Starting phenix.real_space_refine on Tue Nov 19 04:53:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgz_37523/11_2024/8wgz_37523.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.012 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 5 5.49 5 S 203 5.16 5 C 32845 2.51 5 N 8741 2.21 5 O 9602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51396 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4280 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4293 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4321 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4305 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 521} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4310 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "F" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4302 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "G" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4221 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 129 Chain: "H" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4267 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 3, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "I" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4257 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 117 Chain: "J" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4230 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 111 Chain: "K" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4272 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "L" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 27, 'TRANS': 522} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 116 Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Time building chain proxies: 30.12, per 1000 atoms: 0.59 Number of scatterers: 51396 At special positions: 0 Unit cell: (132.72, 132.72, 288.12, 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 203 16.00 P 5 15.00 O 9602 8.00 N 8741 7.00 C 32845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 6.5 seconds 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12624 Finding SS restraints... Secondary structure from input PDB file: 292 helices and 95 sheets defined 39.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 258 through 262 removed outlier: 4.472A pdb=" N ASN A 262 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 4.717A pdb=" N SER A 313 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.731A pdb=" N ARG A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.564A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.004A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.536A pdb=" N THR A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.572A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 653 through 661 removed outlier: 4.038A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.892A pdb=" N GLY A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Proline residue: A 715 - end of helix Processing helix chain 'A' and resid 716 through 724 removed outlier: 4.332A pdb=" N LYS A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.798A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.959A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.775A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.978A pdb=" N GLY B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 4.102A pdb=" N ASP B 534 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.547A pdb=" N ALA B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 577 removed outlier: 4.136A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 652 through 661 removed outlier: 4.554A pdb=" N ASP B 656 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 Processing helix chain 'B' and resid 695 through 705 removed outlier: 4.381A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.569A pdb=" N LEU B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 717 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 717' Processing helix chain 'B' and resid 735 through 744 Processing helix chain 'B' and resid 748 through 762 removed outlier: 4.139A pdb=" N PHE B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 372 removed outlier: 3.527A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.929A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 431 through 434 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.941A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 520 removed outlier: 4.144A pdb=" N THR C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 4.172A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 533 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 571 through 576 removed outlier: 3.595A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.659A pdb=" N MET C 618 " --> pdb=" O ASP C 614 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 614 through 619' Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.786A pdb=" N ALA C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 679 Processing helix chain 'C' and resid 689 through 694 removed outlier: 3.924A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 695 through 704 removed outlier: 4.516A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 717 removed outlier: 3.671A pdb=" N LEU C 716 " --> pdb=" O HIS C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 743 Processing helix chain 'C' and resid 744 through 746 No H-bonds generated for 'chain 'C' and resid 744 through 746' Processing helix chain 'C' and resid 752 through 763 Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'D' and resid 242 through 255 removed outlier: 3.562A pdb=" N ILE D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.747A pdb=" N ASN D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 385 through 399 Processing helix chain 'D' and resid 431 through 436 removed outlier: 3.605A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 431 through 436' Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.635A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 488 removed outlier: 4.150A pdb=" N LYS D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN D 478 " --> pdb=" O GLU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.632A pdb=" N GLY D 521 " --> pdb=" O LYS D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.926A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 576 removed outlier: 3.538A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.756A pdb=" N ARG D 619 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 664 through 679 Processing helix chain 'D' and resid 694 through 705 removed outlier: 4.485A pdb=" N PHE D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 716 through 723 removed outlier: 3.917A pdb=" N LYS D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 744 removed outlier: 3.698A pdb=" N SER D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.552A pdb=" N PHE D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS D 754 " --> pdb=" O ARG D 750 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 784 Processing helix chain 'E' and resid 243 through 253 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.648A pdb=" N PHE E 261 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN E 262 " --> pdb=" O ILE E 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 262' Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.814A pdb=" N LEU E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP E 335 " --> pdb=" O GLN E 331 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.683A pdb=" N LEU E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 378 through 384 removed outlier: 3.807A pdb=" N SER E 381 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU E 383 " --> pdb=" O SER E 380 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.777A pdb=" N LYS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 488 removed outlier: 4.359A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN E 478 " --> pdb=" O GLU E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 533 Processing helix chain 'E' and resid 541 through 546 Processing helix chain 'E' and resid 571 through 577 removed outlier: 3.507A pdb=" N LYS E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 620 removed outlier: 3.609A pdb=" N ARG E 619 " --> pdb=" O ALA E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 654 through 661 Processing helix chain 'E' and resid 664 through 679 Processing helix chain 'E' and resid 695 through 705 removed outlier: 4.622A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 703 " --> pdb=" O TYR E 699 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR E 704 " --> pdb=" O LEU E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 717 removed outlier: 3.544A pdb=" N MET E 717 " --> pdb=" O ILE E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 744 removed outlier: 3.608A pdb=" N SER E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 242 through 253 removed outlier: 4.112A pdb=" N ALA F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 379 through 383 Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.530A pdb=" N LEU F 400 " --> pdb=" O ILE F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.521A pdb=" N ALA F 433 " --> pdb=" O GLY F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.733A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.502A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.554A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.718A pdb=" N MET F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 619' Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 652 through 660 removed outlier: 3.737A pdb=" N ASP F 656 " --> pdb=" O ASP F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 679 Processing helix chain 'F' and resid 693 through 695 No H-bonds generated for 'chain 'F' and resid 693 through 695' Processing helix chain 'F' and resid 696 through 704 Processing helix chain 'F' and resid 713 through 717 Processing helix chain 'F' and resid 735 through 744 Processing helix chain 'F' and resid 748 through 751 Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 779 through 784 Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.545A pdb=" N ILE G 255 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 Processing helix chain 'G' and resid 363 through 371 Processing helix chain 'G' and resid 372 through 375 Processing helix chain 'G' and resid 376 through 381 removed outlier: 3.867A pdb=" N SER G 381 " --> pdb=" O LYS G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 400 Processing helix chain 'G' and resid 430 through 435 Processing helix chain 'G' and resid 455 through 469 Processing helix chain 'G' and resid 475 through 488 Processing helix chain 'G' and resid 508 through 521 Processing helix chain 'G' and resid 529 through 533 Processing helix chain 'G' and resid 541 through 545 Processing helix chain 'G' and resid 570 through 577 removed outlier: 3.571A pdb=" N ILE G 574 " --> pdb=" O ARG G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 619 No H-bonds generated for 'chain 'G' and resid 617 through 619' Processing helix chain 'G' and resid 632 through 634 No H-bonds generated for 'chain 'G' and resid 632 through 634' Processing helix chain 'G' and resid 635 through 641 removed outlier: 3.678A pdb=" N ASN G 641 " --> pdb=" O GLU G 637 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 661 removed outlier: 3.960A pdb=" N GLY G 657 " --> pdb=" O GLU G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 679 removed outlier: 4.070A pdb=" N PHE G 666 " --> pdb=" O ASN G 662 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA G 667 " --> pdb=" O ARG G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 705 removed outlier: 4.416A pdb=" N TYR G 699 " --> pdb=" O ASP G 695 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR G 704 " --> pdb=" O LEU G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 710 through 715 Proline residue: G 715 - end of helix Processing helix chain 'G' and resid 716 through 722 removed outlier: 4.302A pdb=" N LYS G 722 " --> pdb=" O THR G 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 735 through 744 Processing helix chain 'G' and resid 752 through 763 Processing helix chain 'G' and resid 779 through 784 Processing helix chain 'H' and resid 242 through 254 Processing helix chain 'H' and resid 324 through 336 Processing helix chain 'H' and resid 363 through 371 Processing helix chain 'H' and resid 376 through 383 removed outlier: 3.566A pdb=" N SER H 380 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 400 Processing helix chain 'H' and resid 431 through 434 Processing helix chain 'H' and resid 455 through 469 Processing helix chain 'H' and resid 472 through 488 removed outlier: 4.430A pdb=" N LYS H 477 " --> pdb=" O ASP H 473 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN H 478 " --> pdb=" O GLU H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 521 Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 541 through 546 Processing helix chain 'H' and resid 570 through 577 Processing helix chain 'H' and resid 614 through 619 removed outlier: 3.536A pdb=" N MET H 618 " --> pdb=" O ASP H 614 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG H 619 " --> pdb=" O ASN H 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 614 through 619' Processing helix chain 'H' and resid 632 through 634 No H-bonds generated for 'chain 'H' and resid 632 through 634' Processing helix chain 'H' and resid 635 through 640 removed outlier: 3.508A pdb=" N ALA H 639 " --> pdb=" O GLY H 635 " (cutoff:3.500A) Processing helix chain 'H' and resid 654 through 661 Processing helix chain 'H' and resid 664 through 679 Processing helix chain 'H' and resid 693 through 695 No H-bonds generated for 'chain 'H' and resid 693 through 695' Processing helix chain 'H' and resid 696 through 704 removed outlier: 3.700A pdb=" N GLY H 703 " --> pdb=" O TYR H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 713 through 715 No H-bonds generated for 'chain 'H' and resid 713 through 715' Processing helix chain 'H' and resid 716 through 721 Processing helix chain 'H' and resid 722 through 724 No H-bonds generated for 'chain 'H' and resid 722 through 724' Processing helix chain 'H' and resid 736 through 744 removed outlier: 3.566A pdb=" N SER H 744 " --> pdb=" O GLN H 740 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 763 Processing helix chain 'H' and resid 779 through 784 Processing helix chain 'I' and resid 242 through 254 removed outlier: 3.742A pdb=" N ALA I 246 " --> pdb=" O SER I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 336 removed outlier: 4.074A pdb=" N THR I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 371 Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.742A pdb=" N SER I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 400 Processing helix chain 'I' and resid 430 through 435 removed outlier: 3.809A pdb=" N LYS I 435 " --> pdb=" O ASP I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 469 Processing helix chain 'I' and resid 475 through 488 Processing helix chain 'I' and resid 508 through 521 Processing helix chain 'I' and resid 530 through 534 removed outlier: 3.812A pdb=" N ASP I 534 " --> pdb=" O ILE I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 546 Processing helix chain 'I' and resid 570 through 578 removed outlier: 3.593A pdb=" N ILE I 574 " --> pdb=" O ARG I 570 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR I 578 " --> pdb=" O ILE I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 619 Processing helix chain 'I' and resid 632 through 634 No H-bonds generated for 'chain 'I' and resid 632 through 634' Processing helix chain 'I' and resid 635 through 641 Processing helix chain 'I' and resid 653 through 660 removed outlier: 4.467A pdb=" N GLY I 657 " --> pdb=" O GLU I 653 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 679 Processing helix chain 'I' and resid 693 through 695 No H-bonds generated for 'chain 'I' and resid 693 through 695' Processing helix chain 'I' and resid 696 through 705 removed outlier: 3.652A pdb=" N GLY I 703 " --> pdb=" O TYR I 699 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR I 704 " --> pdb=" O LEU I 700 " (cutoff:3.500A) Processing helix chain 'I' and resid 713 through 715 No H-bonds generated for 'chain 'I' and resid 713 through 715' Processing helix chain 'I' and resid 716 through 721 Processing helix chain 'I' and resid 722 through 724 No H-bonds generated for 'chain 'I' and resid 722 through 724' Processing helix chain 'I' and resid 736 through 744 Processing helix chain 'I' and resid 752 through 763 Processing helix chain 'I' and resid 779 through 784 removed outlier: 3.688A pdb=" N SER I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 255 removed outlier: 3.583A pdb=" N ALA J 246 " --> pdb=" O SER J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 314 removed outlier: 4.700A pdb=" N SER J 313 " --> pdb=" O ASN J 310 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS J 314 " --> pdb=" O PRO J 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 310 through 314' Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.651A pdb=" N THR J 336 " --> pdb=" O ARG J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 371 removed outlier: 4.142A pdb=" N LYS J 366 " --> pdb=" O PRO J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 375 removed outlier: 4.018A pdb=" N LEU J 375 " --> pdb=" O ARG J 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 376 through 384 removed outlier: 4.905A pdb=" N SER J 381 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 383 " --> pdb=" O SER J 380 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU J 384 " --> pdb=" O SER J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 400 removed outlier: 3.775A pdb=" N LEU J 400 " --> pdb=" O ILE J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 436 removed outlier: 3.783A pdb=" N LYS J 434 " --> pdb=" O GLY J 430 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS J 435 " --> pdb=" O ASP J 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR J 436 " --> pdb=" O ASP J 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 430 through 436' Processing helix chain 'J' and resid 455 through 469 Processing helix chain 'J' and resid 475 through 488 Processing helix chain 'J' and resid 489 through 491 No H-bonds generated for 'chain 'J' and resid 489 through 491' Processing helix chain 'J' and resid 508 through 521 Processing helix chain 'J' and resid 529 through 533 Processing helix chain 'J' and resid 541 through 546 removed outlier: 3.653A pdb=" N ALA J 545 " --> pdb=" O ASN J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 577 removed outlier: 3.506A pdb=" N LEU J 577 " --> pdb=" O ASN J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 619 removed outlier: 3.534A pdb=" N MET J 618 " --> pdb=" O ASP J 614 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG J 619 " --> pdb=" O ASN J 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 614 through 619' Processing helix chain 'J' and resid 632 through 634 No H-bonds generated for 'chain 'J' and resid 632 through 634' Processing helix chain 'J' and resid 635 through 640 removed outlier: 3.505A pdb=" N ALA J 639 " --> pdb=" O GLY J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 654 through 661 Processing helix chain 'J' and resid 664 through 679 Processing helix chain 'J' and resid 695 through 705 removed outlier: 4.238A pdb=" N TYR J 699 " --> pdb=" O ASP J 695 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY J 703 " --> pdb=" O TYR J 699 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 704 " --> pdb=" O LEU J 700 " (cutoff:3.500A) Processing helix chain 'J' and resid 713 through 717 Processing helix chain 'J' and resid 720 through 724 Processing helix chain 'J' and resid 736 through 744 Processing helix chain 'J' and resid 752 through 763 Processing helix chain 'J' and resid 779 through 784 Processing helix chain 'K' and resid 242 through 255 removed outlier: 3.531A pdb=" N ALA K 246 " --> pdb=" O SER K 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE K 254 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE K 255 " --> pdb=" O SER K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 314 removed outlier: 4.649A pdb=" N SER K 313 " --> pdb=" O ASN K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 336 removed outlier: 3.668A pdb=" N ASP K 335 " --> pdb=" O GLN K 331 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR K 336 " --> pdb=" O ARG K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 371 Processing helix chain 'K' and resid 372 through 375 removed outlier: 4.051A pdb=" N LEU K 375 " --> pdb=" O ARG K 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 376 through 381 removed outlier: 4.162A pdb=" N SER K 381 " --> pdb=" O LYS K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 384 No H-bonds generated for 'chain 'K' and resid 382 through 384' Processing helix chain 'K' and resid 385 through 400 Processing helix chain 'K' and resid 431 through 434 Processing helix chain 'K' and resid 455 through 469 Processing helix chain 'K' and resid 475 through 489 Processing helix chain 'K' and resid 508 through 521 Processing helix chain 'K' and resid 541 through 546 removed outlier: 3.556A pdb=" N ASN K 546 " --> pdb=" O PRO K 542 " (cutoff:3.500A) Processing helix chain 'K' and resid 570 through 577 removed outlier: 3.705A pdb=" N ILE K 574 " --> pdb=" O ARG K 570 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 619 Processing helix chain 'K' and resid 632 through 634 No H-bonds generated for 'chain 'K' and resid 632 through 634' Processing helix chain 'K' and resid 635 through 641 Processing helix chain 'K' and resid 652 through 661 removed outlier: 4.401A pdb=" N ASP K 656 " --> pdb=" O ASP K 652 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY K 657 " --> pdb=" O GLU K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 664 through 679 Processing helix chain 'K' and resid 694 through 705 removed outlier: 4.176A pdb=" N PHE K 698 " --> pdb=" O PRO K 694 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR K 699 " --> pdb=" O ASP K 695 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY K 703 " --> pdb=" O TYR K 699 " (cutoff:3.500A) Processing helix chain 'K' and resid 713 through 715 No H-bonds generated for 'chain 'K' and resid 713 through 715' Processing helix chain 'K' and resid 716 through 722 removed outlier: 3.530A pdb=" N LEU K 720 " --> pdb=" O LEU K 716 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS K 722 " --> pdb=" O THR K 718 " (cutoff:3.500A) Processing helix chain 'K' and resid 736 through 747 removed outlier: 3.581A pdb=" N LYS K 745 " --> pdb=" O GLN K 741 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR K 746 " --> pdb=" O LYS K 742 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE K 747 " --> pdb=" O ILE K 743 " (cutoff:3.500A) Processing helix chain 'K' and resid 752 through 763 Processing helix chain 'K' and resid 779 through 784 Processing helix chain 'L' and resid 242 through 255 Processing helix chain 'L' and resid 324 through 334 Processing helix chain 'L' and resid 335 through 337 No H-bonds generated for 'chain 'L' and resid 335 through 337' Processing helix chain 'L' and resid 363 through 371 Processing helix chain 'L' and resid 376 through 380 Processing helix chain 'L' and resid 385 through 400 Processing helix chain 'L' and resid 430 through 436 removed outlier: 4.338A pdb=" N TYR L 436 " --> pdb=" O ASP L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 469 removed outlier: 4.006A pdb=" N GLU L 459 " --> pdb=" O SER L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 488 Processing helix chain 'L' and resid 489 through 491 No H-bonds generated for 'chain 'L' and resid 489 through 491' Processing helix chain 'L' and resid 508 through 521 Processing helix chain 'L' and resid 570 through 577 removed outlier: 3.610A pdb=" N LEU L 577 " --> pdb=" O ASN L 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 632 through 634 No H-bonds generated for 'chain 'L' and resid 632 through 634' Processing helix chain 'L' and resid 635 through 640 Processing helix chain 'L' and resid 654 through 661 Processing helix chain 'L' and resid 664 through 679 Processing helix chain 'L' and resid 695 through 705 removed outlier: 4.169A pdb=" N TYR L 699 " --> pdb=" O ASP L 695 " (cutoff:3.500A) Processing helix chain 'L' and resid 710 through 717 Proline residue: L 715 - end of helix Processing helix chain 'L' and resid 720 through 724 Processing helix chain 'L' and resid 736 through 744 removed outlier: 3.647A pdb=" N SER L 744 " --> pdb=" O GLN L 740 " (cutoff:3.500A) Processing helix chain 'L' and resid 752 through 763 Processing helix chain 'L' and resid 779 through 784 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 299 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 413 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.762A pdb=" N ILE A 602 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA6, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA7, first strand: chain 'A' and resid 706 through 708 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA9, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.859A pdb=" N GLN B 295 " --> pdb=" O TYR B 306 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 304 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B 317 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB3, first strand: chain 'B' and resid 499 through 502 removed outlier: 3.856A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 604 " --> pdb=" O PHE B 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB5, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB6, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AB7, first strand: chain 'C' and resid 294 through 298 Processing sheet with id=AB8, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AB9, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AC1, first strand: chain 'C' and resid 524 through 526 removed outlier: 3.955A pdb=" N PHE C 554 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 499 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC3, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AC4, first strand: chain 'C' and resid 706 through 707 Processing sheet with id=AC5, first strand: chain 'C' and resid 726 through 728 removed outlier: 4.368A pdb=" N LEU C 734 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 774 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 294 through 298 removed outlier: 3.685A pdb=" N SER D 297 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 341 through 342 removed outlier: 3.587A pdb=" N ASP D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AC9, first strand: chain 'D' and resid 524 through 527 removed outlier: 3.521A pdb=" N PHE D 554 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AD2, first strand: chain 'D' and resid 630 through 631 Processing sheet with id=AD3, first strand: chain 'D' and resid 706 through 708 removed outlier: 3.585A pdb=" N VAL D 707 " --> pdb=" O ILE D 777 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD5, first strand: chain 'D' and resid 764 through 765 Processing sheet with id=AD6, first strand: chain 'E' and resid 294 through 297 Processing sheet with id=AD7, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD8, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD9, first strand: chain 'E' and resid 524 through 525 removed outlier: 3.650A pdb=" N PHE E 554 " --> pdb=" O VAL E 525 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 626 " --> pdb=" O PHE E 502 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AE2, first strand: chain 'E' and resid 706 through 708 removed outlier: 3.504A pdb=" N VAL E 707 " --> pdb=" O ILE E 777 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AE4, first strand: chain 'F' and resid 294 through 298 Processing sheet with id=AE5, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AE6, first strand: chain 'F' and resid 412 through 414 removed outlier: 3.624A pdb=" N LEU F 413 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.069A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 628 through 631 removed outlier: 5.744A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 706 through 708 Processing sheet with id=AF1, first strand: chain 'F' and resid 726 through 728 Processing sheet with id=AF2, first strand: chain 'F' and resid 764 through 765 removed outlier: 4.070A pdb=" N TYR F 773 " --> pdb=" O LYS F 765 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 294 through 299 removed outlier: 4.119A pdb=" N LYS G 317 " --> pdb=" O ILE G 305 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 339 through 341 removed outlier: 3.521A pdb=" N LEU G 340 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 412 through 414 Processing sheet with id=AF6, first strand: chain 'G' and resid 524 through 526 removed outlier: 3.522A pdb=" N THR G 499 " --> pdb=" O ILE G 600 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE G 602 " --> pdb=" O THR G 499 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU G 498 " --> pdb=" O ALA G 622 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 581 through 583 Processing sheet with id=AF8, first strand: chain 'G' and resid 628 through 631 removed outlier: 6.003A pdb=" N HIS G 629 " --> pdb=" O LYS G 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'G' and resid 706 through 708 Processing sheet with id=AG1, first strand: chain 'G' and resid 726 through 728 Processing sheet with id=AG2, first strand: chain 'G' and resid 765 through 766 Processing sheet with id=AG3, first strand: chain 'H' and resid 294 through 299 removed outlier: 3.713A pdb=" N GLU H 299 " --> pdb=" O ALA H 302 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 354 through 357 removed outlier: 8.574A pdb=" N VAL H 404 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU H 341 " --> pdb=" O VAL H 404 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 412 through 414 Processing sheet with id=AG6, first strand: chain 'H' and resid 524 through 527 Processing sheet with id=AG7, first strand: chain 'H' and resid 581 through 583 Processing sheet with id=AG8, first strand: chain 'H' and resid 629 through 631 Processing sheet with id=AG9, first strand: chain 'H' and resid 706 through 708 Processing sheet with id=AH1, first strand: chain 'H' and resid 726 through 728 removed outlier: 3.560A pdb=" N LEU H 734 " --> pdb=" O LEU H 774 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 294 through 299 Processing sheet with id=AH3, first strand: chain 'I' and resid 354 through 356 removed outlier: 6.605A pdb=" N LEU I 341 " --> pdb=" O VAL I 404 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 412 through 415 Processing sheet with id=AH5, first strand: chain 'I' and resid 524 through 527 removed outlier: 3.791A pdb=" N ILE I 601 " --> pdb=" O VAL I 553 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 628 through 631 removed outlier: 6.003A pdb=" N HIS I 629 " --> pdb=" O LYS I 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'I' and resid 706 through 708 Processing sheet with id=AH8, first strand: chain 'I' and resid 726 through 728 Processing sheet with id=AH9, first strand: chain 'J' and resid 294 through 299 removed outlier: 3.508A pdb=" N TYR J 306 " --> pdb=" O GLN J 295 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 354 through 356 removed outlier: 6.728A pdb=" N LEU J 341 " --> pdb=" O VAL J 404 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 412 through 415 Processing sheet with id=AI3, first strand: chain 'J' and resid 524 through 527 removed outlier: 4.045A pdb=" N THR J 499 " --> pdb=" O ILE J 600 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE J 602 " --> pdb=" O THR J 499 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR J 604 " --> pdb=" O PHE J 501 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE J 500 " --> pdb=" O VAL J 624 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 581 through 582 Processing sheet with id=AI5, first strand: chain 'J' and resid 628 through 631 removed outlier: 3.798A pdb=" N SER J 631 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AI7, first strand: chain 'J' and resid 726 through 728 Processing sheet with id=AI8, first strand: chain 'K' and resid 257 through 258 removed outlier: 4.409A pdb=" N SER K 257 " --> pdb=" O ASP K 277 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP K 277 " --> pdb=" O SER K 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'K' and resid 273 through 274 removed outlier: 3.534A pdb=" N SER K 297 " --> pdb=" O ARG K 304 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE K 303 " --> pdb=" O VAL K 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS K 317 " --> pdb=" O ILE K 305 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 339 through 341 Processing sheet with id=AJ2, first strand: chain 'K' and resid 412 through 414 Processing sheet with id=AJ3, first strand: chain 'K' and resid 524 through 527 removed outlier: 3.618A pdb=" N VAL K 525 " --> pdb=" O SER K 552 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS K 555 " --> pdb=" O ILE K 601 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP K 603 " --> pdb=" O CYS K 555 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU K 498 " --> pdb=" O ALA K 622 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL K 624 " --> pdb=" O LEU K 498 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE K 500 " --> pdb=" O VAL K 624 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 628 through 631 removed outlier: 5.605A pdb=" N HIS K 629 " --> pdb=" O LYS K 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'K' and resid 706 through 708 Processing sheet with id=AJ6, first strand: chain 'K' and resid 726 through 728 Processing sheet with id=AJ7, first strand: chain 'L' and resid 294 through 299 removed outlier: 3.731A pdb=" N ILE L 303 " --> pdb=" O VAL L 319 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 354 through 357 removed outlier: 8.782A pdb=" N VAL L 404 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU L 341 " --> pdb=" O VAL L 404 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 412 through 414 Processing sheet with id=AK1, first strand: chain 'L' and resid 524 through 526 removed outlier: 3.617A pdb=" N PHE L 554 " --> pdb=" O VAL L 525 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR L 499 " --> pdb=" O ILE L 600 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 602 " --> pdb=" O THR L 499 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU L 498 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL L 624 " --> pdb=" O LEU L 498 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE L 500 " --> pdb=" O VAL L 624 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 581 through 583 Processing sheet with id=AK3, first strand: chain 'L' and resid 629 through 631 removed outlier: 6.029A pdb=" N HIS L 629 " --> pdb=" O LYS L 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'L' and resid 706 through 708 Processing sheet with id=AK5, first strand: chain 'L' and resid 726 through 728 removed outlier: 4.045A pdb=" N TYR L 773 " --> pdb=" O LYS L 765 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS L 765 " --> pdb=" O TYR L 773 " (cutoff:3.500A) 1768 hydrogen bonds defined for protein. 4950 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: 25.97 Time building geometry restraints manager: 14.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 15374 1.33 - 1.45: 7811 1.45 - 1.57: 29069 1.57 - 1.69: 9 1.69 - 1.81: 269 Bond restraints: 52532 Sorted by residual: bond pdb=" CB VAL A 392 " pdb=" CG1 VAL A 392 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.79e+00 bond pdb=" C ILE C 348 " pdb=" N VAL C 349 " ideal model delta sigma weight residual 1.329 1.290 0.039 1.63e-02 3.76e+03 5.79e+00 bond pdb=" CB VAL F 392 " pdb=" CG2 VAL F 392 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.76e+00 bond pdb=" CG1 ILE D 329 " pdb=" CD1 ILE D 329 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.63e+00 bond pdb=" CB VAL D 392 " pdb=" CG1 VAL D 392 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.59e+00 ... (remaining 52527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 70679 2.61 - 5.22: 555 5.22 - 7.84: 38 7.84 - 10.45: 8 10.45 - 13.06: 1 Bond angle restraints: 71281 Sorted by residual: angle pdb=" C PHE C 240 " pdb=" N ILE C 241 " pdb=" CA ILE C 241 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" N ILE D 592 " pdb=" CA ILE D 592 " pdb=" C ILE D 592 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 angle pdb=" CA LEU E 400 " pdb=" CB LEU E 400 " pdb=" CG LEU E 400 " ideal model delta sigma weight residual 116.30 129.36 -13.06 3.50e+00 8.16e-02 1.39e+01 angle pdb=" N ILE C 241 " pdb=" CA ILE C 241 " pdb=" CB ILE C 241 " ideal model delta sigma weight residual 109.84 114.73 -4.89 1.32e+00 5.74e-01 1.37e+01 angle pdb=" N THR D 485 " pdb=" CA THR D 485 " pdb=" C THR D 485 " ideal model delta sigma weight residual 113.01 108.83 4.18 1.20e+00 6.94e-01 1.21e+01 ... (remaining 71276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 30604 27.69 - 55.39: 1080 55.39 - 83.08: 79 83.08 - 110.77: 15 110.77 - 138.47: 3 Dihedral angle restraints: 31781 sinusoidal: 12358 harmonic: 19423 Sorted by residual: dihedral pdb=" CA LYS C 356 " pdb=" C LYS C 356 " pdb=" N PHE C 357 " pdb=" CA PHE C 357 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASP E 322 " pdb=" C ASP E 322 " pdb=" N GLY E 323 " pdb=" CA GLY E 323 " ideal model delta harmonic sigma weight residual 180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ILE B 276 " pdb=" C ILE B 276 " pdb=" N ASP B 277 " pdb=" CA ASP B 277 " ideal model delta harmonic sigma weight residual 180.00 159.58 20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 31778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 6432 0.051 - 0.103: 1444 0.103 - 0.154: 236 0.154 - 0.206: 20 0.206 - 0.257: 2 Chirality restraints: 8134 Sorted by residual: chirality pdb=" CB VAL F 392 " pdb=" CA VAL F 392 " pdb=" CG1 VAL F 392 " pdb=" CG2 VAL F 392 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE B 241 " pdb=" N ILE B 241 " pdb=" C ILE B 241 " pdb=" CB ILE B 241 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 305 " pdb=" N ILE A 305 " pdb=" C ILE A 305 " pdb=" CB ILE A 305 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 8131 not shown) Planarity restraints: 9156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 413 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO C 414 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 240 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C PHE D 240 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE D 240 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE D 241 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 681 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO H 682 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 682 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 682 " -0.032 5.00e-02 4.00e+02 ... (remaining 9153 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 944 2.67 - 3.23: 51063 3.23 - 3.78: 78615 3.78 - 4.34: 105618 4.34 - 4.90: 168136 Nonbonded interactions: 404376 Sorted by model distance: nonbonded pdb=" O THR F 505 " pdb=" OH TYR F 645 " model vdw 2.111 3.040 nonbonded pdb=" NE2 GLN E 529 " pdb=" O SER E 556 " model vdw 2.133 3.120 nonbonded pdb=" NZ LYS B 307 " pdb=" O ASN B 310 " model vdw 2.143 3.120 nonbonded pdb=" OG1 THR J 365 " pdb=" OE1 GLU J 393 " model vdw 2.146 3.040 nonbonded pdb=" OG SER G 571 " pdb=" O ARG G 612 " model vdw 2.152 3.040 ... (remaining 404371 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 246 or (res \ id 247 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 or (resid 261 and (name N or name C \ A or name C or name O or name CB )) or resid 262 or (resid 263 through 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 or (resid 268 t \ hrough 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 through 284 or (resid 285 through 288 and (name N or name CA or \ name C or name O or name CB )) or resid 289 through 290 or (resid 291 through 2 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 294 or (res \ id 295 through 296 and (name N or name CA or name C or name O or name CB )) or r \ esid 297 through 298 or (resid 299 and (name N or name CA or name C or name O or \ name CB )) or resid 300 through 303 or (resid 304 through 307 and (name N or na \ me CA or name C or name O or name CB )) or resid 308 through 311 or (resid 312 t \ hrough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ or (resid 315 through 319 and (name N or name CA or name C or name O or name CB \ )) or resid 320 or (resid 321 through 322 and (name N or name CA or name C or n \ ame O or name CB )) or resid 323 through 327 or (resid 328 and (name N or name C \ A or name C or name O or name CB )) or resid 329 through 330 or (resid 331 throu \ gh 333 and (name N or name CA or name C or name O or name CB )) or resid 334 or \ (resid 335 and (name N or name CA or name C or name O or name CB )) or resid 336 \ through 338 or (resid 339 and (name N or name CA or name C or name O or name CB \ )) or resid 340 through 348 or (resid 349 and (name N or name CA or name C or n \ ame O or name CB )) or resid 350 through 351 or (resid 352 and (name N or name C \ A or name C or name O or name CB )) or resid 353 through 355 or (resid 356 and ( \ name N or name CA or name C or name O or name CB )) or resid 357 through 358 or \ (resid 359 through 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB \ )) or resid 364 through 365 or (resid 366 through 367 and (name N or name CA or \ name C or name O or name CB )) or resid 368 through 369 or (resid 370 through 3 \ 72 and (name N or name CA or name C or name O or name CB )) or resid 373 or (res \ id 374 through 378 and (name N or name CA or name C or name O or name CB )) or r \ esid 379 through 386 or (resid 387 and (name N or name CA or name C or name O or \ name CB )) or resid 388 through 389 or (resid 390 and (name N or name CA or nam \ e C or name O or name CB )) or resid 391 through 392 or (resid 393 through 401 a \ nd (name N or name CA or name C or name O or name CB )) or resid 402 through 404 \ or (resid 405 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 408 through 410 or (resid 411 through 413 and (name N or name CA or \ name C or name O or name CB )) or resid 414 through 416 or (resid 417 and (name \ N or name CA or name C or name O or name CB )) or resid 418 through 419 or (res \ id 420 through 421 and (name N or name CA or name C or name O or name CB )) or r \ esid 422 through 423 or (resid 424 and (name N or name CA or name C or name O or \ name CB )) or resid 425 or (resid 426 through 428 and (name N or name CA or nam \ e C or name O or name CB )) or resid 429 through 431 or (resid 432 through 436 a \ nd (name N or name CA or name C or name O or name CB )) or resid 437 through 439 \ or (resid 440 and (name N or name CA or name C or name O or name CB )) or resid \ 441 through 444 or (resid 445 through 447 and (name N or name CA or name C or n \ ame O or name CB )) or resid 448 through 449 or (resid 450 through 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 or (resid 453 throu \ gh 454 and (name N or name CA or name C or name O or name CB )) or resid 455 or \ (resid 456 through 463 and (name N or name CA or name C or name O or name CB )) \ or resid 464 through 465 or (resid 466 through 467 and (name N or name CA or nam \ e C or name O or name CB )) or resid 468 or (resid 469 and (name N or name CA or \ name C or name O or name CB )) or resid 470 or (resid 471 through 474 and (name \ N or name CA or name C or name O or name CB )) or resid 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 479 or (resid 480 and (name N or name CA or name C or name O or name CB )) \ or resid 481 or (resid 482 and (name N or name CA or name C or name O or name CB \ )) or resid 483 or (resid 484 and (name N or name CA or name C or name O or nam \ e CB )) or resid 485 through 489 or (resid 490 and (name N or name CA or name C \ or name O or name CB )) or resid 491 through 496 or (resid 497 and (name N or na \ me CA or name C or name O or name CB )) or resid 498 or (resid 499 through 501 a \ nd (name N or name CA or name C or name O or name CB )) or resid 502 through 503 \ or (resid 504 through 506 and (name N or name CA or name C or name O or name CB \ )) or resid 507 through 508 or (resid 509 and (name N or name CA or name C or n \ ame O or name CB )) or resid 510 through 512 or (resid 513 through 514 and (name \ N or name CA or name C or name O or name CB )) or resid 515 through 516 or (res \ id 517 and (name N or name CA or name C or name O or name CB )) or resid 518 thr \ ough 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 or (resid 522 through 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 528 or (resid 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 through 531 or (resid 532 through 5 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 539 or (res \ id 540 through 541 and (name N or name CA or name C or name O or name CB )) or r \ esid 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) \ or resid 544 through 545 or (resid 546 through 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 or (resid 549 through 551 and (name N o \ r name CA or name C or name O or name 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or name O or \ name CB )) or resid 706 through 724 or (resid 725 and (name N or name CA or nam \ e C or name O or name CB )) or resid 726 through 738 or (resid 739 through 740 a \ nd (name N or name CA or name C or name O or name CB )) or resid 741 through 742 \ or (resid 743 and (name N or name CA or name C or name O or name CB )) or resid \ 744 through 747 or (resid 748 and (name N or name CA or name C or name O or nam \ e CB )) or resid 749 through 755 or (resid 756 and (name N or name CA or name C \ or name O or name CB )) or resid 757 through 758 or (resid 759 through 760 and ( \ name N or name CA or name C or name O or name CB )) or resid 761 through 762 or \ (resid 763 through 764 and (name N or name CA or name C or name O or name CB )) \ or resid 765 through 773 or (resid 774 through 776 and (name N or name CA or nam \ e C or name O or name CB )) or resid 777 or (resid 778 and (name N or name CA or \ name C or name O or name CB )) or resid 779 through 785)) selection = (chain 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CA or name C or name O or name CB )) or resid 329 through \ 330 or (resid 331 through 333 and (name N or name CA or name C or name O or nam \ e CB )) or resid 334 or (resid 335 and (name N or name CA or name C or name O or \ name CB )) or resid 336 through 338 or (resid 339 and (name N or name CA or nam \ e C or name O or name CB )) or resid 340 through 348 or (resid 349 and (name N o \ r name CA or name C or name O or name CB )) or resid 350 through 351 or (resid 3 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 353 through \ 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or r \ esid 357 through 358 or (resid 359 through 361 and (name N or name CA or name C \ or name O or name CB )) or resid 362 or (resid 363 and (name N or name CA or nam \ e C or name O or name CB )) or resid 364 through 365 or (resid 366 through 367 a \ nd (name N or name CA or name C or name O or name CB )) or resid 368 through 369 \ or (resid 370 through 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 or (resid 374 through 378 and (name N or name CA or name C or n \ ame O or name CB )) or resid 379 through 386 or (resid 387 and (name N or name C \ A or name C or name O or name CB )) or resid 388 through 389 or (resid 390 and ( \ name N or name CA or name C or name O or name CB )) or resid 391 through 392 or \ (resid 393 through 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 through 404 or (resid 405 through 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 through 410 or (resid 411 through 413 a \ nd (name N or name CA or name C or name O or name CB )) or resid 414 through 415 \ or (resid 416 through 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 through 419 or (resid 420 through 421 and (name N or name CA or \ name C or name O or name CB )) or resid 422 through 423 or (resid 424 and (name \ N or name CA or name C or name O or name 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name C or name O or name CB \ )) or resid 475 or (resid 476 through 477 and (name N or name CA or name C or n \ ame O or name CB )) or resid 478 or (resid 479 through 480 and (name N or name C \ A or name C or name O or name CB )) or resid 481 or (resid 482 and (name N or na \ me CA or name C or name O or name CB )) or resid 483 or (resid 484 and (name N o \ r name CA or name C or name O or name CB )) or resid 485 through 489 or (resid 4 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 491 through \ 496 or (resid 497 and (name N or name CA or name C or name O or name CB )) or r \ esid 498 or (resid 499 through 501 and (name N or name CA or name C or name O or \ name CB )) or resid 502 through 503 or (resid 504 through 506 and (name N or na \ me CA or name C or name O or name CB )) or resid 507 through 508 or (resid 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 512 \ or (resid 513 through 514 and (name N or name CA or name C or name O or name CB \ )) or resid 515 through 519 or (resid 520 and (name N or name CA or name C or n \ ame O or name CB )) or resid 521 or (resid 522 through 526 and (name N or name C \ A or name C or name O or name CB )) or resid 527 through 528 or (resid 529 and ( \ name N or name CA or name C or name O or name CB )) or resid 530 through 531 or \ (resid 532 through 538 and (name N or name CA or name C or name O or name CB )) \ or (resid 539 through 541 and (name N or name CA or name C or name O or name CB \ )) or resid 542 through 545 or (resid 546 through 547 and (name N or name CA or \ name C or name O or name CB )) or resid 548 or (resid 549 through 551 and (name \ N or name CA or name C or name O or name CB )) or resid 552 through 554 or (resi \ d 555 and (name N or name CA or name C or name O or name CB )) or resid 556 or ( \ resid 557 through 558 and (name N or name CA or name C or name O or name CB )) o \ r resid 559 through 566 or (resid 567 through 570 and (name N or name CA or name \ C or name O or name CB )) or resid 571 or (resid 572 through 573 and (name N or \ name CA or name C or name O or name CB )) or resid 574 through 575 or (resid 57 \ 6 through 577 and (name N or name CA or name C or name O or name CB )) or resid \ 578 through 581 or (resid 582 through 583 and (name N or name CA or name C or na \ me O or name CB )) or resid 584 through 590 or (resid 591 through 592 and (name \ N or name CA or name C or name O or name CB )) or resid 593 or (resid 594 throug \ h 598 and (name N or name CA or name C or name O or name CB )) or resid 599 or ( \ resid 600 and (name N or name CA or name C or name O or name CB )) or resid 601 \ or (resid 602 through 605 and (name N or name CA or name C or name O or name CB \ )) or resid 606 through 612 or (resid 613 through 620 and (name N or name CA or \ name C or name O or name CB )) or resid 621 through 622 or (resid 623 and (name \ N or name CA or name C or name O or name CB )) or resid 624 or (resid 625 and (n \ 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through 681 and (name N or name CA or name C or name O or name CB )) or re \ sid 682 or (resid 683 and (name N or name CA or name C or name O or name CB )) o \ r resid 684 through 685 or (resid 686 through 687 and (name N or name CA or name \ C or name O or name CB )) or resid 688 through 690 or (resid 691 through 692 an \ d (name N or name CA or name C or name O or name CB )) or resid 693 through 698 \ or (resid 699 and (name N or name CA or name C or name O or name CB )) or resid \ 700 or (resid 701 through 702 and (name N or name CA or name C or name O or name \ CB )) or resid 703 through 704 or (resid 705 and (name N or name CA or name C o \ r name O or name CB )) or resid 706 through 718 or (resid 719 and (name N or nam \ e CA or name C or name O or name CB )) or resid 720 through 721 or (resid 722 an \ d (name N or name CA or name C or name O or name CB )) or resid 723 through 724 \ or (resid 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 741 or (resid 742 through 743 and (name N or name CA or name C or na \ me O or name CB )) or resid 744 through 747 or (resid 748 and (name N or name CA \ or name C or name O or name CB )) or resid 749 or (resid 750 through 751 and (n \ ame N or name CA or name C or name O or name CB )) or resid 752 through 758 or ( \ resid 759 through 760 and (name N or name CA or name C or name O or name CB )) o \ r resid 761 through 762 or (resid 763 through 764 and (name N or name CA or name \ C or name O or name CB )) or resid 765 or (resid 766 through 769 and (name N or \ name CA or name C or name O or name CB )) or resid 770 or (resid 771 through 77 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 777 or (resi \ d 778 and (name N or name CA or name C or name O or name CB )) or resid 779 thro \ ugh 784 or (resid 785 and (name N or name CA or name C or name O or name CB )))) \ selection = (chain 'C' and ((resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 246 or (res \ id 247 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 or (resid 261 and (name N or name C \ A or name C or name O or name CB )) or resid 262 through 263 or (resid 264 throu \ gh 266 and (name N or name CA or name C or name O or name CB )) or resid 267 thr \ ough 268 or (resid 269 through 277 and (name N or name CA or name C or name O or \ name CB )) or resid 278 through 279 or (resid 280 and (name N or name CA or nam \ e C or name O or name CB )) or resid 281 through 284 or (resid 285 through 288 a \ nd (name N or name CA or name C or name O or name CB )) or resid 289 through 290 \ or (resid 291 through 293 and (name N or name CA or name C or name O or name CB \ )) or resid 294 or (resid 295 through 296 and (name N or name CA or name C or n \ ame O or name CB )) or resid 297 or (resid 298 through 299 and (name N or name C \ A or name C or name O or name CB )) or resid 300 through 303 or (resid 304 throu \ gh 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thr \ ough 310 or (resid 311 through 313 and (name N or name CA or name C or name O or \ name CB )) or resid 314 or (resid 315 through 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 or (resid 321 through 322 and (name N o \ r name CA or name C or name O or name CB )) or resid 323 through 327 or (resid 3 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 329 through \ 330 or (resid 331 through 333 and (name N or name CA or name C or name O or nam \ e CB )) or resid 334 or (resid 335 and (name N or name CA or name C or name O or \ name CB )) or resid 336 through 338 or (resid 339 and (name N or name CA or nam \ e C or name O or name CB )) or resid 340 through 348 or (resid 349 and (name N o \ r name CA or name C or name O or name CB )) or resid 350 through 351 or (resid 3 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 353 through \ 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or r \ esid 357 through 358 or (resid 359 through 361 and (name N or name CA or name C \ or name O or name CB )) or resid 362 or (resid 363 and (name N or name CA or nam \ e C or name O or name CB )) or resid 364 through 365 or (resid 366 through 367 a \ nd (name N or name CA or name C or name O or name CB )) or resid 368 through 369 \ or (resid 370 through 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 or (resid 374 through 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name C or name O or name CB )) or r \ esid 437 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 444 or (resid 445 through 447 and (name N or na \ me CA or name C or name O or name CB )) or resid 448 through 449 or (resid 450 t \ hrough 451 and (name N or name CA or name C or name O or name CB )) or resid 452 \ or (resid 453 through 454 and (name N or name CA or name C or name O or name CB \ )) or resid 455 or (resid 456 through 463 and (name N or name CA or name C or n \ ame O or name CB )) or resid 464 or (resid 465 through 467 and (name N or name C \ A or name C or name O or name CB )) or resid 468 or (resid 469 and (name N or na \ me CA or name C or name O or name CB )) or resid 470 or (resid 471 through 474 a \ nd (name N or name CA or name C or name O or name CB )) or resid 475 or (resid 4 \ 76 through 477 and (name N or name CA or name C or name O or name CB )) or resid \ 478 or (resid 479 through 480 and (name N or name CA or name C or name O or nam \ e CB )) or resid 481 or (resid 482 and (name N or name CA or name C or name O or \ name CB )) or resid 483 or (resid 484 and (name N or name CA or name C or name \ O or name CB )) or resid 485 through 489 or (resid 490 and (name N or name CA or \ name C or name O or name CB )) or resid 491 through 496 or (resid 497 and (name \ N or name CA or name C or name O or name CB )) or resid 498 or (resid 499 throu \ gh 501 and (name N or name CA or name C or name O or name CB )) or resid 502 thr \ ough 503 or (resid 504 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 through 508 or (resid 509 and (name N or name CA or nam \ e C or name O or name CB )) or resid 510 through 513 or (resid 514 and (name N o \ r name CA or name C or name O or name CB )) or resid 515 through 516 or (resid 5 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 518 through \ 519 or (resid 520 and (name N or name CA or name C or name O or 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)) or resid 765 or (resid 7 \ 66 through 769 and (name N or name CA or name C or name O or name CB )) or resid \ 770 or (resid 771 through 776 and (name N or name CA or name C or name O or nam \ e CB )) or resid 777 through 784 or (resid 785 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and ((resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 246 or (res \ id 247 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name 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or name C or name O or name CB )) or resid 314 \ through 315 or (resid 316 through 319 and (name N or name CA or name C or name \ O or name CB )) or resid 320 or (resid 321 through 322 and (name N or name CA or \ name C or name O or name CB )) or resid 323 through 327 or (resid 328 and (name \ N or name CA or name C or name O or name CB )) or resid 329 through 330 or (res \ id 331 through 333 and (name N or name CA or name C or name O or name CB )) or r \ esid 334 or (resid 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 338 or (resid 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 through 348 or (resid 349 and (name N or name CA or \ name C or name O or name CB )) or resid 350 through 351 or (resid 352 and (name \ N or name CA or name C or name O or name CB )) or resid 353 through 355 or (res \ id 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 358 or (resid 359 through 361 and (name N 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(name N or name C \ A or name C or name O or name CB )) or resid 468 through 470 or (resid 471 throu \ gh 474 and (name N or name CA or name C or name O or name CB )) or resid 475 or \ (resid 476 through 477 and (name N or name CA or name C or name O or name CB )) \ or resid 478 or (resid 479 through 480 and (name N or name CA or name C or name \ O or name CB )) or resid 481 or (resid 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 or (resid 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 489 or (resid 490 and (name N or na \ me CA or name C or name O or name CB )) or resid 491 through 496 or (resid 497 a \ nd (name N or name CA or name C or name O or name CB )) or resid 498 or (resid 4 \ 99 through 501 and (name N or name CA or name C or name O or name CB )) or resid \ 502 through 503 or (resid 504 through 506 and (name N or name CA or name C or n \ ame O or name CB )) or resid 507 through 508 or (resid 509 and (name N or name C \ A or name C or name O or name CB )) or resid 510 through 512 or (resid 513 throu \ gh 514 and (name N or name CA or name C or name O or name CB )) or resid 515 thr \ ough 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 or (resid 522 through 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 528 or (resid 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 or (resid 531 through 538 and (name \ N or name CA or name C or name O or name CB )) or resid 539 or (resid 540 throu \ gh 541 and (name N or name CA or name C or name O or name CB )) or resid 542 or \ (resid 543 and (name N or name CA or name C or name O or name CB )) or resid 544 \ through 545 or (resid 546 through 547 and (name N or name CA or name C or name \ O or name CB )) or resid 548 or (resid 549 through 551 and (name N or name CA or \ name C or name O or name CB )) or resid 552 through 554 or (resid 555 and (name \ 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)) or resid 770 or (resid 771 through 776 and ( \ name N or name CA or name C or name O or name CB )) or resid 777 or (resid 778 a \ nd (name N or name CA or name C or name O or name CB )) or resid 779 through 784 \ or (resid 785 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 246 or (res \ id 247 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 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through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 246 or (res \ id 247 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 or (resid 261 and (name N or name C \ A or name C or name O or name CB )) or resid 262 or (resid 263 through 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 or (resid 268 t \ hrough 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 279 or (resid 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 through 284 or (resid 285 through 288 and (name N or name CA or \ name C or name O or name CB )) or resid 289 through 290 or (resid 291 through 2 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 294 through \ 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) or r \ esid 297 or (resid 298 through 299 and (name N or name CA or name C or name O or \ name CB )) or resid 300 through 304 or (resid 305 through 307 and (name N or na \ me CA or name C or name O or name CB )) or resid 308 through 310 or (resid 311 t \ hrough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ or (resid 315 through 319 and (name N or name CA or name C or name O or name CB \ )) or resid 320 or (resid 321 through 322 and (name N or name CA or name C or n \ ame O or name CB )) or resid 323 through 327 or (resid 328 and (name N or name C \ A or name C or name O or name CB )) or resid 329 through 330 or (resid 331 throu \ gh 333 and (name N or name CA or name C or name O or name CB )) or resid 334 or \ (resid 335 and (name N or name CA or name C or name O or name CB )) or resid 336 \ through 338 or (resid 339 and (name N or name CA or name C or name O or name CB \ )) or resid 340 through 348 or (resid 349 and (name N or name CA or name C or n \ ame O or name CB )) or resid 350 through 351 or (resid 352 and (name N or name C \ A or name C or name O or name CB )) or resid 353 through 355 or (resid 356 and ( \ name N or name CA or name C or name O or name CB )) or resid 357 through 358 or \ (resid 359 through 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 369 or (resid 370 through 372 a \ nd (name N or name CA or name C or name O or name CB )) or resid 373 or (resid 3 \ 74 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 through 386 or (resid 387 and (name N or name CA or name C or name O or nam \ e CB )) or resid 388 through 389 or (resid 390 and (name N or name CA or name C \ or name O or name CB )) or resid 391 through 392 or (resid 393 through 401 and ( \ name N or name CA or name C or name O or name CB )) or resid 402 through 415 or \ (resid 416 through 417 and (name N or name CA or name C or name O or name CB )) \ or resid 418 through 433 or (resid 434 through 436 and (name N or name CA or nam \ e C or name O or name CB )) or resid 437 through 439 or (resid 440 and (name N o \ r name CA or name C or name O or name CB )) or resid 441 through 444 or (resid 4 \ 45 through 447 and (name N or name CA or name C or name O or name CB )) or resid \ 448 through 449 or (resid 450 through 451 and (name N or name CA or name C or n \ ame O or name CB )) or resid 452 or (resid 453 through 454 and (name N or name C \ A or name C or name O or name CB )) or resid 455 or (resid 456 through 463 and ( \ name N or name CA or name C or name O or name CB )) or resid 464 or (resid 465 t \ hrough 467 and (name N or name CA or name C or name O or name CB )) or resid 468 \ or (resid 469 and (name N or name CA or name C or name O or name CB )) or resid \ 470 or (resid 471 through 474 and (name N or name CA or name C or name O or nam \ e CB )) or resid 475 or (resid 476 through 477 and (name N or name CA or name C \ or name O or name CB )) or resid 478 or (resid 479 through 480 and (name N or na \ me CA or name C or name O or name CB )) or resid 481 or (resid 482 and (name N o \ r name CA or name C or name O or name CB )) or resid 483 or (resid 484 and (name \ N or name CA or name C or name O or name CB )) or resid 485 through 496 or (res \ id 497 and (name N or name CA or name C or name O or name CB )) or resid 498 or \ (resid 499 through 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 503 or (resid 504 through 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 508 or (resid 509 and (name N o \ r name CA or name C or name O or name CB )) or resid 510 through 512 or (resid 5 \ 13 through 514 and (name N or name CA or name C or name O or name CB )) or resid \ 515 through 516 or (resid 517 and (name N or name CA or name C or name O or nam \ e CB )) or resid 518 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 or (resid 522 through 526 and (name N or na \ me CA or name C or name O or name CB )) or resid 527 through 528 or (resid 529 a \ nd (name N or name CA or name C or name O or name CB )) or resid 530 or (resid 5 \ 31 through 538 and (name N or name CA or name C or name O or name CB )) or resid \ 539 or (resid 540 through 541 and (name N or name CA or name C or name O or nam \ e CB )) or resid 542 or (resid 543 and (name N or name CA or name C or name O or \ name CB )) or resid 544 through 545 or (resid 546 through 547 and (name N or na \ me CA or name C or name O or name CB )) or resid 548 through 549 or (resid 550 t \ hrough 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 554 or (resid 555 and (name N or name CA or name C or name O or name CB \ )) or resid 556 or (resid 557 through 558 and (name N or name CA or name C or n \ ame O or name CB )) or resid 559 through 566 or (resid 567 through 570 and (name \ N or name CA or name C or name O or name CB )) or resid 571 or (resid 572 throu \ gh 573 and (name N or name CA or name C or name O or name CB )) or resid 574 or \ (resid 575 through 577 and (name N or name CA or name C or name O or name CB )) \ or resid 578 through 581 or (resid 582 through 583 and (name N or name CA or nam \ e C or name O or name CB )) or resid 584 through 586 or (resid 587 and (name N o \ r name CA or name C or name O or name CB )) or resid 588 through 590 or (resid 5 \ 91 through 592 and (name N or name CA or name C or name O or name CB )) or resid \ 593 or (resid 594 through 598 and (name N or name CA or name C or name O or nam \ e CB )) or resid 599 or (resid 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 or (resid 602 through 605 and (name N or name CA or nam \ e C or name O or name CB )) or resid 606 through 612 or (resid 613 through 620 a \ nd (name N or name CA or name C or name O or name CB )) or resid 621 through 622 \ or (resid 623 and (name N or name CA or name C or name O or name CB )) or resid \ 624 through 626 or (resid 627 and (name N or name CA or name C or name O or nam \ e CB )) or resid 628 through 631 or (resid 632 and (name N or name CA or name C \ or name O or name CB )) or resid 633 through 644 or (resid 645 and (name N or na \ me CA or name C or name O or name CB )) or resid 646 through 651 or (resid 652 t \ hrough 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ or (resid 655 through 656 and (name N or name CA or name C or name O or name CB \ )) or resid 657 through 659 or (resid 660 through 668 and (name N or name CA or \ name C or name O or name CB )) or resid 669 through 670 or (resid 671 through 6 \ 72 and (name N or name CA or name C or name O or name CB )) or resid 673 or (res \ id 674 and (name N or name CA or name C or name O or name CB )) or resid 675 thr \ ough 677 or (resid 678 through 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 or (resid 683 and (name N or name CA or name C or name \ O or name CB )) or resid 684 through 685 or (resid 686 through 687 and (name N o \ r name CA or name C or name O or name CB )) or resid 688 through 690 or (resid 6 \ 91 through 692 and (name N or name CA or name C or name O or name CB )) or resid \ 693 through 698 or (resid 699 and (name N or name CA or name C or name O or nam \ e CB )) or resid 700 through 701 or (resid 702 and (name N or name CA or name C \ or name O or name CB )) or resid 703 through 718 or (resid 719 and (name N or na \ me CA or name C or name O or name CB )) or resid 720 through 721 or (resid 722 a \ nd (name N or name CA or name C or name O or name CB )) or resid 723 through 724 \ or (resid 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 738 or (resid 739 through 740 and (name N or name CA or name C or n \ ame O or name CB )) or resid 741 or (resid 742 through 743 and (name N or name C \ A or name C or name O or name CB )) or resid 744 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB )) or resid 749 or (resid 750 t \ hrough 751 and (name N or name CA or name C or name O or name CB )) or resid 752 \ through 755 or (resid 756 and (name N or name CA or name C or name O or name CB \ )) or resid 757 through 758 or (resid 759 through 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 or (resid 762 through 764 and (name \ N or name CA or name C or name O or name CB )) or resid 765 or (resid 766 throu \ gh 769 and (name N or name CA or name C or name O or name CB )) or resid 770 or \ (resid 771 through 776 and (name N or name CA or name C or name O or name CB )) \ or resid 777 or (resid 778 and (name N or name CA or name C or name O or name CB \ )) or resid 779 through 784 or (resid 785 and (name N or name CA or name C or n \ ame O or name CB )))) selection = (chain 'L' and ((resid 236 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 239 or (resid 240 through 241 and (name N or name CA or \ name C or name O or name CB )) or resid 242 or (resid 243 through 244 and (name \ N or name CA or name C or name O or name CB )) or resid 245 through 248 or (res \ id 249 through 250 and (name N or name CA or name C or name O or name CB )) or r \ esid 251 or (resid 252 through 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 or (resid 261 and (name N or name CA or \ name C or name O or name CB )) or resid 262 or (resid 263 through 266 and (name \ N or name CA or name C or name O or name CB )) or resid 267 or (resid 268 throu \ gh 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thr \ ough 285 or (resid 286 through 288 and (name N or name CA or name C or name O or \ name CB )) or resid 289 through 290 or (resid 291 through 293 and (name N or na \ me CA or name C or name O or name CB )) or resid 294 or (resid 295 through 296 a \ nd (name N or name CA or name C or name O or name CB )) or resid 297 or (resid 2 \ 98 through 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 303 or (resid 304 through 307 and (name N or name CA or name C or n \ ame O or name CB )) or resid 308 through 310 or (resid 311 through 313 and (name \ N or name CA or name C or name O or name CB )) or resid 314 or (resid 315 throu \ gh 319 and (name N or name CA or name C or name O or name CB )) or resid 320 or \ (resid 321 through 322 and (name N or name CA or name C or name O or name CB )) \ or resid 323 through 330 or (resid 331 through 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 or (resid 335 and (name N or name CA or \ name C or name O or name CB )) or resid 336 through 338 or (resid 339 and (name \ N or name CA or name C or name O or name CB )) or resid 340 through 348 or (res \ id 349 and (name N or name CA or name C or name O or name CB )) or resid 350 thr \ ough 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) \ or resid 353 through 355 or (resid 356 and (name N or name CA or name C or name \ O or name CB )) or resid 357 through 358 or (resid 359 through 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 or (resid 363 and (name \ N or name CA or name C or name O or name CB )) or resid 364 through 365 or (res \ id 366 through 367 and (name N or name CA or name C or name O or name CB )) or r \ esid 368 through 369 or (resid 370 through 372 and (name N or name CA or name C \ or name O or name CB )) or resid 373 or (resid 374 through 378 and (name N or na \ me CA or name C or name O or name CB )) or resid 379 through 386 or (resid 387 a \ nd (name N or name CA or name C or name O or name CB )) or resid 388 through 400 \ or (resid 401 and (name N or name CA or name C or name O or name CB )) or resid \ 402 through 404 or (resid 405 through 407 and (name N or name CA or name C or n \ ame O or name CB )) or resid 408 through 410 or (resid 411 through 413 and (name \ N or name CA or name C or name O or name CB )) or resid 414 through 415 or (res \ id 416 through 417 and (name N or name CA or name C or name O or name CB )) or r \ esid 418 through 419 or (resid 420 through 421 and (name N or name CA or name C \ or name O or name CB )) or resid 422 through 423 or (resid 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 or (resid 426 through 428 a \ nd (name N or name CA or name C or name O or name CB )) or resid 429 through 431 \ or (resid 432 through 436 and (name N or name CA or name C or name O or name CB \ )) or resid 437 through 444 or (resid 445 through 447 and (name N or name CA or \ name C or name O or name CB )) or resid 448 through 450 or (resid 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 or (resid 453 throu \ gh 454 and (name N or name CA or name C or name O or name CB )) or resid 455 or \ (resid 456 through 463 and (name N or name CA or name C or name O or name CB )) \ or resid 464 or (resid 465 through 467 and (name N or name CA or name C or name \ O or name CB )) or resid 468 or (resid 469 and (name N or name CA or name C or n \ ame O or name CB )) or resid 470 or (resid 471 through 474 and (name N or name C \ A or name C or name O or name CB )) or resid 475 or (resid 476 through 477 and ( \ name N or name CA or name C or name O or name CB )) or resid 478 or (resid 479 t \ hrough 480 and (name N or name CA or name C or name O or name CB )) or resid 481 \ or (resid 482 and (name N or name CA or name C or name O or name CB )) or resid \ 483 or (resid 484 and (name N or name CA or name C or name O or name CB )) or r \ esid 485 through 489 or (resid 490 and (name N or name CA or name C or name O or \ name CB )) or resid 491 through 496 or (resid 497 and (name N or name CA or nam \ e C or name O or name CB )) or resid 498 or (resid 499 through 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 through 503 or (resid 5 \ 04 through 506 and (name N or name CA or name C or name O or name CB )) or resid \ 507 through 508 or (resid 509 and (name N or name CA or name C or name O or nam \ e CB )) or resid 510 through 512 or (resid 513 through 514 and (name N or name C \ A or name C or name O or name CB )) or resid 515 through 516 or (resid 517 and ( \ name N or name CA or name C or name O or name CB )) or resid 518 through 519 or \ (resid 520 and (name N or name CA or name C or name O or name CB )) or resid 521 \ or (resid 522 through 526 and (name N or name CA or name C or name O or name CB \ )) or resid 527 through 528 or (resid 529 and (name N or name CA or name C or n \ ame O or name CB )) or resid 530 or (resid 531 through 538 and (name N or name C \ A or name C or name O or name CB )) or resid 539 or (resid 540 through 541 and ( \ name N or name CA or name C or name O or name CB )) or resid 542 or (resid 543 a \ nd (name N or name CA or name C or name O or name CB )) or resid 544 through 546 \ or (resid 547 and (name N or name CA or name C or name O or name CB )) or resid \ 548 through 554 or (resid 555 and (name N or name CA or name C or name O or nam \ e CB )) or resid 556 or (resid 557 through 558 and (name N or name CA or name C \ or name O or name CB )) or resid 559 through 566 or (resid 567 through 570 and ( \ name N or name CA or name C or name O or name CB )) or resid 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 through 581 or (resid 582 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 586 or (resid 587 and (name \ N or name CA or name C or name O or name CB )) or resid 588 through 590 or (res \ id 591 through 592 and (name N or name CA or name C or name O or name CB )) or r \ esid 593 or (resid 594 through 598 and (name N or name CA or name C or name O or \ name CB )) or resid 599 or (resid 600 and (name N or name CA or name C or name \ O or name CB )) or resid 601 or (resid 602 through 605 and (name N or name CA or \ name C or name O or name CB )) or resid 606 through 612 or (resid 613 through 6 \ 20 and (name N or name CA or name C or name O or name CB )) or resid 621 through \ 622 or (resid 623 and (name N or name CA or name C or name O or name CB )) or r \ esid 624 through 626 or (resid 627 and (name N or name CA or name C or name O or \ name CB )) or resid 628 through 644 or (resid 645 and (name N or name CA or nam \ e C or name O or name CB )) or resid 646 through 649 or (resid 650 and (name N o \ r name CA or name C or name O or name CB )) or resid 651 or (resid 652 through 6 \ 53 and (name N or name CA or name C or name O or name CB )) or resid 654 or (res \ id 655 through 656 and (name N or name CA or name C or name O or name CB )) or r \ esid 657 through 659 or (resid 660 through 668 and (name N or name CA or name C \ or name O or name CB )) or resid 669 through 673 or (resid 674 and (name N or na \ me CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 t \ hrough 681 and (name N or name CA or name C or name O or name CB )) or resid 682 \ or (resid 683 and (name N or name CA or name C or name O or name CB )) or resid \ 684 through 685 or (resid 686 through 687 and (name N or name CA or name C or n \ ame O or name CB )) or resid 688 through 690 or (resid 691 through 692 and (name \ N or name CA or name C or name O or name CB )) or resid 693 through 698 or (res \ id 699 and (name N or name CA or name C or name O or name CB )) or resid 700 or \ (resid 701 through 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 704 or (resid 705 and (name N or name CA or name C or name \ O or name CB )) or resid 706 through 718 or (resid 719 and (name N or name CA or \ name C or name O or name CB )) or resid 720 through 721 or (resid 722 and (name \ N or name CA or name C or name O or name CB )) or resid 723 through 724 or (res \ id 725 and (name N or name CA or name C or name O or name CB )) or resid 726 thr \ ough 738 or (resid 739 through 740 and (name N or name CA or name C or name O or \ name CB )) or resid 741 or (resid 742 through 743 and (name N or name CA or nam \ e C or name O or name CB )) or resid 744 through 747 or (resid 748 and (name N o \ r name CA or name C or name O or name CB )) or resid 749 or (resid 750 through 7 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 752 through \ 755 or (resid 756 and (name N or name CA or name C or name O or name CB )) or r \ esid 757 through 758 or (resid 759 through 760 and (name N or name CA or name C \ or name O or name CB )) or resid 761 or (resid 762 through 764 and (name N or na \ me CA or name C or name O or name CB )) or resid 765 or (resid 766 through 769 a \ nd (name N or name CA or name C or name O or name CB )) or resid 770 or (resid 7 \ 71 through 776 and (name N or name CA or name C or name O or name CB )) or resid \ 777 or (resid 778 and (name N or name CA or name C or name O or name CB )) or r \ esid 779 through 784 or (resid 785 and (name N or name CA or name C or name O or \ name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.730 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 118.120 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4449 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 : 0.005 0.093 52532 Z= 0.301 Angle : 0.609 13.062 71281 Z= 0.325 Chirality : 0.044 0.257 8134 Planarity : 0.005 0.090 9156 Dihedral : 13.613 138.466 19157 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 6576 helix: 0.21 (0.11), residues: 2168 sheet: -0.56 (0.20), residues: 702 loop : -0.73 (0.10), residues: 3706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 236 HIS 0.011 0.001 HIS E 597 PHE 0.036 0.002 PHE B 254 TYR 0.030 0.001 TYR D 676 ARG 0.011 0.000 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 5.823 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: F 458 MET cc_start: 0.3739 (mmt) cc_final: 0.3251 (mmt) REVERT: I 618 MET cc_start: 0.4303 (ptm) cc_final: 0.3846 (tmm) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.6340 time to fit residues: 441.7407 Evaluate side-chains 268 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 5.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 5.9990 chunk 500 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 170 optimal weight: 40.0000 chunk 337 optimal weight: 10.0000 chunk 267 optimal weight: 40.0000 chunk 517 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 599 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 597 HIS F 741 GLN G 290 HIS ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 HIS ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN J 632 GLN J 662 ASN ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 353 ASN K 680 HIS ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4521 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 52532 Z= 0.420 Angle : 0.661 15.379 71281 Z= 0.342 Chirality : 0.047 0.449 8134 Planarity : 0.005 0.070 9156 Dihedral : 5.969 140.313 7099 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.13 % Favored : 93.78 % Rotamer: Outliers : 0.89 % Allowed : 7.90 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 6576 helix: -0.17 (0.11), residues: 2282 sheet: -0.73 (0.20), residues: 720 loop : -0.87 (0.10), residues: 3574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 236 HIS 0.010 0.001 HIS E 597 PHE 0.037 0.002 PHE B 254 TYR 0.022 0.002 TYR C 409 ARG 0.007 0.001 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 458 MET cc_start: 0.3963 (mmt) cc_final: 0.3439 (mmt) REVERT: I 618 MET cc_start: 0.4774 (ptm) cc_final: 0.4295 (tmm) REVERT: J 550 LYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4523 (mmmm) REVERT: J 567 LYS cc_start: 0.3250 (tttm) cc_final: 0.2960 (tptt) outliers start: 49 outliers final: 41 residues processed: 323 average time/residue: 0.5886 time to fit residues: 332.9337 Evaluate side-chains 288 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 431 ASP Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain J residue 771 ASP Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain L residue 375 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 498 optimal weight: 0.0050 chunk 408 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 600 optimal weight: 0.0770 chunk 648 optimal weight: 10.0000 chunk 534 optimal weight: 5.9990 chunk 595 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 481 optimal weight: 5.9990 overall best weight: 2.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 ASN D 641 ASN ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 ASN ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4486 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 52532 Z= 0.287 Angle : 0.563 12.138 71281 Z= 0.293 Chirality : 0.044 0.307 8134 Planarity : 0.005 0.057 9156 Dihedral : 5.732 139.728 7099 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.25 % Allowed : 10.90 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.10), residues: 6576 helix: 0.05 (0.11), residues: 2280 sheet: -0.92 (0.19), residues: 733 loop : -0.82 (0.10), residues: 3563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 350 HIS 0.007 0.001 HIS E 597 PHE 0.026 0.001 PHE B 254 TYR 0.014 0.001 TYR B 670 ARG 0.005 0.000 ARG J 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 280 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 ILE cc_start: 0.7783 (mt) cc_final: 0.7578 (mt) REVERT: D 341 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8374 (pt) REVERT: F 458 MET cc_start: 0.4007 (mmt) cc_final: 0.3458 (mmt) REVERT: I 618 MET cc_start: 0.4797 (ptm) cc_final: 0.4371 (tmm) REVERT: I 716 LEU cc_start: 0.1415 (OUTLIER) cc_final: 0.0260 (tp) REVERT: J 567 LYS cc_start: 0.3226 (tttm) cc_final: 0.2952 (tptt) REVERT: L 259 ILE cc_start: 0.1978 (OUTLIER) cc_final: 0.1738 (mp) outliers start: 69 outliers final: 48 residues processed: 339 average time/residue: 0.5676 time to fit residues: 339.2479 Evaluate side-chains 299 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 716 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 771 ASP Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain L residue 259 ILE Chi-restraints excluded: chain L residue 544 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 6.9990 chunk 451 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 chunk 403 optimal weight: 4.9990 chunk 602 optimal weight: 4.9990 chunk 637 optimal weight: 40.0000 chunk 314 optimal weight: 6.9990 chunk 571 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN G 290 HIS ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 HIS ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 662 ASN ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4471 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 52532 Z= 0.244 Angle : 0.533 11.411 71281 Z= 0.277 Chirality : 0.043 0.254 8134 Planarity : 0.004 0.055 9156 Dihedral : 5.591 138.991 7099 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 2.11 % Allowed : 12.46 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 6576 helix: 0.20 (0.11), residues: 2286 sheet: -0.91 (0.19), residues: 765 loop : -0.78 (0.11), residues: 3525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 350 HIS 0.005 0.001 HIS E 597 PHE 0.021 0.001 PHE B 254 TYR 0.014 0.001 TYR E 645 ARG 0.006 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 281 time to evaluate : 5.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6024 (m-10) REVERT: C 334 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8315 (mp) REVERT: D 341 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8306 (pt) REVERT: F 684 MET cc_start: 0.4149 (mmm) cc_final: 0.3935 (mmt) REVERT: I 618 MET cc_start: 0.4660 (ptm) cc_final: 0.4059 (tmm) REVERT: J 662 ASN cc_start: 0.3378 (m110) cc_final: 0.3063 (m-40) REVERT: K 458 MET cc_start: 0.4769 (mmm) cc_final: 0.4525 (mmt) outliers start: 116 outliers final: 77 residues processed: 383 average time/residue: 0.5655 time to fit residues: 383.8384 Evaluate side-chains 338 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 431 ASP Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 771 ASP Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain L residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 475 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 544 optimal weight: 10.0000 chunk 440 optimal weight: 0.0000 chunk 0 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 572 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 632 GLN H 352 ASN I 768 ASN ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4483 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 52532 Z= 0.256 Angle : 0.538 11.593 71281 Z= 0.279 Chirality : 0.043 0.291 8134 Planarity : 0.004 0.054 9156 Dihedral : 5.572 139.169 7099 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.10), residues: 6576 helix: 0.26 (0.11), residues: 2275 sheet: -0.96 (0.19), residues: 751 loop : -0.76 (0.11), residues: 3550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 350 HIS 0.009 0.001 HIS D 680 PHE 0.021 0.001 PHE E 240 TYR 0.017 0.001 TYR B 687 ARG 0.004 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 277 time to evaluate : 5.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.6009 (m-10) REVERT: C 334 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8308 (mp) REVERT: D 341 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8312 (pt) REVERT: F 458 MET cc_start: 0.3957 (mmt) cc_final: 0.3545 (mmt) REVERT: G 290 HIS cc_start: 0.4356 (OUTLIER) cc_final: 0.2709 (t-90) REVERT: I 618 MET cc_start: 0.4738 (ptm) cc_final: 0.4115 (tmm) REVERT: I 716 LEU cc_start: 0.1250 (OUTLIER) cc_final: 0.0123 (tp) REVERT: J 550 LYS cc_start: 0.4790 (OUTLIER) cc_final: 0.3753 (mmmm) REVERT: J 661 ASN cc_start: 0.3249 (m110) cc_final: 0.2262 (t0) outliers start: 150 outliers final: 97 residues processed: 406 average time/residue: 0.5455 time to fit residues: 391.5943 Evaluate side-chains 361 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 258 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 431 ASP Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain I residue 716 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 7.9990 chunk 574 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 374 optimal weight: 0.0060 chunk 157 optimal weight: 8.9990 chunk 638 optimal weight: 10.0000 chunk 530 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 573 ASN H 661 ASN ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 662 ASN ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 HIS L 310 ASN ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 52532 Z= 0.419 Angle : 0.639 12.946 71281 Z= 0.332 Chirality : 0.046 0.420 8134 Planarity : 0.005 0.059 9156 Dihedral : 5.967 142.569 7099 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 2.85 % Allowed : 14.47 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.10), residues: 6576 helix: -0.08 (0.11), residues: 2251 sheet: -1.05 (0.19), residues: 748 loop : -0.97 (0.10), residues: 3577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 350 HIS 0.008 0.001 HIS A 312 PHE 0.033 0.002 PHE E 240 TYR 0.022 0.002 TYR B 670 ARG 0.007 0.001 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 271 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 334 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8384 (mp) REVERT: D 341 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8438 (pt) REVERT: E 254 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5020 (t80) REVERT: E 626 PHE cc_start: 0.2362 (OUTLIER) cc_final: 0.0425 (m-10) REVERT: G 290 HIS cc_start: 0.4502 (OUTLIER) cc_final: 0.2766 (t-90) REVERT: I 284 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5245 (tt) REVERT: J 716 LEU cc_start: 0.0242 (OUTLIER) cc_final: -0.0647 (mp) REVERT: L 740 GLN cc_start: 0.4899 (mm-40) cc_final: 0.4539 (mt0) outliers start: 157 outliers final: 117 residues processed: 413 average time/residue: 0.5711 time to fit residues: 421.7725 Evaluate side-chains 381 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 257 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 PHE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 626 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 771 ASP Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain K residue 716 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 569 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 363 optimal weight: 0.9990 chunk 466 optimal weight: 20.0000 chunk 361 optimal weight: 30.0000 chunk 537 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 636 optimal weight: 5.9990 chunk 398 optimal weight: 0.0570 chunk 387 optimal weight: 0.0010 chunk 293 optimal weight: 2.9990 overall best weight: 0.9508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN E 593 ASN G 290 HIS ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4468 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 52532 Z= 0.187 Angle : 0.527 10.990 71281 Z= 0.273 Chirality : 0.042 0.181 8134 Planarity : 0.004 0.057 9156 Dihedral : 5.579 139.967 7099 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 2.12 % Allowed : 15.89 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.10), residues: 6576 helix: 0.28 (0.11), residues: 2274 sheet: -1.00 (0.19), residues: 775 loop : -0.81 (0.11), residues: 3527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 675 HIS 0.015 0.001 HIS A 548 PHE 0.020 0.001 PHE E 240 TYR 0.019 0.001 TYR B 687 ARG 0.008 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 287 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6055 (m-10) REVERT: C 334 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 341 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8276 (pt) REVERT: E 254 PHE cc_start: 0.5632 (OUTLIER) cc_final: 0.4911 (t80) REVERT: H 684 MET cc_start: 0.2404 (mmm) cc_final: 0.2119 (mmt) REVERT: J 550 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.3598 (mmmm) outliers start: 117 outliers final: 85 residues processed: 388 average time/residue: 0.5777 time to fit residues: 398.6440 Evaluate side-chains 356 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 266 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 PHE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 292 HIS Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain J residue 771 ASP Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 716 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 569 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 123 optimal weight: 0.6980 chunk 404 optimal weight: 0.6980 chunk 433 optimal weight: 0.0070 chunk 314 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 500 optimal weight: 40.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 ASN F 741 GLN G 290 HIS ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4440 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 52532 Z= 0.169 Angle : 0.515 9.925 71281 Z= 0.265 Chirality : 0.042 0.190 8134 Planarity : 0.004 0.069 9156 Dihedral : 5.420 138.504 7099 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 16.29 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.10), residues: 6576 helix: 0.50 (0.11), residues: 2268 sheet: -0.88 (0.19), residues: 766 loop : -0.73 (0.11), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 675 HIS 0.023 0.001 HIS G 290 PHE 0.017 0.001 PHE E 240 TYR 0.013 0.001 TYR B 776 ARG 0.021 0.000 ARG E 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 276 time to evaluate : 5.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5844 (m-10) REVERT: C 334 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8249 (mp) REVERT: D 341 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8238 (pt) REVERT: F 458 MET cc_start: 0.3968 (mmt) cc_final: 0.3588 (mmt) REVERT: H 684 MET cc_start: 0.2423 (mmm) cc_final: 0.2072 (mmt) REVERT: I 284 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5223 (tt) REVERT: I 369 LEU cc_start: 0.6517 (tt) cc_final: 0.6276 (tp) REVERT: I 618 MET cc_start: 0.4742 (ptm) cc_final: 0.4080 (tmm) outliers start: 114 outliers final: 91 residues processed: 377 average time/residue: 0.5586 time to fit residues: 373.0034 Evaluate side-chains 354 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 259 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain I residue 766 PHE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 558 LEU Chi-restraints excluded: chain K residue 716 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 348 ILE Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 569 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 20.0000 chunk 609 optimal weight: 9.9990 chunk 556 optimal weight: 9.9990 chunk 592 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 465 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 535 optimal weight: 0.9990 chunk 560 optimal weight: 5.9990 chunk 590 optimal weight: 40.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN D 475 ASN D 478 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 605 ASN ** G 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 713 HIS ** J 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 52532 Z= 0.528 Angle : 0.709 12.076 71281 Z= 0.365 Chirality : 0.049 0.567 8134 Planarity : 0.005 0.077 9156 Dihedral : 6.053 143.205 7099 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 2.49 % Allowed : 16.49 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 6576 helix: -0.13 (0.11), residues: 2257 sheet: -1.15 (0.20), residues: 698 loop : -0.99 (0.10), residues: 3621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP G 355 HIS 0.010 0.001 HIS A 312 PHE 0.035 0.002 PHE F 254 TYR 0.024 0.002 TYR B 670 ARG 0.008 0.001 ARG C 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 261 time to evaluate : 6.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 334 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8393 (mp) REVERT: D 341 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8443 (pt) REVERT: E 254 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.4759 (t80) REVERT: F 684 MET cc_start: 0.4019 (mmm) cc_final: 0.3689 (mmm) REVERT: H 426 MET cc_start: 0.1508 (ppp) cc_final: 0.1245 (ppp) REVERT: I 284 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5358 (tt) REVERT: J 550 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.3918 (mmmm) outliers start: 137 outliers final: 110 residues processed: 382 average time/residue: 0.5857 time to fit residues: 398.5146 Evaluate side-chains 361 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 246 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 PHE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain I residue 766 PHE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain K residue 558 LEU Chi-restraints excluded: chain K residue 716 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 348 ILE Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 569 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 8.9990 chunk 626 optimal weight: 0.0170 chunk 382 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 chunk 435 optimal weight: 0.1980 chunk 657 optimal weight: 5.9990 chunk 605 optimal weight: 8.9990 chunk 523 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 overall best weight: 3.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN E 593 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS G 290 HIS G 353 ASN ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 713 HIS ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4604 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 52532 Z= 0.447 Angle : 0.663 12.875 71281 Z= 0.341 Chirality : 0.047 0.503 8134 Planarity : 0.005 0.060 9156 Dihedral : 6.052 144.518 7099 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.39 % Favored : 93.49 % Rotamer: Outliers : 2.40 % Allowed : 16.80 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.10), residues: 6576 helix: -0.18 (0.11), residues: 2242 sheet: -1.21 (0.19), residues: 755 loop : -1.02 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP G 355 HIS 0.007 0.001 HIS C 629 PHE 0.032 0.002 PHE E 240 TYR 0.022 0.002 TYR C 482 ARG 0.011 0.001 ARG E 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 258 time to evaluate : 5.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 334 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 341 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8396 (pt) REVERT: E 254 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.4727 (t80) REVERT: F 426 MET cc_start: 0.4781 (tpp) cc_final: 0.4449 (tpt) REVERT: F 684 MET cc_start: 0.4089 (mmm) cc_final: 0.3745 (mmm) REVERT: J 550 LYS cc_start: 0.4866 (OUTLIER) cc_final: 0.3549 (mmmm) outliers start: 132 outliers final: 116 residues processed: 376 average time/residue: 0.5599 time to fit residues: 375.3042 Evaluate side-chains 372 residues out of total 6072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 252 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 254 PHE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 754 HIS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 374 GLN Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 511 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 583 ILE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain F residue 236 TRP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 411 ASP Chi-restraints excluded: chain G residue 600 ILE Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 553 VAL Chi-restraints excluded: chain H residue 669 LEU Chi-restraints excluded: chain I residue 272 VAL Chi-restraints excluded: chain I residue 292 HIS Chi-restraints excluded: chain I residue 393 GLU Chi-restraints excluded: chain I residue 531 ILE Chi-restraints excluded: chain I residue 766 PHE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 550 LYS Chi-restraints excluded: chain J residue 684 MET Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain K residue 558 LEU Chi-restraints excluded: chain K residue 716 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 348 ILE Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 569 ILE Chi-restraints excluded: chain L residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 0.9990 chunk 557 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 482 optimal weight: 0.0370 chunk 77 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 524 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 538 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 662 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS G 290 HIS G 353 ASN ** G 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 662 ASN ** K 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.218147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.199649 restraints weight = 104322.974| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 2.59 r_work: 0.4583 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.4562 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 52532 Z= 0.338 Angle : 0.615 14.049 71281 Z= 0.315 Chirality : 0.045 0.373 8134 Planarity : 0.005 0.057 9156 Dihedral : 5.901 144.213 7099 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.31 % Allowed : 17.14 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 6576 helix: -0.00 (0.11), residues: 2245 sheet: -1.16 (0.19), residues: 779 loop : -0.97 (0.10), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP G 355 HIS 0.006 0.001 HIS C 629 PHE 0.032 0.002 PHE F 261 TYR 0.020 0.001 TYR B 670 ARG 0.007 0.000 ARG C 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10295.79 seconds wall clock time: 200 minutes 42.92 seconds (12042.92 seconds total)