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8181 (mtt180) REVERT: 4 740 ILE cc_start: 0.5932 (pt) cc_final: 0.5670 (pt) REVERT: 5 51 ARG cc_start: 0.4679 (mtp85) cc_final: 0.3068 (mtp85) REVERT: 5 65 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5555 (tp) REVERT: 5 88 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7389 (m) REVERT: 5 220 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6845 (tp40) REVERT: 5 259 LEU cc_start: 0.7347 (mt) cc_final: 0.7089 (mt) REVERT: 5 508 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8252 (tt) REVERT: 5 589 ARG cc_start: 0.4683 (OUTLIER) cc_final: 0.4406 (ptt180) REVERT: 6 151 MET cc_start: 0.0103 (ppp) cc_final: -0.0384 (tmm) REVERT: 6 167 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5411 (pttt) REVERT: 6 194 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4626 (m-80) REVERT: 6 519 MET cc_start: 0.4640 (ptt) cc_final: 0.4086 (ptp) REVERT: 7 31 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: 7 48 ILE cc_start: 0.5124 (OUTLIER) cc_final: 0.4442 (pt) REVERT: 7 72 ARG cc_start: 0.2356 (OUTLIER) cc_final: 0.1731 (ttm170) REVERT: 7 269 ASP cc_start: 0.5699 (m-30) cc_final: 0.4913 (t0) REVERT: 7 369 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.4150 (mtt) REVERT: 7 598 MET cc_start: 0.6349 (mmt) cc_final: 0.6127 (mmp) REVERT: A 86 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7330 (tp) REVERT: A 221 LEU cc_start: 0.4577 (OUTLIER) cc_final: 0.4194 (tp) REVERT: A 284 THR cc_start: 0.8515 (t) cc_final: 0.8145 (p) REVERT: A 342 TYR cc_start: 0.6162 (t80) cc_final: 0.5858 (t80) REVERT: A 541 LYS cc_start: 0.8044 (tptt) cc_final: 0.7580 (tmtt) REVERT: H 76 ARG cc_start: 0.3801 (tpt170) cc_final: 0.2221 (ptm-80) REVERT: H 80 CYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6901 (p) REVERT: H 81 LEU cc_start: 0.7993 (tp) cc_final: 0.7748 (tp) REVERT: H 198 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6382 (tt) REVERT: L 8 PHE cc_start: 0.2600 (m-80) cc_final: 0.1919 (m-80) REVERT: L 100 MET cc_start: 0.8197 (mpp) cc_final: 0.7931 (mpp) REVERT: L 114 ARG cc_start: 0.6400 (tmt170) cc_final: 0.5007 (mmm-85) REVERT: L 171 GLN cc_start: 0.5030 (OUTLIER) cc_final: 0.4425 (tp-100) REVERT: M 91 HIS cc_start: 0.4222 (OUTLIER) cc_final: 0.3866 (m170) REVERT: M 131 HIS cc_start: 0.5916 (t70) cc_final: 0.5680 (t70) outliers start: 217 outliers final: 133 residues processed: 801 average time/residue: 0.2425 time to fit residues: 319.9636 Evaluate side-chains 741 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 588 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 361 ILE Chi-restraints excluded: chain 2 residue 363 LEU 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 438 VAL Chi-restraints excluded: chain 2 residue 448 THR 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 521 THR Chi-restraints excluded: chain 2 residue 584 SER Chi-restraints excluded: chain 2 residue 590 GLU Chi-restraints excluded: chain 2 residue 612 ILE Chi-restraints excluded: chain 2 residue 697 LEU 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 46 VAL Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 347 SER 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 464 ILE Chi-restraints excluded: chain 3 residue 619 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 4 residue 276 SER 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 448 VAL Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 88 THR Chi-restraints excluded: chain 5 residue 123 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN 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 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 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 313 THR Chi-restraints excluded: chain 6 residue 362 LEU Chi-restraints excluded: chain 6 residue 368 VAL Chi-restraints excluded: chain 6 residue 387 VAL Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 616 MET Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 31 PHE 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 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 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 382 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 604 ARG Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 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 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 221 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU 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 36 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU 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 70 THR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 210 optimal weight: 2.9990 chunk 290 optimal weight: 0.0670 chunk 75 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 421 optimal weight: 0.9980 chunk 362 optimal weight: 0.9980 chunk 379 optimal weight: 0.6980 chunk 238 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 181 optimal weight: 0.0870 chunk 262 optimal weight: 10.0000 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 4 223 GLN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN 6 203 GLN 6 592 HIS 6 630 ASN ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS N 147 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.282156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.256981 restraints weight = 62043.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.258545 restraints weight = 52077.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.260208 restraints weight = 39946.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.261059 restraints weight = 31214.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.261191 restraints weight = 28749.306| |-----------------------------------------------------------------------------| r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40475 Z= 0.137 Angle : 0.734 13.405 54828 Z= 0.368 Chirality : 0.045 0.258 6193 Planarity : 0.005 0.065 6950 Dihedral : 11.556 128.993 5810 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 5.29 % Allowed : 23.35 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.45 (0.11), residues: 4789 helix: -1.03 (0.13), residues: 1581 sheet: -2.55 (0.20), residues: 534 loop : -3.17 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 4 531 TYR 0.017 0.001 TYR 5 50 PHE 0.043 0.002 PHE 6 185 TRP 0.051 0.002 TRP A 297 HIS 0.024 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (40466) covalent geometry : angle 0.73403 / 0.37 (54822) SS BOND : bond 0.00115 / 0.06 ( 3) SS BOND : angle 1.04162 / 0.43 ( 6) hydrogen bonds : bond 0.03922 / 2.62 ( 1028) hydrogen bonds : angle 5.54287 / 3.76 ( 2934) Misc. bond : bond 0.00125 / 0.07 ( 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 851 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 625 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash 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 TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 2 250 ASP cc_start: 0.7343 (t0) cc_final: 0.6988 (t0) REVERT: 2 350 MET cc_start: 0.3396 (mmt) cc_final: 0.3066 (ptp) REVERT: 2 723 MET cc_start: 0.4184 (mmt) cc_final: 0.3500 (ptt) REVERT: 2 775 MET cc_start: 0.3305 (ppp) cc_final: 0.2794 (tmm) REVERT: 2 794 THR cc_start: 0.6543 (OUTLIER) cc_final: 0.5957 (m) REVERT: 3 73 PHE cc_start: 0.6540 (m-80) cc_final: 0.6285 (m-80) REVERT: 3 619 SER cc_start: 0.7925 (t) cc_final: 0.7659 (t) REVERT: 4 242 MET cc_start: 0.1698 (tpp) cc_final: 0.0245 (ptt) REVERT: 4 247 MET cc_start: 0.7486 (ttp) cc_final: 0.6321 (tpt) REVERT: 4 380 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5754 (m-30) REVERT: 4 397 TYR cc_start: 0.3168 (OUTLIER) cc_final: 0.2008 (m-80) REVERT: 4 697 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8081 (mtt180) REVERT: 4 740 ILE cc_start: 0.5890 (pt) cc_final: 0.5621 (pt) REVERT: 5 51 ARG cc_start: 0.4738 (mtp85) cc_final: 0.3062 (mtp85) REVERT: 5 65 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5807 (tp) REVERT: 5 220 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7145 (tp40) REVERT: 5 259 LEU cc_start: 0.7524 (mt) cc_final: 0.7228 (mt) REVERT: 5 308 TYR cc_start: 0.2533 (OUTLIER) cc_final: 0.2056 (m-10) REVERT: 5 344 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7242 (ptp-170) REVERT: 5 508 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8276 (tt) REVERT: 5 581 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5827 (mp) REVERT: 5 589 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.4498 (ptt180) REVERT: 5 616 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6164 (mt) REVERT: 6 151 MET cc_start: 0.0196 (ppp) cc_final: -0.0219 (tmm) REVERT: 6 167 LYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5418 (pttt) REVERT: 6 194 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: 6 519 MET cc_start: 0.4732 (ptt) cc_final: 0.4186 (ptp) REVERT: 7 31 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: 7 48 ILE cc_start: 0.5177 (OUTLIER) cc_final: 0.4455 (pt) REVERT: 7 72 ARG cc_start: 0.2439 (OUTLIER) cc_final: 0.1821 (ttm170) REVERT: 7 269 ASP cc_start: 0.5824 (m-30) cc_final: 0.4970 (t0) REVERT: 7 281 MET cc_start: 0.6483 (tmm) cc_final: 0.5266 (mtt) REVERT: 7 369 MET cc_start: 0.4340 (OUTLIER) cc_final: 0.3881 (mtt) REVERT: 7 466 THR cc_start: 0.4087 (OUTLIER) cc_final: 0.3781 (m) REVERT: 7 598 MET cc_start: 0.6295 (mmt) cc_final: 0.6091 (mmp) REVERT: A 86 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7259 (tp) REVERT: A 221 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4239 (tp) REVERT: A 249 ILE cc_start: 0.1855 (OUTLIER) cc_final: 0.1649 (mt) REVERT: A 284 THR cc_start: 0.8395 (t) cc_final: 0.8099 (p) REVERT: A 342 TYR cc_start: 0.6070 (t80) cc_final: 0.5801 (t80) REVERT: A 541 LYS cc_start: 0.7937 (tptt) cc_final: 0.7544 (tmtt) REVERT: H 76 ARG cc_start: 0.3826 (tpt170) cc_final: 0.2366 (ptt180) REVERT: H 80 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6796 (p) REVERT: H 81 LEU cc_start: 0.7978 (tp) cc_final: 0.7737 (tp) REVERT: H 86 TYR cc_start: 0.5560 (OUTLIER) cc_final: 0.4544 (t80) REVERT: H 198 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6426 (tt) REVERT: L 100 MET cc_start: 0.8149 (mpp) cc_final: 0.7605 (mpp) REVERT: L 114 ARG cc_start: 0.6431 (tmt170) cc_final: 0.5289 (mmm-85) REVERT: L 171 GLN cc_start: 0.5056 (OUTLIER) cc_final: 0.4575 (tp-100) REVERT: M 91 HIS cc_start: 0.4776 (OUTLIER) cc_final: 0.4387 (m170) REVERT: M 108 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6917 (tt) outliers start: 226 outliers final: 145 residues processed: 787 average time/residue: 0.2398 time to fit residues: 312.3003 Evaluate side-chains 770 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 599 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 294 LEU 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 419 VAL Chi-restraints excluded: chain 2 residue 424 ILE 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 521 THR 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 612 ILE Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 750 MET Chi-restraints excluded: chain 2 residue 794 THR Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 347 SER 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 557 LEU Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 4 residue 316 THR Chi-restraints excluded: chain 4 residue 347 SER Chi-restraints excluded: chain 4 residue 380 ASP 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 451 LEU Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 693 ILE Chi-restraints excluded: chain 4 residue 736 LEU Chi-restraints excluded: chain 4 residue 752 SER Chi-restraints excluded: chain 5 residue 48 TYR 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 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 263 ILE Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU 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 581 LEU Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 616 ILE Chi-restraints excluded: chain 5 residue 619 SER Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 313 THR Chi-restraints excluded: chain 6 residue 368 VAL Chi-restraints excluded: chain 6 residue 382 ILE Chi-restraints excluded: chain 6 residue 401 VAL Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 508 LEU 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 48 ILE 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 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL 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 369 MET Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 466 THR Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 604 ARG 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 221 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU 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 36 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU 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 142 TYR Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 50 MET 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 113 GLU 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: 10.0000 chunk 332 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 417 optimal weight: 0.0370 chunk 403 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 179 optimal weight: 0.0870 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 355 ASN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 501 ASN 6 101 GLN 6 198 GLN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.281570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.255624 restraints weight = 61361.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.256927 restraints weight = 47916.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.258023 restraints weight = 40447.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.259145 restraints weight = 32969.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.259386 restraints weight = 30145.313| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.6075 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= 0.134 Angle : 0.731 13.050 54828 Z= 0.364 Chirality : 0.045 0.219 6193 Planarity : 0.005 0.082 6950 Dihedral : 11.346 130.137 5809 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 5.13 % Allowed : 23.73 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.11), residues: 4789 helix: -0.95 (0.13), residues: 1587 sheet: -2.36 (0.21), residues: 539 loop : -3.12 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 128 TYR 0.019 0.001 TYR 7 182 PHE 0.041 0.002 PHE 6 185 TRP 0.036 0.002 TRP A 297 HIS 0.025 0.001 HIS 7 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (40466) covalent geometry : angle 0.73066 / 0.36 (54822) SS BOND : bond 0.00091 / 0.05 ( 3) SS BOND : angle 0.62761 / 0.30 ( 6) hydrogen bonds : bond 0.03822 / 2.55 ( 1028) hydrogen bonds : angle 5.48120 / 3.72 ( 2934) Misc. bond : bond 0.00112 / 0.06 ( 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 863 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 644 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "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: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7436 (t0) cc_final: 0.7039 (t0) REVERT: 2 350 MET cc_start: 0.3717 (mmt) cc_final: 0.3218 (ptp) REVERT: 2 397 LEU cc_start: 0.6960 (mt) cc_final: 0.6687 (tp) REVERT: 2 455 ASP cc_start: 0.6571 (t0) cc_final: 0.6357 (t0) REVERT: 2 723 MET cc_start: 0.4336 (mmt) cc_final: 0.3591 (ptt) REVERT: 2 775 MET cc_start: 0.3754 (ppp) cc_final: 0.3384 (tmm) REVERT: 3 73 PHE cc_start: 0.6578 (m-80) cc_final: 0.6334 (m-80) REVERT: 3 203 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6643 (pt0) REVERT: 3 464 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7354 (mt) REVERT: 3 557 LEU cc_start: 0.2342 (OUTLIER) cc_final: 0.2092 (tt) REVERT: 3 572 MET cc_start: 0.5738 (mmm) cc_final: 0.5220 (ppp) REVERT: 3 619 SER cc_start: 0.8014 (t) cc_final: 0.7727 (t) REVERT: 4 242 MET cc_start: 0.1675 (tpp) cc_final: 0.0422 (ptt) REVERT: 4 247 MET cc_start: 0.7649 (ttp) cc_final: 0.6439 (tpt) REVERT: 4 380 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5852 (m-30) REVERT: 4 397 TYR cc_start: 0.3137 (OUTLIER) cc_final: 0.1848 (m-80) REVERT: 4 697 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8113 (mtt180) REVERT: 4 740 ILE cc_start: 0.6122 (pt) cc_final: 0.5837 (pt) REVERT: 5 65 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5953 (tp) REVERT: 5 220 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7184 (tp40) REVERT: 5 259 LEU cc_start: 0.7459 (mt) cc_final: 0.7168 (mt) REVERT: 5 308 TYR cc_start: 0.2526 (OUTLIER) cc_final: 0.2032 (m-10) REVERT: 5 344 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7111 (ptp-170) REVERT: 5 508 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8345 (tt) REVERT: 5 581 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5972 (mp) REVERT: 5 589 ARG cc_start: 0.4692 (OUTLIER) cc_final: 0.4433 (ptt180) REVERT: 5 616 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6713 (mt) REVERT: 6 151 MET cc_start: 0.0079 (ppp) cc_final: -0.0446 (tmm) REVERT: 6 167 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5392 (pttt) REVERT: 6 194 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.4797 (m-80) REVERT: 6 519 MET cc_start: 0.5031 (ptt) cc_final: 0.4479 (ptp) REVERT: 7 31 PHE cc_start: 0.6305 (m-80) cc_final: 0.5777 (m-80) REVERT: 7 48 ILE cc_start: 0.5156 (OUTLIER) cc_final: 0.4527 (pt) REVERT: 7 72 ARG cc_start: 0.2694 (OUTLIER) cc_final: 0.1771 (ttm170) REVERT: 7 269 ASP cc_start: 0.5837 (m-30) cc_final: 0.4882 (t0) REVERT: 7 358 LEU cc_start: 0.6251 (mp) cc_final: 0.6042 (mp) REVERT: 7 369 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3994 (mtt) REVERT: 7 397 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6827 (mm) REVERT: 7 559 MET cc_start: 0.4127 (mtt) cc_final: 0.3835 (mtt) REVERT: 7 585 TYR cc_start: 0.6373 (t80) cc_final: 0.6131 (t80) REVERT: 7 598 MET cc_start: 0.6567 (mmt) cc_final: 0.6246 (mmp) REVERT: A 221 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4549 (tp) REVERT: A 284 THR cc_start: 0.8446 (t) cc_final: 0.8040 (p) REVERT: A 342 TYR cc_start: 0.6037 (t80) cc_final: 0.5762 (t80) REVERT: A 522 VAL cc_start: 0.7078 (p) cc_final: 0.6836 (t) REVERT: A 541 LYS cc_start: 0.7954 (tptt) cc_final: 0.7586 (tmtt) REVERT: H 76 ARG cc_start: 0.3967 (tpt170) cc_final: 0.2606 (ptm-80) REVERT: H 80 CYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6828 (p) REVERT: H 81 LEU cc_start: 0.8005 (tp) cc_final: 0.7754 (tp) REVERT: H 86 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.4582 (t80) REVERT: H 130 MET cc_start: 0.5199 (ptp) cc_final: 0.4680 (ptp) REVERT: H 198 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6363 (tt) REVERT: L 84 PHE cc_start: 0.6056 (m-10) cc_final: 0.5504 (m-80) REVERT: L 114 ARG cc_start: 0.6257 (tmt170) cc_final: 0.5500 (mmm-85) REVERT: L 171 GLN cc_start: 0.5143 (OUTLIER) cc_final: 0.4893 (tp-100) REVERT: M 91 HIS cc_start: 0.4761 (OUTLIER) cc_final: 0.4378 (m170) REVERT: N 107 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7155 (t) outliers start: 219 outliers final: 153 residues processed: 798 average time/residue: 0.2384 time to fit residues: 315.0461 Evaluate side-chains 788 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 610 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 294 LEU Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 363 LEU Chi-restraints excluded: chain 2 residue 375 ILE Chi-restraints excluded: chain 2 residue 381 VAL 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 424 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR 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 520 TYR Chi-restraints excluded: chain 2 residue 521 THR 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 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 697 LEU Chi-restraints excluded: chain 2 residue 698 ARG 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 105 ASN Chi-restraints excluded: chain 3 residue 121 MET Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 232 VAL Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 315 LEU Chi-restraints excluded: chain 3 residue 347 SER 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 157 THR Chi-restraints excluded: chain 4 residue 211 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 380 ASP 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 451 LEU Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 671 LEU Chi-restraints excluded: chain 4 residue 693 ILE 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 53 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 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 308 TYR Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU 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 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 581 LEU Chi-restraints excluded: chain 5 residue 589 ARG Chi-restraints excluded: chain 5 residue 608 THR Chi-restraints excluded: chain 5 residue 616 ILE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 152 CYS Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 313 THR Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 368 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 426 VAL 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 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP 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 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 93 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 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 604 ARG Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 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 205 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 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 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 198 LEU 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 70 THR Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 30 MET Chi-restraints excluded: chain N residue 50 MET 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 107 CYS Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 234 optimal weight: 3.9990 chunk 384 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 323 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 211 ASN 2 286 HIS 2 606 GLN 2 754 HIS 3 448 ASN ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN 6 337 ASN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.278476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.251581 restraints weight = 60450.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.253091 restraints weight = 49890.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.254403 restraints weight = 37991.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.255629 restraints weight = 30686.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.255720 restraints weight = 28403.013| |-----------------------------------------------------------------------------| r_work (final): 0.4883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40475 Z= 0.155 Angle : 0.752 12.208 54828 Z= 0.376 Chirality : 0.046 0.278 6193 Planarity : 0.005 0.081 6950 Dihedral : 11.243 130.116 5806 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.04 % Allowed : 24.48 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.11), residues: 4789 helix: -0.87 (0.13), residues: 1588 sheet: -2.30 (0.21), residues: 542 loop : -3.08 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 128 TYR 0.031 0.002 TYR 6 236 PHE 0.035 0.002 PHE A 440 TRP 0.069 0.003 TRP A 297 HIS 0.015 0.001 HIS 7 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (40466) covalent geometry : angle 0.75150 / 0.38 (54822) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.98916 / 0.41 ( 6) hydrogen bonds : bond 0.03888 / 2.62 ( 1028) hydrogen bonds : angle 5.45240 / 3.68 ( 2934) Misc. bond : bond 0.00121 / 0.06 ( 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 863 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 648 time to evaluate : 1.445 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 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: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7281 (t0) cc_final: 0.6919 (t0) REVERT: 2 350 MET cc_start: 0.3677 (mmt) cc_final: 0.3128 (ptp) REVERT: 2 397 LEU cc_start: 0.7376 (mt) cc_final: 0.7103 (tp) REVERT: 2 723 MET cc_start: 0.4645 (mmt) cc_final: 0.4028 (ptt) REVERT: 2 728 ARG cc_start: 0.5112 (tmm160) cc_final: 0.4801 (tmm160) REVERT: 2 775 MET cc_start: 0.4114 (ppp) cc_final: 0.3894 (tmm) REVERT: 3 203 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6511 (pt0) REVERT: 3 464 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7465 (mt) REVERT: 3 619 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7850 (t) REVERT: 4 242 MET cc_start: 0.1436 (tpp) cc_final: 0.0307 (ptt) REVERT: 4 247 MET cc_start: 0.7759 (ttp) cc_final: 0.6673 (tpt) REVERT: 4 397 TYR cc_start: 0.2797 (OUTLIER) cc_final: 0.1467 (m-80) REVERT: 4 740 ILE cc_start: 0.6306 (pt) cc_final: 0.6060 (pt) REVERT: 5 65 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6327 (tp) REVERT: 5 220 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: 5 259 LEU cc_start: 0.7720 (mt) cc_final: 0.7444 (mt) REVERT: 5 308 TYR cc_start: 0.2604 (OUTLIER) cc_final: 0.2030 (m-10) REVERT: 5 340 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5946 (pt) REVERT: 5 344 ARG cc_start: 0.7250 (mtm180) cc_final: 0.7048 (ptp-170) REVERT: 5 508 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8411 (tt) REVERT: 5 581 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5988 (mp) REVERT: 5 589 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.4251 (ptt180) REVERT: 5 616 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6954 (mt) REVERT: 6 151 MET cc_start: 0.0006 (ppp) cc_final: -0.0382 (tmm) REVERT: 6 167 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5328 (ttpt) REVERT: 6 194 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: 6 519 MET cc_start: 0.5421 (ptt) cc_final: 0.4803 (ptp) REVERT: 6 623 MET cc_start: 0.6568 (ptp) cc_final: 0.6287 (mpp) REVERT: 7 31 PHE cc_start: 0.6304 (m-80) cc_final: 0.5874 (m-80) REVERT: 7 48 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4592 (pt) REVERT: 7 72 ARG cc_start: 0.2730 (OUTLIER) cc_final: 0.1881 (ttm170) REVERT: 7 281 MET cc_start: 0.6460 (tmm) cc_final: 0.5108 (mtt) REVERT: 7 358 LEU cc_start: 0.6439 (mp) cc_final: 0.6188 (mp) REVERT: 7 369 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4185 (mtt) REVERT: 7 380 MET cc_start: 0.5527 (tpt) cc_final: 0.5296 (tpt) REVERT: 7 397 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6840 (mm) REVERT: 7 475 MET cc_start: 0.3889 (pmm) cc_final: 0.3082 (pmm) REVERT: 7 559 MET cc_start: 0.4176 (mtt) cc_final: 0.3855 (mtt) REVERT: 7 601 THR cc_start: 0.6130 (OUTLIER) cc_final: 0.5788 (p) REVERT: A 108 ASN cc_start: 0.7187 (m-40) cc_final: 0.6913 (t0) REVERT: A 249 ILE cc_start: 0.2628 (OUTLIER) cc_final: 0.2406 (mt) REVERT: A 284 THR cc_start: 0.8500 (t) cc_final: 0.8038 (p) REVERT: A 541 LYS cc_start: 0.7935 (tptt) cc_final: 0.7559 (tmtt) REVERT: H 76 ARG cc_start: 0.4243 (tpt170) cc_final: 0.2748 (ptt180) REVERT: H 80 CYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6787 (p) REVERT: H 81 LEU cc_start: 0.8103 (tp) cc_final: 0.7853 (tp) REVERT: H 86 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.4632 (t80) REVERT: H 130 MET cc_start: 0.4941 (ptp) cc_final: 0.4321 (ptp) REVERT: L 27 HIS cc_start: 0.4058 (OUTLIER) cc_final: 0.3639 (t70) REVERT: L 84 PHE cc_start: 0.6209 (m-10) cc_final: 0.5684 (m-80) REVERT: L 114 ARG cc_start: 0.6401 (tmt170) cc_final: 0.5434 (mmt90) REVERT: L 171 GLN cc_start: 0.5575 (OUTLIER) cc_final: 0.5180 (tp40) REVERT: M 91 HIS cc_start: 0.4732 (OUTLIER) cc_final: 0.4387 (m170) REVERT: N 107 CYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7435 (t) outliers start: 215 outliers final: 146 residues processed: 799 average time/residue: 0.2389 time to fit residues: 316.6119 Evaluate side-chains 781 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 609 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 294 LEU 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 419 VAL Chi-restraints excluded: chain 2 residue 424 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 THR 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 494 GLU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 521 THR Chi-restraints excluded: chain 2 residue 545 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 612 ILE Chi-restraints excluded: chain 2 residue 616 ASN Chi-restraints excluded: chain 2 residue 647 VAL Chi-restraints excluded: chain 2 residue 698 ARG Chi-restraints excluded: chain 2 residue 741 VAL Chi-restraints excluded: chain 2 residue 750 MET Chi-restraints excluded: chain 2 residue 793 SER Chi-restraints excluded: chain 3 residue 20 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 232 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 347 SER 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 464 ILE Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 3 residue 619 SER Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU 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 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 448 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL 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 53 THR Chi-restraints excluded: chain 5 residue 65 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 308 TYR Chi-restraints excluded: chain 5 residue 314 ASP Chi-restraints excluded: chain 5 residue 340 ILE Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU 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 568 HIS 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 616 ILE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 313 THR Chi-restraints excluded: chain 6 residue 368 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 426 VAL 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 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP 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 72 ARG Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 601 THR Chi-restraints excluded: chain 7 residue 604 ARG Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET 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 205 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 256 LEU 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 373 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 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 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR 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 27 HIS Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 113 LEU 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 91 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 51 CYS Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 GLU 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: 0.6980 chunk 264 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 338 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 135 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 464 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 400 optimal weight: 0.7980 chunk 479 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN 6 340 GLN 6 341 ASN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.279836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.253214 restraints weight = 60502.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.254354 restraints weight = 49139.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.255737 restraints weight = 39390.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.256872 restraints weight = 32422.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.257112 restraints weight = 29653.448| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 40475 Z= 0.133 Angle : 0.745 13.431 54828 Z= 0.368 Chirality : 0.046 0.532 6193 Planarity : 0.005 0.077 6950 Dihedral : 11.132 129.078 5804 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.98 % Allowed : 25.93 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.11), residues: 4789 helix: -0.75 (0.13), residues: 1587 sheet: -2.27 (0.21), residues: 544 loop : -3.02 (0.11), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 128 TYR 0.046 0.001 TYR 3 588 PHE 0.029 0.002 PHE 2 663 TRP 0.051 0.002 TRP A 297 HIS 0.045 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (40466) covalent geometry : angle 0.74497 / 0.37 (54822) SS BOND : bond 0.00112 / 0.06 ( 3) SS BOND : angle 0.77331 / 0.33 ( 6) hydrogen bonds : bond 0.03681 / 2.47 ( 1028) hydrogen bonds : angle 5.36852 / 3.63 ( 2934) Misc. bond : bond 0.00704 / 0.47 ( 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 797 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 627 time to evaluate : 1.654 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 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: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7253 (t0) cc_final: 0.6924 (t0) REVERT: 2 350 MET cc_start: 0.3690 (mmt) cc_final: 0.3114 (ptp) REVERT: 2 397 LEU cc_start: 0.7511 (mt) cc_final: 0.7136 (tp) REVERT: 2 499 ARG cc_start: 0.5363 (mtm180) cc_final: 0.5086 (ptt90) REVERT: 2 723 MET cc_start: 0.4710 (mmt) cc_final: 0.4006 (ptt) REVERT: 3 464 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7605 (mt) REVERT: 3 619 SER cc_start: 0.8167 (OUTLIER) cc_final: 0.7884 (t) REVERT: 4 242 MET cc_start: 0.1481 (tpp) cc_final: 0.0293 (ptt) REVERT: 4 247 MET cc_start: 0.7809 (ttp) cc_final: 0.6690 (tpt) REVERT: 4 397 TYR cc_start: 0.3011 (OUTLIER) cc_final: 0.1658 (m-80) REVERT: 4 744 GLU cc_start: 0.6805 (pt0) cc_final: 0.6561 (pt0) REVERT: 5 65 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6352 (tp) REVERT: 5 220 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7247 (tp40) REVERT: 5 259 LEU cc_start: 0.7484 (mt) cc_final: 0.7188 (mt) REVERT: 5 308 TYR cc_start: 0.2600 (OUTLIER) cc_final: 0.2051 (m-10) REVERT: 5 340 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5790 (pt) REVERT: 5 344 ARG cc_start: 0.7210 (mtm180) cc_final: 0.6960 (ptp-170) REVERT: 5 508 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8417 (tt) REVERT: 5 581 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6019 (mp) REVERT: 5 589 ARG cc_start: 0.4717 (OUTLIER) cc_final: 0.4327 (ptt180) REVERT: 5 616 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6756 (mt) REVERT: 6 151 MET cc_start: 0.0049 (ppp) cc_final: -0.0417 (tmm) REVERT: 6 167 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5344 (ttpt) REVERT: 6 194 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.4979 (m-80) REVERT: 6 519 MET cc_start: 0.5478 (ptt) cc_final: 0.4889 (ptp) REVERT: 7 31 PHE cc_start: 0.6282 (m-80) cc_final: 0.5890 (m-80) REVERT: 7 48 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4566 (pt) REVERT: 7 72 ARG cc_start: 0.2530 (OUTLIER) cc_final: 0.1714 (ttm170) REVERT: 7 167 VAL cc_start: 0.6166 (OUTLIER) cc_final: 0.5962 (t) REVERT: 7 358 LEU cc_start: 0.6583 (mp) cc_final: 0.6349 (mp) REVERT: 7 369 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4534 (mtt) REVERT: 7 397 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6874 (mm) REVERT: 7 475 MET cc_start: 0.3897 (pmm) cc_final: 0.3063 (pmm) REVERT: 7 559 MET cc_start: 0.4063 (mtt) cc_final: 0.3786 (mtp) REVERT: 7 573 ILE cc_start: 0.5730 (pt) cc_final: 0.5524 (tp) REVERT: A 86 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 284 THR cc_start: 0.8468 (t) cc_final: 0.8033 (p) REVERT: A 541 LYS cc_start: 0.7996 (tptt) cc_final: 0.7631 (tmtt) REVERT: H 76 ARG cc_start: 0.4184 (tpt170) cc_final: 0.2818 (ptt180) REVERT: H 80 CYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6694 (p) REVERT: H 81 LEU cc_start: 0.8105 (tp) cc_final: 0.7877 (tp) REVERT: H 86 TYR cc_start: 0.5504 (OUTLIER) cc_final: 0.4403 (t80) REVERT: H 130 MET cc_start: 0.4800 (ptp) cc_final: 0.4236 (ptp) REVERT: L 84 PHE cc_start: 0.6342 (m-10) cc_final: 0.5841 (m-80) REVERT: L 114 ARG cc_start: 0.6407 (tmt170) cc_final: 0.5523 (mmt90) REVERT: L 171 GLN cc_start: 0.5308 (OUTLIER) cc_final: 0.5025 (tp-100) outliers start: 170 outliers final: 124 residues processed: 744 average time/residue: 0.2366 time to fit residues: 292.8751 Evaluate side-chains 745 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 599 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 294 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 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 494 GLU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 521 THR Chi-restraints excluded: chain 2 residue 574 PHE 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 698 ARG 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 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 232 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 347 SER 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 488 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 3 residue 591 LEU Chi-restraints excluded: chain 3 residue 619 SER Chi-restraints excluded: chain 4 residue 211 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 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 448 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL Chi-restraints excluded: chain 4 residue 693 ILE 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 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 308 TYR Chi-restraints excluded: chain 5 residue 340 ILE Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU 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 568 HIS 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 616 ILE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 426 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP 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 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 604 ARG Chi-restraints excluded: chain A residue 21 ILE 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 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 221 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 570 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 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR 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 94 VAL Chi-restraints excluded: chain L residue 95 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 115 HIS Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 411 optimal weight: 0.0970 chunk 412 optimal weight: 8.9990 chunk 68 optimal weight: 0.0370 chunk 216 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 338 optimal weight: 0.9980 chunk 445 optimal weight: 0.7980 chunk 416 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 245 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 616 ASN ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 134 GLN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 446 ASN ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 GLN L 91 HIS ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.280132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.253631 restraints weight = 60613.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.255178 restraints weight = 50527.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.256642 restraints weight = 38198.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.257551 restraints weight = 30531.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.257880 restraints weight = 28890.615| |-----------------------------------------------------------------------------| r_work (final): 0.4894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40475 Z= 0.132 Angle : 0.738 14.652 54828 Z= 0.366 Chirality : 0.046 0.353 6193 Planarity : 0.005 0.070 6950 Dihedral : 11.030 128.314 5801 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.87 % Allowed : 26.61 % Favored : 69.52 % 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: -3.06 (0.11), residues: 4789 helix: -0.65 (0.13), residues: 1575 sheet: -2.12 (0.21), residues: 546 loop : -3.00 (0.11), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 128 TYR 0.034 0.001 TYR 3 588 PHE 0.030 0.002 PHE 2 663 TRP 0.046 0.002 TRP A 297 HIS 0.019 0.001 HIS 2 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (40466) covalent geometry : angle 0.73799 / 0.37 (54822) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.64706 / 0.25 ( 6) hydrogen bonds : bond 0.03675 / 2.46 ( 1028) hydrogen bonds : angle 5.28838 / 3.57 ( 2934) Misc. bond : bond 0.00195 / 0.13 ( 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 785 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 620 time to evaluate : 1.472 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 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: "THR M 174 " (corrupted residue). Skipping it. REVERT: 2 250 ASP cc_start: 0.7241 (t0) cc_final: 0.6900 (t0) REVERT: 2 350 MET cc_start: 0.3703 (mmt) cc_final: 0.3197 (ptp) REVERT: 2 397 LEU cc_start: 0.7537 (mt) cc_final: 0.6970 (tt) REVERT: 2 494 GLU cc_start: 0.4791 (OUTLIER) cc_final: 0.4265 (tt0) REVERT: 2 723 MET cc_start: 0.4682 (mmt) cc_final: 0.4109 (ptt) REVERT: 3 203 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: 3 464 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7585 (mt) REVERT: 3 619 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7730 (t) REVERT: 4 242 MET cc_start: 0.1073 (tpp) cc_final: 0.0248 (ptt) REVERT: 4 247 MET cc_start: 0.7821 (ttp) cc_final: 0.6742 (tpt) REVERT: 4 397 TYR cc_start: 0.3008 (OUTLIER) cc_final: 0.1801 (m-80) REVERT: 4 744 GLU cc_start: 0.6778 (pt0) cc_final: 0.6560 (pt0) REVERT: 5 65 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6463 (tp) REVERT: 5 220 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7100 (tp40) REVERT: 5 259 LEU cc_start: 0.7546 (mt) cc_final: 0.7245 (mt) REVERT: 5 308 TYR cc_start: 0.2724 (OUTLIER) cc_final: 0.2119 (m-10) REVERT: 5 340 ILE cc_start: 0.6147 (OUTLIER) cc_final: 0.5825 (pt) REVERT: 5 344 ARG cc_start: 0.7284 (mtm180) cc_final: 0.7063 (ptp-170) REVERT: 5 461 GLN cc_start: 0.7273 (mt0) cc_final: 0.6878 (mm-40) REVERT: 5 508 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8432 (tt) REVERT: 5 581 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6325 (mp) REVERT: 5 589 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.4294 (ptt180) REVERT: 5 616 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6821 (mt) REVERT: 6 151 MET cc_start: -0.0200 (ppp) cc_final: -0.0681 (tmm) REVERT: 6 167 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5403 (ttpt) REVERT: 6 194 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: 6 236 TYR cc_start: 0.4686 (m-10) cc_final: 0.4422 (m-10) REVERT: 6 445 ASP cc_start: 0.6478 (t0) cc_final: 0.6150 (t0) REVERT: 6 446 ASN cc_start: 0.4975 (OUTLIER) cc_final: 0.4654 (m110) REVERT: 6 519 MET cc_start: 0.5618 (ptt) cc_final: 0.5017 (ptp) REVERT: 6 621 GLU cc_start: 0.3562 (pp20) cc_final: 0.2980 (pt0) REVERT: 6 623 MET cc_start: 0.6528 (ptp) cc_final: 0.6254 (mpp) REVERT: 7 31 PHE cc_start: 0.6371 (m-80) cc_final: 0.5940 (m-80) REVERT: 7 48 ILE cc_start: 0.5156 (OUTLIER) cc_final: 0.4513 (pt) REVERT: 7 72 ARG cc_start: 0.2600 (OUTLIER) cc_final: 0.1811 (ttm170) REVERT: 7 167 VAL cc_start: 0.6161 (OUTLIER) cc_final: 0.5929 (t) REVERT: 7 358 LEU cc_start: 0.6614 (mp) cc_final: 0.6372 (mp) REVERT: 7 369 MET cc_start: 0.4803 (OUTLIER) cc_final: 0.4392 (mtt) REVERT: 7 397 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6751 (mm) REVERT: 7 475 MET cc_start: 0.3825 (pmm) cc_final: 0.3072 (pmm) REVERT: 7 559 MET cc_start: 0.4193 (mtt) cc_final: 0.3920 (mtp) REVERT: A 86 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7308 (tp) REVERT: A 201 MET cc_start: 0.5808 (mtp) cc_final: 0.5400 (mmm) REVERT: A 284 THR cc_start: 0.8466 (t) cc_final: 0.8059 (p) REVERT: A 313 LEU cc_start: 0.7035 (mt) cc_final: 0.6699 (mt) REVERT: A 528 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.4900 (tpp80) REVERT: A 541 LYS cc_start: 0.7920 (tptt) cc_final: 0.7601 (tmtt) REVERT: H 76 ARG cc_start: 0.4321 (tpt170) cc_final: 0.3135 (ptm-80) REVERT: H 80 CYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6557 (p) REVERT: H 81 LEU cc_start: 0.8149 (tp) cc_final: 0.7933 (tp) REVERT: H 86 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4337 (t80) REVERT: H 130 MET cc_start: 0.4899 (ptp) cc_final: 0.4215 (ptp) REVERT: L 84 PHE cc_start: 0.6263 (m-10) cc_final: 0.5876 (m-80) REVERT: L 114 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5672 (mmm-85) REVERT: M 128 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5579 (ttp80) outliers start: 165 outliers final: 128 residues processed: 733 average time/residue: 0.2376 time to fit residues: 289.4057 Evaluate side-chains 746 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 593 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 204 ILE Chi-restraints excluded: chain 2 residue 207 MET Chi-restraints excluded: chain 2 residue 282 PHE Chi-restraints excluded: chain 2 residue 294 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 424 ILE 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 494 GLU Chi-restraints excluded: chain 2 residue 520 TYR Chi-restraints excluded: chain 2 residue 521 THR Chi-restraints excluded: chain 2 residue 574 PHE 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 698 ARG 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 122 VAL Chi-restraints excluded: chain 3 residue 128 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 232 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 347 SER Chi-restraints excluded: chain 3 residue 394 VAL Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 488 VAL Chi-restraints excluded: chain 3 residue 557 LEU Chi-restraints excluded: chain 3 residue 619 SER Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 4 residue 211 LEU 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 393 VAL Chi-restraints excluded: chain 4 residue 396 ILE Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 448 VAL Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 652 VAL 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 53 THR Chi-restraints excluded: chain 5 residue 65 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 308 TYR Chi-restraints excluded: chain 5 residue 340 ILE Chi-restraints excluded: chain 5 residue 376 LEU Chi-restraints excluded: chain 5 residue 377 LEU 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 568 HIS 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 616 ILE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 58 SER Chi-restraints excluded: chain 6 residue 113 THR Chi-restraints excluded: chain 6 residue 167 LYS Chi-restraints excluded: chain 6 residue 187 LEU 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 410 TYR Chi-restraints excluded: chain 6 residue 426 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 446 ASN Chi-restraints excluded: chain 7 residue 6 TYR Chi-restraints excluded: chain 7 residue 25 ASP 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 72 ARG Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 149 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 198 LEU Chi-restraints excluded: chain 7 residue 203 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 295 GLU Chi-restraints excluded: chain 7 residue 369 MET Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 540 VAL Chi-restraints excluded: chain 7 residue 604 ARG 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 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 221 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 570 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 49 VAL Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 86 TYR 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 95 VAL Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain M residue 58 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 115 HIS 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 88 VAL Chi-restraints excluded: chain N residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 154 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 339 optimal weight: 1.9990 chunk 420 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 194 optimal weight: 0.0570 chunk 24 optimal weight: 0.1980 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN ** 6 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 446 ASN ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.279961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.253136 restraints weight = 61321.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.255384 restraints weight = 49423.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.256778 restraints weight = 37706.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.257265 restraints weight = 30335.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.257695 restraints weight = 27638.792| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 40475 Z= 0.229 Angle : 0.875 59.200 54828 Z= 0.493 Chirality : 0.049 1.197 6193 Planarity : 0.006 0.159 6950 Dihedral : 11.032 128.303 5800 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 3.94 % Allowed : 26.63 % Favored : 69.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.11), residues: 4789 helix: -0.65 (0.13), residues: 1575 sheet: -2.12 (0.21), residues: 546 loop : -3.01 (0.11), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 5 56 TYR 0.026 0.001 TYR 3 588 PHE 0.022 0.002 PHE 2 663 TRP 0.039 0.002 TRP A 297 HIS 0.247 0.002 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.23 (40466) covalent geometry : angle 0.87518 / 0.49 (54822) SS BOND : bond 0.00092 / 0.05 ( 3) SS BOND : angle 0.65847 / 0.26 ( 6) hydrogen bonds : bond 0.03677 / 2.46 ( 1028) hydrogen bonds : angle 5.28818 / 3.57 ( 2934) Misc. bond : bond 0.00111 / 0.06 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8407.54 seconds wall clock time: 146 minutes 3.61 seconds (8763.61 seconds total)