Starting phenix.real_space_refine on Tue Mar 19 22:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrb_34966/03_2024/8hrb_34966_neut_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 126 5.49 5 S 440 5.16 5 C 60562 2.51 5 N 16638 2.21 5 O 18586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 291": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F GLU 789": "OE1" <-> "OE2" Residue "K GLU 529": "OE1" <-> "OE2" Residue "K GLU 596": "OE1" <-> "OE2" Residue "L GLU 294": "OE1" <-> "OE2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "M GLU 202": "OE1" <-> "OE2" Residue "M GLU 668": "OE1" <-> "OE2" Residue "M GLU 714": "OE1" <-> "OE2" Residue "M GLU 891": "OE1" <-> "OE2" Residue "P GLU 151": "OE1" <-> "OE2" Residue "P GLU 202": "OE1" <-> "OE2" Residue "P GLU 565": "OE1" <-> "OE2" Residue "Q GLU 198": "OE1" <-> "OE2" Residue "Q GLU 326": "OE1" <-> "OE2" Residue "Q GLU 437": "OE1" <-> "OE2" Residue "Q GLU 526": "OE1" <-> "OE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "R GLU 275": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "B GLU 800": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H GLU 529": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 96352 Number of models: 1 Model: "" Number of chains: 28 Chain: "F" Number of atoms: 6785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6785 Classifications: {'peptide': 851} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 826} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "L" Number of atoms: 6778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6778 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 23, 'TRANS': 827} Chain breaks: 4 Chain: "M" Number of atoms: 6762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6762 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 23, 'TRANS': 825} Chain breaks: 4 Chain: "P" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6654 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "Q" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "R" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "A" Number of atoms: 6785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6785 Classifications: {'peptide': 851} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 826} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "C" Number of atoms: 6778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6778 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 23, 'TRANS': 827} Chain breaks: 4 Chain: "D" Number of atoms: 6762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6762 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 23, 'TRANS': 825} Chain breaks: 4 Chain: "E" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6654 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "G" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "H" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "V" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "W" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "Y" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "a" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 37.41, per 1000 atoms: 0.39 Number of scatterers: 96352 At special positions: 0 Unit cell: (257.58, 174.9, 172.78, 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 440 16.00 P 126 15.00 O 18586 8.00 N 16638 7.00 C 60562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 30.82 Conformation dependent library (CDL) restraints added in 14.6 seconds 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 539 helices and 35 sheets defined 53.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.52 Creating SS restraints... Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 35 through 49 removed outlier: 3.651A pdb=" N ILE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 121 through 138 removed outlier: 3.502A pdb=" N LYS F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 167 removed outlier: 3.661A pdb=" N ARG F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 163 " --> pdb=" O GLN F 159 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU F 166 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 180 removed outlier: 3.651A pdb=" N SER F 178 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 Processing helix chain 'F' and resid 227 through 240 removed outlier: 4.103A pdb=" N GLY F 230 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU F 235 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG F 238 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.831A pdb=" N LEU F 260 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 276 No H-bonds generated for 'chain 'F' and resid 273 through 276' Processing helix chain 'F' and resid 282 through 301 removed outlier: 3.518A pdb=" N TYR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 313 through 316 No H-bonds generated for 'chain 'F' and resid 313 through 316' Processing helix chain 'F' and resid 344 through 355 removed outlier: 3.554A pdb=" N ILE F 348 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP F 350 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 354 " --> pdb=" O ASP F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 373 removed outlier: 4.140A pdb=" N MET F 366 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 368 " --> pdb=" O ALA F 364 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 392 removed outlier: 3.739A pdb=" N GLN F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 422 Processing helix chain 'F' and resid 426 through 432 Processing helix chain 'F' and resid 443 through 457 removed outlier: 3.912A pdb=" N LYS F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP F 449 " --> pdb=" O SER F 445 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 473 through 476 No H-bonds generated for 'chain 'F' and resid 473 through 476' Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.626A pdb=" N SER F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 502 removed outlier: 3.891A pdb=" N MET F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 515 removed outlier: 4.305A pdb=" N VAL F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER F 509 " --> pdb=" O CYS F 505 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN F 512 " --> pdb=" O VAL F 508 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE F 514 " --> pdb=" O ILE F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 538 Processing helix chain 'F' and resid 547 through 559 removed outlier: 4.735A pdb=" N ALA F 556 " --> pdb=" O ASN F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 595 No H-bonds generated for 'chain 'F' and resid 593 through 595' Processing helix chain 'F' and resid 598 through 607 removed outlier: 3.904A pdb=" N SER F 606 " --> pdb=" O ALA F 602 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER F 607 " --> pdb=" O ALA F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 634 removed outlier: 4.575A pdb=" N ALA F 634 " --> pdb=" O ALA F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 649 removed outlier: 3.774A pdb=" N ASN F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 649 " --> pdb=" O ALA F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 666 through 670 Processing helix chain 'F' and resid 705 through 726 removed outlier: 3.629A pdb=" N ASP F 708 " --> pdb=" O GLU F 705 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 715 " --> pdb=" O LYS F 712 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 717 " --> pdb=" O GLU F 714 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 720 " --> pdb=" O LEU F 717 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 721 " --> pdb=" O LYS F 718 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU F 722 " --> pdb=" O ASN F 719 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 725 " --> pdb=" O GLU F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 754 removed outlier: 3.525A pdb=" N GLY F 735 " --> pdb=" O ALA F 731 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA F 749 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 750 " --> pdb=" O ASN F 746 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 751 " --> pdb=" O ASN F 747 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 754 " --> pdb=" O ASP F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 793 removed outlier: 3.994A pdb=" N VAL F 779 " --> pdb=" O MET F 775 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA F 785 " --> pdb=" O ALA F 781 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 792 " --> pdb=" O VAL F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 831 removed outlier: 3.798A pdb=" N LYS F 820 " --> pdb=" O GLU F 816 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE F 821 " --> pdb=" O PHE F 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F 829 " --> pdb=" O GLY F 825 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP F 831 " --> pdb=" O LYS F 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 841 through 846 Processing helix chain 'F' and resid 849 through 855 Proline residue: F 853 - end of helix No H-bonds generated for 'chain 'F' and resid 849 through 855' Processing helix chain 'F' and resid 865 through 882 removed outlier: 4.443A pdb=" N ASN F 869 " --> pdb=" O VAL F 865 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LYS F 870 " --> pdb=" O LYS F 866 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 876 " --> pdb=" O THR F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 896 Processing helix chain 'K' and resid 35 through 49 removed outlier: 3.825A pdb=" N SER K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN K 47 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 94 removed outlier: 3.933A pdb=" N SER K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 139 removed outlier: 3.707A pdb=" N MET K 132 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS K 138 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 167 removed outlier: 4.223A pdb=" N LYS K 148 " --> pdb=" O ASN K 144 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN K 149 " --> pdb=" O ASP K 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS K 156 " --> pdb=" O GLN K 152 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY K 163 " --> pdb=" O GLN K 159 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N HIS K 165 " --> pdb=" O GLN K 161 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU K 166 " --> pdb=" O ARG K 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU K 167 " --> pdb=" O GLY K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 180 removed outlier: 4.463A pdb=" N SER K 178 " --> pdb=" O GLU K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 211 removed outlier: 3.599A pdb=" N LEU K 203 " --> pdb=" O ILE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 239 Processing helix chain 'K' and resid 254 through 268 removed outlier: 3.764A pdb=" N GLU K 267 " --> pdb=" O GLY K 263 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.871A pdb=" N GLU K 275 " --> pdb=" O LYS K 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 271 through 275' Processing helix chain 'K' and resid 280 through 301 removed outlier: 3.547A pdb=" N MET K 289 " --> pdb=" O GLU K 285 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU K 291 " --> pdb=" O GLY K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 306 No H-bonds generated for 'chain 'K' and resid 304 through 306' Processing helix chain 'K' and resid 313 through 317 Processing helix chain 'K' and resid 344 through 356 removed outlier: 4.286A pdb=" N ALA K 351 " --> pdb=" O ALA K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 372 removed outlier: 3.880A pdb=" N TYR K 367 " --> pdb=" O ASP K 363 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 394 removed outlier: 3.717A pdb=" N MET K 380 " --> pdb=" O VAL K 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN K 381 " --> pdb=" O ARG K 377 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS K 392 " --> pdb=" O THR K 388 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 432 removed outlier: 3.742A pdb=" N GLY K 423 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER K 427 " --> pdb=" O GLY K 423 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER K 428 " --> pdb=" O SER K 424 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE K 429 " --> pdb=" O MET K 425 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR K 430 " --> pdb=" O LEU K 426 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG K 431 " --> pdb=" O SER K 427 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA K 432 " --> pdb=" O SER K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 457 removed outlier: 3.815A pdb=" N CYS K 447 " --> pdb=" O MET K 443 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS K 448 " --> pdb=" O ASP K 444 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE K 451 " --> pdb=" O CYS K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 465 No H-bonds generated for 'chain 'K' and resid 463 through 465' Processing helix chain 'K' and resid 473 through 490 removed outlier: 3.809A pdb=" N ILE K 480 " --> pdb=" O ARG K 476 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR K 481 " --> pdb=" O ASN K 477 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS K 490 " --> pdb=" O VAL K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 516 removed outlier: 3.508A pdb=" N LEU K 502 " --> pdb=" O LEU K 498 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER K 507 " --> pdb=" O VAL K 503 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL K 508 " --> pdb=" O GLY K 504 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE K 511 " --> pdb=" O SER K 507 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN K 512 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN K 513 " --> pdb=" O SER K 509 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE K 514 " --> pdb=" O ILE K 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 539 removed outlier: 3.533A pdb=" N SER K 533 " --> pdb=" O GLU K 529 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU K 534 " --> pdb=" O GLN K 530 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL K 536 " --> pdb=" O ILE K 532 " (cutoff:3.500A) Processing helix chain 'K' and resid 547 through 559 removed outlier: 4.291A pdb=" N ALA K 556 " --> pdb=" O ASN K 552 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL K 557 " --> pdb=" O ARG K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 601 through 606 Processing helix chain 'K' and resid 622 through 632 removed outlier: 3.779A pdb=" N ALA K 630 " --> pdb=" O ILE K 626 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP K 631 " --> pdb=" O GLY K 627 " (cutoff:3.500A) Processing helix chain 'K' and resid 644 through 647 No H-bonds generated for 'chain 'K' and resid 644 through 647' Processing helix chain 'K' and resid 659 through 661 No H-bonds generated for 'chain 'K' and resid 659 through 661' Processing helix chain 'K' and resid 705 through 726 removed outlier: 4.298A pdb=" N ALA K 709 " --> pdb=" O GLU K 705 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR K 711 " --> pdb=" O SER K 707 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS K 712 " --> pdb=" O ASP K 708 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE K 725 " --> pdb=" O ASN K 721 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY K 726 " --> pdb=" O GLU K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 749 removed outlier: 3.819A pdb=" N TRP K 738 " --> pdb=" O ILE K 734 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER K 739 " --> pdb=" O GLY K 735 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 792 removed outlier: 3.817A pdb=" N LEU K 787 " --> pdb=" O LEU K 783 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 830 removed outlier: 3.722A pdb=" N LYS K 820 " --> pdb=" O GLU K 816 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU K 826 " --> pdb=" O LYS K 822 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS K 827 " --> pdb=" O ILE K 823 " (cutoff:3.500A) Processing helix chain 'K' and resid 835 through 838 No H-bonds generated for 'chain 'K' and resid 835 through 838' Processing helix chain 'K' and resid 840 through 846 removed outlier: 3.891A pdb=" N LEU K 845 " --> pdb=" O LEU K 841 " (cutoff:3.500A) Processing helix chain 'K' and resid 849 through 855 Proline residue: K 853 - end of helix No H-bonds generated for 'chain 'K' and resid 849 through 855' Processing helix chain 'K' and resid 867 through 881 removed outlier: 3.532A pdb=" N GLU K 871 " --> pdb=" O LEU K 868 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR K 872 " --> pdb=" O ASN K 869 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN K 875 " --> pdb=" O THR K 872 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS K 876 " --> pdb=" O SER K 873 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU K 877 " --> pdb=" O PHE K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 891 through 896 removed outlier: 3.918A pdb=" N LEU K 895 " --> pdb=" O GLU K 891 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 27 No H-bonds generated for 'chain 'L' and resid 25 through 27' Processing helix chain 'L' and resid 35 through 49 removed outlier: 3.572A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 95 removed outlier: 3.587A pdb=" N SER L 92 " --> pdb=" O SER L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 138 Processing helix chain 'L' and resid 143 through 162 removed outlier: 3.576A pdb=" N GLN L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU L 151 " --> pdb=" O ARG L 147 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN L 152 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA L 158 " --> pdb=" O GLN L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 180 Processing helix chain 'L' and resid 196 through 211 removed outlier: 3.561A pdb=" N PHE L 200 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 209 " --> pdb=" O LYS L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 239 removed outlier: 4.010A pdb=" N GLY L 230 " --> pdb=" O PHE L 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP L 231 " --> pdb=" O ASP L 228 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP L 232 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 234 " --> pdb=" O TRP L 231 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 235 " --> pdb=" O ASP L 232 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG L 238 " --> pdb=" O GLU L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 267 removed outlier: 3.659A pdb=" N ARG L 262 " --> pdb=" O SER L 258 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY L 263 " --> pdb=" O GLN L 259 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU L 267 " --> pdb=" O GLY L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 removed outlier: 3.505A pdb=" N GLU L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 301 removed outlier: 4.225A pdb=" N GLU L 285 " --> pdb=" O VAL L 281 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU L 291 " --> pdb=" O GLY L 287 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS L 292 " --> pdb=" O TYR L 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN L 296 " --> pdb=" O HIS L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 306 No H-bonds generated for 'chain 'L' and resid 304 through 306' Processing helix chain 'L' and resid 314 through 317 No H-bonds generated for 'chain 'L' and resid 314 through 317' Processing helix chain 'L' and resid 344 through 356 Processing helix chain 'L' and resid 363 through 371 removed outlier: 3.641A pdb=" N TYR L 367 " --> pdb=" O ASP L 363 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 368 " --> pdb=" O ALA L 364 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU L 370 " --> pdb=" O MET L 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 393 removed outlier: 3.753A pdb=" N MET L 380 " --> pdb=" O VAL L 376 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN L 381 " --> pdb=" O ARG L 377 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR L 387 " --> pdb=" O LEU L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 422 removed outlier: 3.603A pdb=" N ASN L 419 " --> pdb=" O ASN L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 431 Processing helix chain 'L' and resid 443 through 457 removed outlier: 3.676A pdb=" N LYS L 448 " --> pdb=" O ASP L 444 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE L 451 " --> pdb=" O CYS L 447 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 465 No H-bonds generated for 'chain 'L' and resid 463 through 465' Processing helix chain 'L' and resid 478 through 489 Processing helix chain 'L' and resid 495 through 499 Processing helix chain 'L' and resid 506 through 509 No H-bonds generated for 'chain 'L' and resid 506 through 509' Processing helix chain 'L' and resid 511 through 514 No H-bonds generated for 'chain 'L' and resid 511 through 514' Processing helix chain 'L' and resid 525 through 539 removed outlier: 3.545A pdb=" N GLU L 529 " --> pdb=" O ARG L 525 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 558 removed outlier: 4.388A pdb=" N ALA L 556 " --> pdb=" O ASN L 552 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL L 557 " --> pdb=" O ARG L 553 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL L 558 " --> pdb=" O CYS L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 595 No H-bonds generated for 'chain 'L' and resid 593 through 595' Processing helix chain 'L' and resid 599 through 605 removed outlier: 3.823A pdb=" N ALA L 603 " --> pdb=" O LEU L 599 " (cutoff:3.500A) Processing helix chain 'L' and resid 622 through 633 removed outlier: 3.798A pdb=" N ASP L 631 " --> pdb=" O GLY L 627 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE L 632 " --> pdb=" O ALA L 628 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 648 removed outlier: 3.654A pdb=" N THR L 643 " --> pdb=" O ARG L 639 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN L 644 " --> pdb=" O SER L 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 664 through 670 removed outlier: 4.485A pdb=" N GLU L 668 " --> pdb=" O ALA L 664 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET L 669 " --> pdb=" O VAL L 665 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS L 670 " --> pdb=" O ARG L 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 664 through 670' Processing helix chain 'L' and resid 707 through 723 removed outlier: 4.786A pdb=" N ASN L 719 " --> pdb=" O GLN L 715 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN L 721 " --> pdb=" O LEU L 717 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU L 722 " --> pdb=" O LYS L 718 " (cutoff:3.500A) Processing helix chain 'L' and resid 731 through 751 removed outlier: 3.936A pdb=" N GLY L 735 " --> pdb=" O ALA L 731 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU L 745 " --> pdb=" O PHE L 741 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA L 749 " --> pdb=" O LEU L 745 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP L 750 " --> pdb=" O ASN L 746 " (cutoff:3.500A) Processing helix chain 'L' and resid 773 through 792 removed outlier: 3.806A pdb=" N PHE L 777 " --> pdb=" O LYS L 773 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE L 782 " --> pdb=" O ASN L 778 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 786 " --> pdb=" O PHE L 782 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER L 791 " --> pdb=" O LEU L 787 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU L 792 " --> pdb=" O VAL L 788 " (cutoff:3.500A) Processing helix chain 'L' and resid 815 through 831 removed outlier: 3.686A pdb=" N LYS L 819 " --> pdb=" O ASP L 815 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS L 820 " --> pdb=" O GLU L 816 " (cutoff:3.500A) Processing helix chain 'L' and resid 840 through 846 Processing helix chain 'L' and resid 849 through 855 Proline residue: L 853 - end of helix No H-bonds generated for 'chain 'L' and resid 849 through 855' Processing helix chain 'L' and resid 868 through 882 removed outlier: 3.598A pdb=" N SER L 873 " --> pdb=" O ASN L 869 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN L 875 " --> pdb=" O GLU L 871 " (cutoff:3.500A) Processing helix chain 'L' and resid 889 through 896 removed outlier: 3.514A pdb=" N TYR L 894 " --> pdb=" O GLU L 890 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 895 " --> pdb=" O GLU L 891 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 35 through 49 removed outlier: 3.669A pdb=" N GLU M 43 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER M 44 " --> pdb=" O GLN M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 99 removed outlier: 4.155A pdb=" N GLN M 97 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP M 98 " --> pdb=" O ASN M 94 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP M 99 " --> pdb=" O SER M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 139 removed outlier: 3.509A pdb=" N MET M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M 138 " --> pdb=" O SER M 134 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 167 removed outlier: 3.842A pdb=" N GLN M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS M 165 " --> pdb=" O GLN M 161 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU M 166 " --> pdb=" O ARG M 162 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU M 167 " --> pdb=" O GLY M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 181 Processing helix chain 'M' and resid 196 through 211 removed outlier: 3.653A pdb=" N GLU M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 209 " --> pdb=" O LYS M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 238 removed outlier: 3.984A pdb=" N GLY M 230 " --> pdb=" O PHE M 227 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP M 232 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M 234 " --> pdb=" O TRP M 231 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU M 235 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG M 238 " --> pdb=" O GLU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 267 removed outlier: 3.642A pdb=" N TYR M 266 " --> pdb=" O ARG M 262 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 276 Processing helix chain 'M' and resid 282 through 301 removed outlier: 3.564A pdb=" N GLN M 296 " --> pdb=" O HIS M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 313 through 317 Processing helix chain 'M' and resid 338 through 340 No H-bonds generated for 'chain 'M' and resid 338 through 340' Processing helix chain 'M' and resid 344 through 355 removed outlier: 3.649A pdb=" N ALA M 351 " --> pdb=" O ALA M 347 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL M 352 " --> pdb=" O ILE M 348 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG M 353 " --> pdb=" O GLY M 349 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 373 removed outlier: 3.893A pdb=" N LYS M 373 " --> pdb=" O ASN M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 393 removed outlier: 3.786A pdb=" N MET M 380 " --> pdb=" O VAL M 376 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN M 381 " --> pdb=" O ARG M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 422 Processing helix chain 'M' and resid 426 through 431 Processing helix chain 'M' and resid 443 through 457 removed outlier: 3.794A pdb=" N CYS M 447 " --> pdb=" O MET M 443 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS M 448 " --> pdb=" O ASP M 444 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN M 456 " --> pdb=" O THR M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 473 through 489 removed outlier: 4.282A pdb=" N ILE M 480 " --> pdb=" O ARG M 476 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR M 481 " --> pdb=" O ASN M 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 502 Processing helix chain 'M' and resid 506 through 514 removed outlier: 3.512A pdb=" N PHE M 511 " --> pdb=" O SER M 507 " (cutoff:3.500A) Processing helix chain 'M' and resid 516 through 518 No H-bonds generated for 'chain 'M' and resid 516 through 518' Processing helix chain 'M' and resid 527 through 539 removed outlier: 3.627A pdb=" N ALA M 537 " --> pdb=" O SER M 533 " (cutoff:3.500A) Processing helix chain 'M' and resid 547 through 560 removed outlier: 3.584A pdb=" N CYS M 555 " --> pdb=" O ALA M 551 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA M 556 " --> pdb=" O ASN M 552 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 559 " --> pdb=" O CYS M 555 " (cutoff:3.500A) Processing helix chain 'M' and resid 593 through 595 No H-bonds generated for 'chain 'M' and resid 593 through 595' Processing helix chain 'M' and resid 598 through 607 removed outlier: 3.658A pdb=" N SER M 606 " --> pdb=" O ALA M 602 " (cutoff:3.500A) Processing helix chain 'M' and resid 622 through 632 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 666 through 670 Processing helix chain 'M' and resid 702 through 726 removed outlier: 3.545A pdb=" N ALA M 709 " --> pdb=" O GLU M 705 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN M 719 " --> pdb=" O GLN M 715 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU M 722 " --> pdb=" O LYS M 718 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE M 725 " --> pdb=" O ASN M 721 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY M 726 " --> pdb=" O GLU M 722 " (cutoff:3.500A) Processing helix chain 'M' and resid 731 through 753 removed outlier: 3.953A pdb=" N GLY M 735 " --> pdb=" O ALA M 731 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP M 750 " --> pdb=" O ASN M 746 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN M 751 " --> pdb=" O ASN M 747 " (cutoff:3.500A) Processing helix chain 'M' and resid 771 through 792 Processing helix chain 'M' and resid 815 through 830 removed outlier: 3.792A pdb=" N LYS M 820 " --> pdb=" O GLU M 816 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY M 825 " --> pdb=" O ILE M 821 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU M 826 " --> pdb=" O LYS M 822 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS M 827 " --> pdb=" O ILE M 823 " (cutoff:3.500A) Processing helix chain 'M' and resid 835 through 838 No H-bonds generated for 'chain 'M' and resid 835 through 838' Processing helix chain 'M' and resid 840 through 846 Processing helix chain 'M' and resid 852 through 855 No H-bonds generated for 'chain 'M' and resid 852 through 855' Processing helix chain 'M' and resid 865 through 882 removed outlier: 4.021A pdb=" N ASN M 869 " --> pdb=" O VAL M 865 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS M 870 " --> pdb=" O LYS M 866 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP M 879 " --> pdb=" O ASN M 875 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU M 880 " --> pdb=" O LYS M 876 " (cutoff:3.500A) Processing helix chain 'M' and resid 889 through 896 removed outlier: 3.655A pdb=" N ASP M 893 " --> pdb=" O ASP M 889 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR M 894 " --> pdb=" O GLU M 890 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU M 895 " --> pdb=" O GLU M 891 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR M 896 " --> pdb=" O TRP M 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 889 through 896' Processing helix chain 'P' and resid 24 through 26 No H-bonds generated for 'chain 'P' and resid 24 through 26' Processing helix chain 'P' and resid 35 through 50 Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 121 through 138 Processing helix chain 'P' and resid 143 through 166 removed outlier: 4.849A pdb=" N GLU P 151 " --> pdb=" O ARG P 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS P 156 " --> pdb=" O GLN P 152 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY P 163 " --> pdb=" O GLN P 159 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS P 165 " --> pdb=" O GLN P 161 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 179 removed outlier: 4.048A pdb=" N SER P 178 " --> pdb=" O GLU P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 211 removed outlier: 3.759A pdb=" N GLU P 201 " --> pdb=" O SER P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 239 removed outlier: 3.578A pdb=" N ASP P 232 " --> pdb=" O ALA P 229 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU P 235 " --> pdb=" O ASP P 232 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG P 238 " --> pdb=" O GLU P 235 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 268 removed outlier: 4.139A pdb=" N GLN P 259 " --> pdb=" O ARG P 255 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY P 263 " --> pdb=" O GLN P 259 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR P 266 " --> pdb=" O ARG P 262 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU P 267 " --> pdb=" O GLY P 263 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN P 268 " --> pdb=" O LYS P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 276 Processing helix chain 'P' and resid 280 through 301 removed outlier: 4.084A pdb=" N GLU P 291 " --> pdb=" O GLY P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 313 through 317 Processing helix chain 'P' and resid 338 through 340 No H-bonds generated for 'chain 'P' and resid 338 through 340' Processing helix chain 'P' and resid 344 through 353 Processing helix chain 'P' and resid 362 through 372 Processing helix chain 'P' and resid 376 through 394 removed outlier: 3.934A pdb=" N GLN P 381 " --> pdb=" O ARG P 377 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 383 " --> pdb=" O LEU P 379 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN P 384 " --> pdb=" O MET P 380 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP P 385 " --> pdb=" O GLN P 381 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR P 388 " --> pdb=" O GLN P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 424 removed outlier: 3.799A pdb=" N GLY P 423 " --> pdb=" O ASN P 419 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 432 removed outlier: 3.709A pdb=" N TYR P 430 " --> pdb=" O LEU P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 457 removed outlier: 3.512A pdb=" N LYS P 448 " --> pdb=" O ASP P 444 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE P 451 " --> pdb=" O CYS P 447 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR P 452 " --> pdb=" O LYS P 448 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR P 453 " --> pdb=" O ASP P 449 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL P 454 " --> pdb=" O ILE P 450 " (cutoff:3.500A) Processing helix chain 'P' and resid 463 through 465 No H-bonds generated for 'chain 'P' and resid 463 through 465' Processing helix chain 'P' and resid 473 through 489 removed outlier: 4.194A pdb=" N CYS P 478 " --> pdb=" O ALA P 474 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER P 479 " --> pdb=" O LEU P 475 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE P 480 " --> pdb=" O ARG P 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR P 481 " --> pdb=" O ASN P 477 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 482 " --> pdb=" O CYS P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 495 through 502 removed outlier: 3.589A pdb=" N MET P 500 " --> pdb=" O LYS P 496 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU P 501 " --> pdb=" O PHE P 497 " (cutoff:3.500A) Processing helix chain 'P' and resid 507 through 514 Processing helix chain 'P' and resid 525 through 539 removed outlier: 3.844A pdb=" N ALA P 537 " --> pdb=" O SER P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 547 through 560 removed outlier: 3.594A pdb=" N ALA P 556 " --> pdb=" O ASN P 552 " (cutoff:3.500A) Processing helix chain 'P' and resid 564 through 566 No H-bonds generated for 'chain 'P' and resid 564 through 566' Processing helix chain 'P' and resid 599 through 605 Processing helix chain 'P' and resid 622 through 634 removed outlier: 4.144A pdb=" N ALA P 634 " --> pdb=" O ALA P 630 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 646 removed outlier: 3.595A pdb=" N PHE P 646 " --> pdb=" O ILE P 642 " (cutoff:3.500A) Processing helix chain 'P' and resid 703 through 726 removed outlier: 4.586A pdb=" N ASP P 708 " --> pdb=" O THR P 704 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA P 709 " --> pdb=" O GLU P 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN P 719 " --> pdb=" O GLN P 715 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE P 725 " --> pdb=" O ASN P 721 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY P 726 " --> pdb=" O GLU P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 753 removed outlier: 4.167A pdb=" N TRP P 738 " --> pdb=" O ILE P 734 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU P 745 " --> pdb=" O PHE P 741 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA P 749 " --> pdb=" O LEU P 745 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS P 753 " --> pdb=" O ALA P 749 " (cutoff:3.500A) Processing helix chain 'P' and resid 771 through 790 removed outlier: 3.557A pdb=" N PHE P 777 " --> pdb=" O LYS P 773 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU P 780 " --> pdb=" O ARG P 776 " (cutoff:3.500A) Processing helix chain 'P' and resid 817 through 830 Processing helix chain 'P' and resid 835 through 838 No H-bonds generated for 'chain 'P' and resid 835 through 838' Processing helix chain 'P' and resid 840 through 846 Processing helix chain 'P' and resid 849 through 855 Proline residue: P 853 - end of helix No H-bonds generated for 'chain 'P' and resid 849 through 855' Processing helix chain 'P' and resid 865 through 882 removed outlier: 3.659A pdb=" N ASN P 869 " --> pdb=" O VAL P 865 " (cutoff:3.500A) Processing helix chain 'P' and resid 889 through 896 removed outlier: 3.778A pdb=" N TYR P 894 " --> pdb=" O GLU P 890 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 895 " --> pdb=" O GLU P 891 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 26 No H-bonds generated for 'chain 'Q' and resid 24 through 26' Processing helix chain 'Q' and resid 36 through 50 removed outlier: 3.505A pdb=" N VAL Q 42 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU Q 43 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 94 removed outlier: 3.699A pdb=" N VAL Q 90 " --> pdb=" O ILE Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 137 removed outlier: 3.784A pdb=" N MET Q 132 " --> pdb=" O ARG Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 162 removed outlier: 3.502A pdb=" N LYS Q 148 " --> pdb=" O ASN Q 144 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU Q 151 " --> pdb=" O ARG Q 147 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS Q 156 " --> pdb=" O GLN Q 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 167 Processing helix chain 'Q' and resid 174 through 181 removed outlier: 3.922A pdb=" N LEU Q 181 " --> pdb=" O SER Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 210 Processing helix chain 'Q' and resid 229 through 240 removed outlier: 3.700A pdb=" N ASP Q 232 " --> pdb=" O ALA Q 229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU Q 235 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG Q 238 " --> pdb=" O GLU Q 235 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE Q 240 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 268 removed outlier: 4.254A pdb=" N GLN Q 259 " --> pdb=" O ARG Q 255 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU Q 267 " --> pdb=" O GLY Q 263 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN Q 268 " --> pdb=" O LYS Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 271 through 276 Processing helix chain 'Q' and resid 280 through 301 removed outlier: 3.672A pdb=" N GLU Q 285 " --> pdb=" O VAL Q 281 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN Q 296 " --> pdb=" O HIS Q 292 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU Q 299 " --> pdb=" O GLN Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 304 through 306 No H-bonds generated for 'chain 'Q' and resid 304 through 306' Processing helix chain 'Q' and resid 313 through 317 removed outlier: 3.666A pdb=" N VAL Q 317 " --> pdb=" O MET Q 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 313 through 317' Processing helix chain 'Q' and resid 344 through 355 removed outlier: 4.197A pdb=" N ALA Q 351 " --> pdb=" O ALA Q 347 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU Q 354 " --> pdb=" O ASP Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 362 through 373 removed outlier: 4.072A pdb=" N TYR Q 367 " --> pdb=" O ASP Q 363 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL Q 368 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 376 through 394 Processing helix chain 'Q' and resid 413 through 424 removed outlier: 3.520A pdb=" N ASN Q 419 " --> pdb=" O ASN Q 415 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Q 420 " --> pdb=" O LEU Q 416 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY Q 423 " --> pdb=" O ASN Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 432 Processing helix chain 'Q' and resid 438 through 440 No H-bonds generated for 'chain 'Q' and resid 438 through 440' Processing helix chain 'Q' and resid 443 through 457 removed outlier: 3.640A pdb=" N LYS Q 448 " --> pdb=" O ASP Q 444 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE Q 451 " --> pdb=" O CYS Q 447 " (cutoff:3.500A) Processing helix chain 'Q' and resid 463 through 465 No H-bonds generated for 'chain 'Q' and resid 463 through 465' Processing helix chain 'Q' and resid 473 through 489 removed outlier: 3.594A pdb=" N ASN Q 489 " --> pdb=" O GLN Q 485 " (cutoff:3.500A) Processing helix chain 'Q' and resid 495 through 502 Processing helix chain 'Q' and resid 506 through 514 removed outlier: 3.902A pdb=" N PHE Q 511 " --> pdb=" O SER Q 507 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 539 removed outlier: 3.736A pdb=" N GLN Q 530 " --> pdb=" O GLU Q 526 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU Q 531 " --> pdb=" O LYS Q 527 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Q 532 " --> pdb=" O PHE Q 528 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA Q 537 " --> pdb=" O SER Q 533 " (cutoff:3.500A) Processing helix chain 'Q' and resid 547 through 559 removed outlier: 4.299A pdb=" N ALA Q 556 " --> pdb=" O ASN Q 552 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 566 No H-bonds generated for 'chain 'Q' and resid 564 through 566' Processing helix chain 'Q' and resid 593 through 595 No H-bonds generated for 'chain 'Q' and resid 593 through 595' Processing helix chain 'Q' and resid 598 through 606 removed outlier: 3.566A pdb=" N ALA Q 603 " --> pdb=" O ALA Q 600 " (cutoff:3.500A) Processing helix chain 'Q' and resid 623 through 632 removed outlier: 3.520A pdb=" N ALA Q 630 " --> pdb=" O ILE Q 626 " (cutoff:3.500A) Processing helix chain 'Q' and resid 640 through 646 Processing helix chain 'Q' and resid 707 through 721 removed outlier: 3.567A pdb=" N LYS Q 718 " --> pdb=" O GLU Q 714 " (cutoff:3.500A) Processing helix chain 'Q' and resid 733 through 753 removed outlier: 4.807A pdb=" N LYS Q 753 " --> pdb=" O ALA Q 749 " (cutoff:3.500A) Processing helix chain 'Q' and resid 771 through 792 removed outlier: 3.535A pdb=" N GLU Q 789 " --> pdb=" O ALA Q 785 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER Q 791 " --> pdb=" O LEU Q 787 " (cutoff:3.500A) Processing helix chain 'Q' and resid 815 through 830 removed outlier: 3.703A pdb=" N ILE Q 821 " --> pdb=" O PHE Q 817 " (cutoff:3.500A) Processing helix chain 'Q' and resid 840 through 846 Processing helix chain 'Q' and resid 849 through 855 Proline residue: Q 853 - end of helix No H-bonds generated for 'chain 'Q' and resid 849 through 855' Processing helix chain 'Q' and resid 867 through 881 removed outlier: 3.907A pdb=" N SER Q 873 " --> pdb=" O ASN Q 869 " (cutoff:3.500A) Processing helix chain 'Q' and resid 889 through 897 removed outlier: 3.512A pdb=" N LEU Q 895 " --> pdb=" O GLU Q 891 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 50 removed outlier: 4.200A pdb=" N ASP R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN R 40 " --> pdb=" O SER R 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG R 46 " --> pdb=" O VAL R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 121 through 134 Processing helix chain 'R' and resid 136 through 139 Processing helix chain 'R' and resid 147 through 168 removed outlier: 3.963A pdb=" N GLN R 152 " --> pdb=" O LYS R 148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU R 157 " --> pdb=" O TRP R 153 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU R 166 " --> pdb=" O ARG R 162 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU R 167 " --> pdb=" O GLY R 163 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.532A pdb=" N SER R 178 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 196 through 211 removed outlier: 3.572A pdb=" N GLU R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 239 removed outlier: 4.055A pdb=" N ASP R 232 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG R 238 " --> pdb=" O LEU R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 268 removed outlier: 4.220A pdb=" N ASN R 268 " --> pdb=" O LYS R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 276 No H-bonds generated for 'chain 'R' and resid 273 through 276' Processing helix chain 'R' and resid 280 through 301 removed outlier: 3.703A pdb=" N GLU R 291 " --> pdb=" O GLY R 287 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN R 296 " --> pdb=" O HIS R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 317 No H-bonds generated for 'chain 'R' and resid 314 through 317' Processing helix chain 'R' and resid 345 through 352 removed outlier: 4.520A pdb=" N ALA R 351 " --> pdb=" O ALA R 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Processing helix chain 'R' and resid 376 through 394 removed outlier: 3.639A pdb=" N GLN R 381 " --> pdb=" O ARG R 377 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL R 382 " --> pdb=" O LEU R 378 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE R 386 " --> pdb=" O VAL R 382 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR R 387 " --> pdb=" O LEU R 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS R 392 " --> pdb=" O THR R 388 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 422 Processing helix chain 'R' and resid 427 through 432 removed outlier: 3.994A pdb=" N ARG R 431 " --> pdb=" O SER R 427 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 427 through 432' Processing helix chain 'R' and resid 443 through 456 removed outlier: 3.884A pdb=" N CYS R 447 " --> pdb=" O MET R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 465 No H-bonds generated for 'chain 'R' and resid 463 through 465' Processing helix chain 'R' and resid 473 through 488 removed outlier: 3.681A pdb=" N SER R 484 " --> pdb=" O ILE R 480 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN R 485 " --> pdb=" O TYR R 481 " (cutoff:3.500A) Processing helix chain 'R' and resid 495 through 516 removed outlier: 4.846A pdb=" N VAL R 508 " --> pdb=" O GLY R 504 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN R 513 " --> pdb=" O SER R 509 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE R 514 " --> pdb=" O ILE R 510 " (cutoff:3.500A) Processing helix chain 'R' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU R 531 " --> pdb=" O LYS R 527 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE R 532 " --> pdb=" O PHE R 528 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL R 536 " --> pdb=" O ILE R 532 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA R 537 " --> pdb=" O SER R 533 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR R 538 " --> pdb=" O GLU R 534 " (cutoff:3.500A) Processing helix chain 'R' and resid 547 through 560 removed outlier: 3.514A pdb=" N ASN R 560 " --> pdb=" O ALA R 556 " (cutoff:3.500A) Processing helix chain 'R' and resid 598 through 607 removed outlier: 3.831A pdb=" N SER R 607 " --> pdb=" O ALA R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 635 removed outlier: 3.957A pdb=" N ASP R 631 " --> pdb=" O GLY R 627 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 633 " --> pdb=" O ILE R 629 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA R 634 " --> pdb=" O ALA R 630 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS R 635 " --> pdb=" O ASP R 631 " (cutoff:3.500A) Processing helix chain 'R' and resid 641 through 646 removed outlier: 3.704A pdb=" N PHE R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 703 through 720 removed outlier: 3.669A pdb=" N SER R 707 " --> pdb=" O ALA R 703 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR R 711 " --> pdb=" O SER R 707 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS R 712 " --> pdb=" O ASP R 708 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL R 713 " --> pdb=" O ALA R 709 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS R 718 " --> pdb=" O GLU R 714 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN R 719 " --> pdb=" O GLN R 715 " (cutoff:3.500A) Processing helix chain 'R' and resid 732 through 754 removed outlier: 4.412A pdb=" N VAL R 737 " --> pdb=" O LEU R 733 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP R 738 " --> pdb=" O ILE R 734 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR R 754 " --> pdb=" O ASP R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 771 through 792 removed outlier: 4.046A pdb=" N PHE R 777 " --> pdb=" O LYS R 773 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 778 " --> pdb=" O ILE R 774 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL R 779 " --> pdb=" O MET R 775 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU R 780 " --> pdb=" O ARG R 776 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL R 786 " --> pdb=" O PHE R 782 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU R 787 " --> pdb=" O LEU R 783 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU R 789 " --> pdb=" O ALA R 785 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU R 790 " --> pdb=" O VAL R 786 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER R 791 " --> pdb=" O LEU R 787 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU R 792 " --> pdb=" O VAL R 788 " (cutoff:3.500A) Processing helix chain 'R' and resid 815 through 829 removed outlier: 3.613A pdb=" N ILE R 821 " --> pdb=" O PHE R 817 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY R 825 " --> pdb=" O ILE R 821 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU R 826 " --> pdb=" O LYS R 822 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS R 827 " --> pdb=" O ILE R 823 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS R 829 " --> pdb=" O GLY R 825 " (cutoff:3.500A) Processing helix chain 'R' and resid 835 through 838 No H-bonds generated for 'chain 'R' and resid 835 through 838' Processing helix chain 'R' and resid 840 through 845 removed outlier: 4.010A pdb=" N LEU R 844 " --> pdb=" O PRO R 840 " (cutoff:3.500A) Processing helix chain 'R' and resid 849 through 855 Proline residue: R 853 - end of helix No H-bonds generated for 'chain 'R' and resid 849 through 855' Processing helix chain 'R' and resid 858 through 860 No H-bonds generated for 'chain 'R' and resid 858 through 860' Processing helix chain 'R' and resid 865 through 882 removed outlier: 3.683A pdb=" N ASN R 869 " --> pdb=" O VAL R 865 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU R 877 " --> pdb=" O SER R 873 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL R 882 " --> pdb=" O ILE R 878 " (cutoff:3.500A) Processing helix chain 'R' and resid 889 through 897 removed outlier: 3.827A pdb=" N TYR R 894 " --> pdb=" O GLU R 890 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR R 896 " --> pdb=" O TRP R 892 " (cutoff:3.500A) Processing helix chain 'R' and resid 916 through 919 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.698A pdb=" N MET A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 167 removed outlier: 3.530A pdb=" N ASN A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.736A pdb=" N SER A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.529A pdb=" N ARG A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.155A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 232 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 235 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 238 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE A 240 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.856A pdb=" N ILE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.573A pdb=" N ARG A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.559A pdb=" N ILE A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.833A pdb=" N MET A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.584A pdb=" N GLN A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.772A pdb=" N LYS A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.664A pdb=" N SER A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 removed outlier: 3.861A pdb=" N MET A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.357A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 547 through 558 removed outlier: 4.652A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 598 through 607 removed outlier: 3.822A pdb=" N SER A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 4.458A pdb=" N ALA A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.667A pdb=" N ASN A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 705 through 725 removed outlier: 3.591A pdb=" N ASP A 708 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 721 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 722 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 754 removed outlier: 3.531A pdb=" N GLY A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 793 removed outlier: 3.935A pdb=" N VAL A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 831 removed outlier: 3.789A pdb=" N LYS A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 849 through 855 Proline residue: A 853 - end of helix No H-bonds generated for 'chain 'A' and resid 849 through 855' Processing helix chain 'A' and resid 865 through 882 removed outlier: 4.363A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 895 Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.770A pdb=" N SER B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.554A pdb=" N SER B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 139 removed outlier: 3.675A pdb=" N MET B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 167 removed outlier: 3.605A pdb=" N HIS B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 4.511A pdb=" N SER B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.592A pdb=" N LYS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.607A pdb=" N TYR B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.764A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.528A pdb=" N GLU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 344 through 356 removed outlier: 4.210A pdb=" N ALA B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.937A pdb=" N TYR B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 394 removed outlier: 3.653A pdb=" N MET B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 432 removed outlier: 3.773A pdb=" N GLY B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.533A pdb=" N PHE B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.997A pdb=" N ILE B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 517 removed outlier: 4.082A pdb=" N SER B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU B 517 " --> pdb=" O GLN B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 removed outlier: 3.892A pdb=" N GLU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 4.194A pdb=" N ALA B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 607 removed outlier: 3.587A pdb=" N SER B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 632 removed outlier: 3.554A pdb=" N ASP B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 647 No H-bonds generated for 'chain 'B' and resid 644 through 647' Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 707 through 726 removed outlier: 3.897A pdb=" N LYS B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.539A pdb=" N TRP B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 739 " --> pdb=" O GLY B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 792 removed outlier: 3.506A pdb=" N ASN B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 830 removed outlier: 3.671A pdb=" N LYS B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 826 " --> pdb=" O LYS B 822 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 838 No H-bonds generated for 'chain 'B' and resid 835 through 838' Processing helix chain 'B' and resid 840 through 846 removed outlier: 3.779A pdb=" N LEU B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Proline residue: B 853 - end of helix No H-bonds generated for 'chain 'B' and resid 849 through 854' Processing helix chain 'B' and resid 867 through 881 removed outlier: 3.550A pdb=" N THR B 872 " --> pdb=" O ASN B 869 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 876 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 877 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 896 removed outlier: 3.995A pdb=" N LEU B 895 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 143 through 162 removed outlier: 3.566A pdb=" N GLN C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.901A pdb=" N GLU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 4.300A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP C 232 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 234 " --> pdb=" O TRP C 231 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 235 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.617A pdb=" N GLY C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 301 removed outlier: 4.128A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS C 292 " --> pdb=" O TYR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.595A pdb=" N TYR C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 393 removed outlier: 3.777A pdb=" N MET C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.641A pdb=" N ASN C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 443 through 457 removed outlier: 3.600A pdb=" N CYS C 447 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C 451 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 473 through 476 No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 505 through 509 removed outlier: 4.160A pdb=" N SER C 509 " --> pdb=" O GLY C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 514 No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.529A pdb=" N GLU C 529 " --> pdb=" O ARG C 525 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 4.159A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 558 " --> pdb=" O CYS C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 599 through 606 removed outlier: 3.948A pdb=" N ALA C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 removed outlier: 3.739A pdb=" N ASP C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 3.709A pdb=" N THR C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 670 removed outlier: 4.380A pdb=" N GLU C 668 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 670 " --> pdb=" O ARG C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 670' Processing helix chain 'C' and resid 707 through 723 removed outlier: 3.527A pdb=" N LYS C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU C 722 " --> pdb=" O LYS C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 751 removed outlier: 3.889A pdb=" N GLY C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 792 removed outlier: 3.810A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 777 " --> pdb=" O LYS C 773 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE C 782 " --> pdb=" O ASN C 778 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 830 removed outlier: 3.589A pdb=" N LYS C 819 " --> pdb=" O ASP C 815 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 846 Processing helix chain 'C' and resid 849 through 855 Proline residue: C 853 - end of helix No H-bonds generated for 'chain 'C' and resid 849 through 855' Processing helix chain 'C' and resid 868 through 882 removed outlier: 3.761A pdb=" N SER C 873 " --> pdb=" O ASN C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 896 removed outlier: 3.545A pdb=" N TYR C 894 " --> pdb=" O GLU C 890 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 895 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 35 through 48 removed outlier: 3.734A pdb=" N GLU D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.947A pdb=" N ASN D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 3.502A pdb=" N MET D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 167 removed outlier: 3.678A pdb=" N ARG D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 150 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.946A pdb=" N GLU D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.964A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP D 232 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 234 " --> pdb=" O TRP D 231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 235 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 239 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 removed outlier: 3.660A pdb=" N TYR D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 282 through 301 removed outlier: 3.619A pdb=" N GLN D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 344 through 355 removed outlier: 3.630A pdb=" N ALA D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG D 353 " --> pdb=" O GLY D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.852A pdb=" N LYS D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 393 removed outlier: 3.787A pdb=" N MET D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 443 through 457 removed outlier: 3.894A pdb=" N CYS D 447 " --> pdb=" O MET D 443 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.205A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.524A pdb=" N PHE D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 527 through 539 removed outlier: 3.670A pdb=" N ALA D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.548A pdb=" N CYS D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 559 " --> pdb=" O CYS D 555 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 598 through 607 removed outlier: 3.690A pdb=" N SER D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 632 Processing helix chain 'D' and resid 639 through 649 Processing helix chain 'D' and resid 666 through 670 Processing helix chain 'D' and resid 702 through 726 removed outlier: 4.020A pdb=" N GLU D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 752 removed outlier: 3.996A pdb=" N GLY D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 792 removed outlier: 3.632A pdb=" N GLU D 789 " --> pdb=" O ALA D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 830 removed outlier: 3.633A pdb=" N LYS D 820 " --> pdb=" O GLU D 816 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 826 " --> pdb=" O LYS D 822 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 840 through 846 Processing helix chain 'D' and resid 849 through 855 Proline residue: D 853 - end of helix No H-bonds generated for 'chain 'D' and resid 849 through 855' Processing helix chain 'D' and resid 865 through 882 removed outlier: 3.991A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 880 " --> pdb=" O LYS D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 896 removed outlier: 3.643A pdb=" N ASP D 893 " --> pdb=" O ASP D 889 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU D 895 " --> pdb=" O GLU D 891 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR D 896 " --> pdb=" O TRP D 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 889 through 896' Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.558A pdb=" N ASN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 Processing helix chain 'E' and resid 143 through 166 removed outlier: 3.906A pdb=" N GLU E 151 " --> pdb=" O ARG E 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N HIS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.100A pdb=" N SER E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 removed outlier: 4.528A pdb=" N GLU E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 239 removed outlier: 3.630A pdb=" N ASP E 232 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 235 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 238 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 4.321A pdb=" N GLN E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 263 " --> pdb=" O GLN E 259 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 301 removed outlier: 3.965A pdb=" N GLU E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 362 through 372 Processing helix chain 'E' and resid 376 through 394 removed outlier: 4.143A pdb=" N GLN E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 383 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN E 384 " --> pdb=" O MET E 380 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR E 388 " --> pdb=" O GLN E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.826A pdb=" N GLY E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 removed outlier: 3.729A pdb=" N TYR E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 457 removed outlier: 3.510A pdb=" N PHE E 451 " --> pdb=" O CYS E 447 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 473 through 489 removed outlier: 4.133A pdb=" N CYS E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 482 " --> pdb=" O CYS E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 503 Processing helix chain 'E' and resid 507 through 514 Processing helix chain 'E' and resid 525 through 539 removed outlier: 3.907A pdb=" N ALA E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 removed outlier: 3.855A pdb=" N ALA E 551 " --> pdb=" O ALA E 547 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 566 No H-bonds generated for 'chain 'E' and resid 564 through 566' Processing helix chain 'E' and resid 622 through 632 Processing helix chain 'E' and resid 640 through 646 removed outlier: 3.585A pdb=" N PHE E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 726 removed outlier: 4.571A pdb=" N ASP E 708 " --> pdb=" O THR E 704 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA E 709 " --> pdb=" O GLU E 705 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE E 725 " --> pdb=" O ASN E 721 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLY E 726 " --> pdb=" O GLU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 753 removed outlier: 3.995A pdb=" N TRP E 738 " --> pdb=" O ILE E 734 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 745 " --> pdb=" O PHE E 741 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 749 " --> pdb=" O LEU E 745 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS E 753 " --> pdb=" O ALA E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 793 removed outlier: 3.656A pdb=" N SER E 791 " --> pdb=" O LEU E 787 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 792 " --> pdb=" O VAL E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 830 Processing helix chain 'E' and resid 835 through 838 No H-bonds generated for 'chain 'E' and resid 835 through 838' Processing helix chain 'E' and resid 840 through 846 Processing helix chain 'E' and resid 849 through 855 Proline residue: E 853 - end of helix No H-bonds generated for 'chain 'E' and resid 849 through 855' Processing helix chain 'E' and resid 865 through 882 removed outlier: 3.648A pdb=" N ASN E 869 " --> pdb=" O VAL E 865 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 880 " --> pdb=" O LYS E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 896 removed outlier: 3.551A pdb=" N TYR E 894 " --> pdb=" O GLU E 890 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.793A pdb=" N GLU G 43 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.708A pdb=" N VAL G 90 " --> pdb=" O ILE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 139 removed outlier: 3.737A pdb=" N MET G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 167 removed outlier: 3.702A pdb=" N GLU G 151 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS G 156 " --> pdb=" O GLN G 152 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N HIS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 180 Processing helix chain 'G' and resid 196 through 210 Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.761A pdb=" N ASP G 232 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU G 235 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 237 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG G 238 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE G 240 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 removed outlier: 4.308A pdb=" N GLN G 259 " --> pdb=" O ARG G 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 267 " --> pdb=" O GLY G 263 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 280 through 301 removed outlier: 3.666A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN G 296 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 299 " --> pdb=" O GLN G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 313 through 317 Processing helix chain 'G' and resid 344 through 355 removed outlier: 3.947A pdb=" N ALA G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU G 354 " --> pdb=" O ASP G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 373 removed outlier: 3.704A pdb=" N VAL G 368 " --> pdb=" O ALA G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 394 Processing helix chain 'G' and resid 413 through 424 removed outlier: 3.522A pdb=" N ASN G 419 " --> pdb=" O ASN G 415 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY G 423 " --> pdb=" O ASN G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 432 Processing helix chain 'G' and resid 443 through 457 removed outlier: 3.553A pdb=" N PHE G 451 " --> pdb=" O CYS G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 473 through 489 Processing helix chain 'G' and resid 494 through 503 Processing helix chain 'G' and resid 506 through 514 removed outlier: 3.986A pdb=" N PHE G 511 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 539 removed outlier: 3.871A pdb=" N GLN G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 531 " --> pdb=" O LYS G 527 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G 532 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 537 " --> pdb=" O SER G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 4.269A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 566 No H-bonds generated for 'chain 'G' and resid 564 through 566' Processing helix chain 'G' and resid 593 through 595 No H-bonds generated for 'chain 'G' and resid 593 through 595' Processing helix chain 'G' and resid 598 through 606 removed outlier: 3.577A pdb=" N ALA G 603 " --> pdb=" O ALA G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 632 removed outlier: 3.572A pdb=" N ILE G 629 " --> pdb=" O LEU G 625 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 630 " --> pdb=" O ILE G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 640 through 646 Processing helix chain 'G' and resid 707 through 721 removed outlier: 3.613A pdb=" N LYS G 718 " --> pdb=" O GLU G 714 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 753 removed outlier: 4.829A pdb=" N LYS G 753 " --> pdb=" O ALA G 749 " (cutoff:3.500A) Processing helix chain 'G' and resid 771 through 792 removed outlier: 3.535A pdb=" N SER G 791 " --> pdb=" O LEU G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 831 removed outlier: 3.520A pdb=" N LYS G 820 " --> pdb=" O GLU G 816 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE G 821 " --> pdb=" O PHE G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 840 through 846 Processing helix chain 'G' and resid 849 through 855 Proline residue: G 853 - end of helix No H-bonds generated for 'chain 'G' and resid 849 through 855' Processing helix chain 'G' and resid 867 through 881 removed outlier: 3.730A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 876 " --> pdb=" O THR G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 889 through 897 Processing helix chain 'H' and resid 35 through 50 removed outlier: 4.130A pdb=" N ASP H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG H 46 " --> pdb=" O VAL H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 121 through 137 removed outlier: 3.898A pdb=" N LYS H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 168 removed outlier: 4.038A pdb=" N GLN H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 179 removed outlier: 3.530A pdb=" N SER H 178 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.517A pdb=" N GLU H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 239 removed outlier: 4.056A pdb=" N ASP H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 238 " --> pdb=" O LEU H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 removed outlier: 4.233A pdb=" N ASN H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.664A pdb=" N GLU H 275 " --> pdb=" O LYS H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 301 removed outlier: 4.181A pdb=" N GLU H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN H 296 " --> pdb=" O HIS H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 317 No H-bonds generated for 'chain 'H' and resid 314 through 317' Processing helix chain 'H' and resid 345 through 352 removed outlier: 4.450A pdb=" N ALA H 351 " --> pdb=" O ALA H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 372 Processing helix chain 'H' and resid 376 through 394 removed outlier: 3.651A pdb=" N GLN H 381 " --> pdb=" O ARG H 377 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE H 386 " --> pdb=" O VAL H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 422 Processing helix chain 'H' and resid 427 through 432 removed outlier: 4.006A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA H 432 " --> pdb=" O SER H 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 427 through 432' Processing helix chain 'H' and resid 443 through 456 Processing helix chain 'H' and resid 463 through 465 No H-bonds generated for 'chain 'H' and resid 463 through 465' Processing helix chain 'H' and resid 473 through 488 removed outlier: 3.591A pdb=" N SER H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN H 485 " --> pdb=" O TYR H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 516 removed outlier: 3.544A pdb=" N SER H 507 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE H 514 " --> pdb=" O ILE H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 538 removed outlier: 4.081A pdb=" N VAL H 536 " --> pdb=" O ILE H 532 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA H 537 " --> pdb=" O SER H 533 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR H 538 " --> pdb=" O GLU H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 560 Processing helix chain 'H' and resid 599 through 607 removed outlier: 4.108A pdb=" N SER H 607 " --> pdb=" O ALA H 603 " (cutoff:3.500A) Processing helix chain 'H' and resid 622 through 635 removed outlier: 4.981A pdb=" N ALA H 634 " --> pdb=" O ALA H 630 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS H 635 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 647 removed outlier: 3.610A pdb=" N PHE H 646 " --> pdb=" O ILE H 642 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN H 647 " --> pdb=" O THR H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 703 through 722 removed outlier: 3.574A pdb=" N SER H 707 " --> pdb=" O ALA H 703 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR H 711 " --> pdb=" O SER H 707 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS H 712 " --> pdb=" O ASP H 708 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL H 713 " --> pdb=" O ALA H 709 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU H 722 " --> pdb=" O LYS H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 731 through 753 removed outlier: 4.312A pdb=" N VAL H 737 " --> pdb=" O LEU H 733 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP H 738 " --> pdb=" O ILE H 734 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 739 " --> pdb=" O GLY H 735 " (cutoff:3.500A) Processing helix chain 'H' and resid 771 through 792 removed outlier: 4.007A pdb=" N PHE H 777 " --> pdb=" O LYS H 773 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN H 778 " --> pdb=" O ILE H 774 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL H 779 " --> pdb=" O MET H 775 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU H 780 " --> pdb=" O ARG H 776 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 786 " --> pdb=" O PHE H 782 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU H 787 " --> pdb=" O LEU H 783 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 788 " --> pdb=" O HIS H 784 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU H 789 " --> pdb=" O ALA H 785 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU H 790 " --> pdb=" O VAL H 786 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER H 791 " --> pdb=" O LEU H 787 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 792 " --> pdb=" O VAL H 788 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 829 removed outlier: 3.808A pdb=" N GLY H 825 " --> pdb=" O ILE H 821 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU H 826 " --> pdb=" O LYS H 822 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS H 827 " --> pdb=" O ILE H 823 " (cutoff:3.500A) Processing helix chain 'H' and resid 835 through 838 No H-bonds generated for 'chain 'H' and resid 835 through 838' Processing helix chain 'H' and resid 842 through 845 No H-bonds generated for 'chain 'H' and resid 842 through 845' Processing helix chain 'H' and resid 852 through 855 No H-bonds generated for 'chain 'H' and resid 852 through 855' Processing helix chain 'H' and resid 858 through 860 No H-bonds generated for 'chain 'H' and resid 858 through 860' Processing helix chain 'H' and resid 865 through 882 removed outlier: 3.715A pdb=" N ASN H 869 " --> pdb=" O VAL H 865 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 875 " --> pdb=" O GLU H 871 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU H 877 " --> pdb=" O SER H 873 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL H 882 " --> pdb=" O ILE H 878 " (cutoff:3.500A) Processing helix chain 'H' and resid 889 through 897 removed outlier: 3.728A pdb=" N TYR H 894 " --> pdb=" O GLU H 890 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR H 896 " --> pdb=" O TRP H 892 " (cutoff:3.500A) Processing helix chain 'H' and resid 916 through 919 Processing sheet with id= A, first strand: chain 'F' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'F' and resid 307 through 309 removed outlier: 8.243A pdb=" N ILE F 308 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE F 73 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N PHE F 72 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 248 " --> pdb=" O PHE F 72 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N VAL F 74 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA F 250 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE F 216 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL F 249 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE F 218 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR F 251 " --> pdb=" O ILE F 218 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 573 through 576 removed outlier: 4.321A pdb=" N ASP F 618 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS F 655 " --> pdb=" O THR F 610 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 307 through 309 removed outlier: 8.603A pdb=" N ILE K 308 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE K 73 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE K 72 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL K 248 " --> pdb=" O PHE K 72 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL K 74 " --> pdb=" O VAL K 248 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA K 250 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE K 216 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL K 249 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE K 218 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR K 251 " --> pdb=" O ILE K 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 573 through 576 removed outlier: 4.426A pdb=" N ASP K 618 " --> pdb=" O LEU K 576 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 72 through 75 removed outlier: 3.917A pdb=" N ALA L 250 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE L 216 " --> pdb=" O VAL L 247 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL L 249 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE L 218 " --> pdb=" O VAL L 249 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR L 251 " --> pdb=" O ILE L 218 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE L 220 " --> pdb=" O THR L 251 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 573 through 576 removed outlier: 4.263A pdb=" N ASP L 618 " --> pdb=" O LEU L 576 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET L 617 " --> pdb=" O VAL L 611 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL L 611 " --> pdb=" O MET L 617 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER L 609 " --> pdb=" O PHE L 619 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 14 through 17 removed outlier: 3.616A pdb=" N ILE M 16 " --> pdb=" O LYS M 329 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 71 through 75 removed outlier: 8.321A pdb=" N PHE M 72 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL M 248 " --> pdb=" O PHE M 72 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL M 74 " --> pdb=" O VAL M 248 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA M 250 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE M 216 " --> pdb=" O VAL M 247 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL M 249 " --> pdb=" O ILE M 216 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE M 218 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR M 251 " --> pdb=" O ILE M 218 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 617 through 620 removed outlier: 3.552A pdb=" N MET M 617 " --> pdb=" O VAL M 611 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 14 through 16 Processing sheet with id= L, first strand: chain 'P' and resid 307 through 309 removed outlier: 8.287A pdb=" N ILE P 308 " --> pdb=" O VAL P 71 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE P 73 " --> pdb=" O ILE P 308 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE P 72 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL P 248 " --> pdb=" O PHE P 72 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL P 74 " --> pdb=" O VAL P 248 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA P 250 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE P 216 " --> pdb=" O VAL P 247 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL P 249 " --> pdb=" O ILE P 216 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE P 218 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR P 251 " --> pdb=" O ILE P 218 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 573 through 576 removed outlier: 4.513A pdb=" N ASP P 618 " --> pdb=" O LEU P 576 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Q' and resid 15 through 17 removed outlier: 7.083A pdb=" N LYS Q 329 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'Q' and resid 307 through 309 removed outlier: 8.521A pdb=" N ILE Q 308 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE Q 73 " --> pdb=" O ILE Q 308 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE Q 72 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL Q 248 " --> pdb=" O PHE Q 72 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 248 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA Q 250 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE Q 216 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL Q 249 " --> pdb=" O ILE Q 216 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE Q 218 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR Q 251 " --> pdb=" O ILE Q 218 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Q' and resid 609 through 611 Processing sheet with id= Q, first strand: chain 'R' and resid 71 through 74 removed outlier: 8.380A pdb=" N PHE R 72 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL R 248 " --> pdb=" O PHE R 72 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL R 74 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA R 250 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE R 216 " --> pdb=" O VAL R 247 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL R 249 " --> pdb=" O ILE R 216 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE R 218 " --> pdb=" O VAL R 249 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR R 251 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 573 through 576 removed outlier: 3.593A pdb=" N CYS R 620 " --> pdb=" O VAL R 574 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP R 618 " --> pdb=" O LEU R 576 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 14 through 16 Processing sheet with id= T, first strand: chain 'A' and resid 307 through 309 removed outlier: 8.246A pdb=" N ILE A 308 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 73 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHE A 72 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 248 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL A 74 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA A 250 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.159A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS A 655 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 307 through 309 removed outlier: 8.653A pdb=" N ILE B 308 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 73 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE B 72 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 248 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 74 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 250 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 216 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL B 249 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 218 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR B 251 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 105 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 573 through 576 removed outlier: 4.406A pdb=" N ASP B 618 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.940A pdb=" N ALA C 250 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 573 through 576 removed outlier: 4.326A pdb=" N ASP C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET C 617 " --> pdb=" O VAL C 611 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 611 " --> pdb=" O MET C 617 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 609 " --> pdb=" O PHE C 619 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 14 through 17 removed outlier: 3.586A pdb=" N ILE D 16 " --> pdb=" O LYS D 329 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 71 through 75 removed outlier: 8.321A pdb=" N PHE D 72 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 248 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL D 74 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 250 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 216 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL D 249 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 218 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR D 251 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 617 through 620 Processing sheet with id= AC, first strand: chain 'E' and resid 307 through 309 removed outlier: 8.301A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N PHE E 72 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL E 248 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 74 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA E 250 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 573 through 576 removed outlier: 4.539A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 15 through 17 removed outlier: 7.085A pdb=" N LYS G 329 " --> pdb=" O ILE G 16 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 307 through 310 removed outlier: 8.512A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU G 310 " --> pdb=" O PHE G 73 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP G 75 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE G 72 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL G 248 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL G 74 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA G 250 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLY G 76 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY G 252 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 609 through 611 Processing sheet with id= AH, first strand: chain 'H' and resid 71 through 74 removed outlier: 8.389A pdb=" N PHE H 72 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL H 248 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL H 74 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA H 250 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL H 249 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 218 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N THR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 573 through 576 removed outlier: 3.503A pdb=" N CYS H 620 " --> pdb=" O VAL H 574 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP H 618 " --> pdb=" O LEU H 576 " (cutoff:3.500A) 3483 hydrogen bonds defined for protein. 9963 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: 38.75 Time building geometry restraints manager: 34.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31351 1.34 - 1.46: 14820 1.46 - 1.58: 51141 1.58 - 1.70: 232 1.70 - 1.82: 670 Bond restraints: 98214 Sorted by residual: bond pdb=" N ILE C 33 " pdb=" CA ILE C 33 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N GLU K 279 " pdb=" CA GLU K 279 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.25e-02 6.40e+03 9.37e+00 bond pdb=" N ASP C 31 " pdb=" CA ASP C 31 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.52e+00 bond pdb=" N GLU P 638 " pdb=" CA GLU P 638 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.06e+00 bond pdb=" N LYS K 278 " pdb=" CA LYS K 278 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.60e+00 ... (remaining 98209 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.93: 2489 106.93 - 115.17: 60096 115.17 - 123.41: 67699 123.41 - 131.65: 2546 131.65 - 139.89: 162 Bond angle restraints: 132992 Sorted by residual: angle pdb=" N GLN C 34 " pdb=" CA GLN C 34 " pdb=" C GLN C 34 " ideal model delta sigma weight residual 114.09 105.31 8.78 1.55e+00 4.16e-01 3.21e+01 angle pdb=" N ILE H 734 " pdb=" CA ILE H 734 " pdb=" C ILE H 734 " ideal model delta sigma weight residual 112.96 107.49 5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" N ILE R 348 " pdb=" CA ILE R 348 " pdb=" C ILE R 348 " ideal model delta sigma weight residual 113.42 107.17 6.25 1.17e+00 7.31e-01 2.86e+01 angle pdb=" N ILE H 348 " pdb=" CA ILE H 348 " pdb=" C ILE H 348 " ideal model delta sigma weight residual 113.42 107.37 6.05 1.17e+00 7.31e-01 2.67e+01 angle pdb=" C GLN M 97 " pdb=" CA GLN M 97 " pdb=" CB GLN M 97 " ideal model delta sigma weight residual 116.63 110.64 5.99 1.16e+00 7.43e-01 2.66e+01 ... (remaining 132987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 53088 17.97 - 35.94: 5580 35.94 - 53.91: 1040 53.91 - 71.88: 299 71.88 - 89.85: 119 Dihedral angle restraints: 60126 sinusoidal: 25696 harmonic: 34430 Sorted by residual: dihedral pdb=" CA GLN E 337 " pdb=" C GLN E 337 " pdb=" N ASP E 338 " pdb=" CA ASP E 338 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLU P 488 " pdb=" C GLU P 488 " pdb=" N ASN P 489 " pdb=" CA ASN P 489 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA HIS F 794 " pdb=" C HIS F 794 " pdb=" N SER F 795 " pdb=" CA SER F 795 " ideal model delta harmonic sigma weight residual -180.00 -158.82 -21.18 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 60123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 12510 0.049 - 0.098: 2162 0.098 - 0.147: 337 0.147 - 0.196: 7 0.196 - 0.245: 2 Chirality restraints: 15018 Sorted by residual: chirality pdb=" CA GLN C 34 " pdb=" N GLN C 34 " pdb=" C GLN C 34 " pdb=" CB GLN C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA TYR A 387 " pdb=" N TYR A 387 " pdb=" C TYR A 387 " pdb=" CB TYR A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU L 32 " pdb=" CB LEU L 32 " pdb=" CD1 LEU L 32 " pdb=" CD2 LEU L 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 15015 not shown) Planarity restraints: 16680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 413 " -0.067 5.00e-02 4.00e+02 1.00e-01 1.62e+01 pdb=" N PRO H 414 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 414 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 414 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 374 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO C 375 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 375 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 375 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 657 " 0.037 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 658 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 658 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 658 " 0.030 5.00e-02 4.00e+02 ... (remaining 16677 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4738 2.73 - 3.27: 102981 3.27 - 3.81: 150750 3.81 - 4.36: 184343 4.36 - 4.90: 303890 Nonbonded interactions: 746702 Sorted by model distance: nonbonded pdb=" OE1 GLN D 513 " pdb=" OH TYR D 742 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASN M 747 " pdb=" NH2 ARG Q 578 " model vdw 2.196 2.520 nonbonded pdb=" OG1 THR M 27 " pdb=" OE1 GLN M 384 " model vdw 2.198 2.440 nonbonded pdb=" O ILE K 45 " pdb=" OG SER K 48 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR D 27 " pdb=" OE1 GLN D 384 " model vdw 2.199 2.440 ... (remaining 746697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 50 or resid 70 through 95 or resid 102 through \ 394 or resid 413 through 517 or resid 524 through 663 or resid 667 or resid 704 \ through 897 or resid 907 through 934)) selection = (chain 'B' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'C' and (resid 13 through 50 or resid 70 through 95 or resid 102 through \ 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'D' and (resid 13 through 95 or resid 102 through 394 or resid 413 throug \ h 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'E' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'F' and (resid 13 through 50 or resid 70 through 95 or resid 102 through \ 394 or resid 413 through 517 or resid 524 through 663 or resid 667 or resid 704 \ through 897 or resid 907 through 934)) selection = (chain 'G' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'H' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 663 or resid 703 through 897 or resid 907 through 934)) selection = (chain 'K' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'L' and (resid 13 through 50 or resid 70 through 95 or resid 102 through \ 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'M' and (resid 13 through 95 or resid 102 through 394 or resid 413 throug \ h 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'P' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'Q' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'R' and (resid 13 through 50 or resid 70 through 394 or resid 413 through \ 663 or resid 703 through 897 or resid 907 through 934)) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 17.730 Check model and map are aligned: 1.100 Set scattering table: 0.730 Process input model: 204.690 Find NCS groups from input model: 6.860 Set up NCS constraints: 0.540 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.002 0.057 98214 Z= 0.139 Angle : 0.479 8.785 132992 Z= 0.257 Chirality : 0.037 0.245 15018 Planarity : 0.003 0.100 16680 Dihedral : 15.520 89.852 37790 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.02 % Allowed : 0.17 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.08), residues: 11606 helix: -0.13 (0.07), residues: 5810 sheet: 0.36 (0.27), residues: 474 loop : -1.16 (0.08), residues: 5322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 141 HIS 0.007 0.001 HIS H 794 PHE 0.024 0.001 PHE B 497 TYR 0.021 0.001 TYR P 436 ARG 0.014 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1159 time to evaluate : 8.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 289 MET cc_start: 0.8486 (tpp) cc_final: 0.8179 (tpp) REVERT: F 765 MET cc_start: 0.8308 (mpp) cc_final: 0.8094 (mpp) REVERT: M 443 MET cc_start: 0.8197 (tpp) cc_final: 0.7909 (tpp) REVERT: M 873 SER cc_start: 0.9035 (m) cc_final: 0.8641 (t) REVERT: P 32 LEU cc_start: 0.8825 (tp) cc_final: 0.8549 (tp) REVERT: P 564 ASP cc_start: 0.8144 (t0) cc_final: 0.7892 (t0) REVERT: P 604 MET cc_start: 0.8498 (tmm) cc_final: 0.8257 (tmm) REVERT: Q 855 ILE cc_start: 0.8496 (mm) cc_final: 0.8277 (mm) REVERT: R 446 LEU cc_start: 0.7894 (tp) cc_final: 0.7583 (tp) REVERT: R 535 TYR cc_start: 0.4730 (m-10) cc_final: 0.4338 (m-80) REVERT: R 539 MET cc_start: 0.4891 (mtm) cc_final: 0.4685 (mtm) REVERT: R 632 ILE cc_start: 0.5930 (mm) cc_final: 0.5721 (mm) REVERT: B 41 LEU cc_start: 0.8628 (tp) cc_final: 0.8368 (tp) REVERT: B 765 MET cc_start: 0.7917 (ppp) cc_final: 0.7208 (mmt) REVERT: B 782 PHE cc_start: 0.7274 (t80) cc_final: 0.6965 (t80) REVERT: C 359 ARG cc_start: 0.7428 (mtt180) cc_final: 0.4714 (ptt90) REVERT: E 32 LEU cc_start: 0.8673 (tp) cc_final: 0.8334 (tp) REVERT: E 443 MET cc_start: 0.9059 (tpt) cc_final: 0.8372 (tpp) REVERT: E 565 GLU cc_start: 0.7386 (pm20) cc_final: 0.7069 (pm20) REVERT: E 604 MET cc_start: 0.8762 (tmm) cc_final: 0.8269 (tmm) REVERT: G 855 ILE cc_start: 0.8561 (mm) cc_final: 0.8345 (mm) outliers start: 2 outliers final: 1 residues processed: 1161 average time/residue: 0.9151 time to fit residues: 1827.0162 Evaluate side-chains 909 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 908 time to evaluate : 8.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 994 optimal weight: 5.9990 chunk 892 optimal weight: 0.0870 chunk 495 optimal weight: 0.4980 chunk 305 optimal weight: 6.9990 chunk 602 optimal weight: 6.9990 chunk 477 optimal weight: 6.9990 chunk 923 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 561 optimal weight: 20.0000 chunk 687 optimal weight: 0.4980 chunk 1069 optimal weight: 6.9990 overall best weight: 2.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 ASN F 165 HIS F 552 ASN F 624 ASN K 22 ASN K 94 ASN ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 GLN K 752 HIS L 719 ASN ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 469 GLN M 869 ASN ** P 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 ASN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN R 575 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 794 HIS A 130 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN E 652 GLN E 747 ASN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 98214 Z= 0.242 Angle : 0.550 8.838 132992 Z= 0.292 Chirality : 0.040 0.318 15018 Planarity : 0.004 0.071 16680 Dihedral : 9.889 89.796 14584 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.95 % Allowed : 8.53 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.08), residues: 11606 helix: 0.37 (0.07), residues: 5884 sheet: 0.39 (0.27), residues: 470 loop : -1.22 (0.08), residues: 5252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 738 HIS 0.010 0.001 HIS F 165 PHE 0.024 0.001 PHE H 741 TYR 0.021 0.001 TYR C 422 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 972 time to evaluate : 8.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 573 MET cc_start: 0.6365 (mmt) cc_final: 0.6145 (mmt) REVERT: K 844 LEU cc_start: 0.8685 (mp) cc_final: 0.8366 (mp) REVERT: L 625 LEU cc_start: 0.8656 (tp) cc_final: 0.8414 (tt) REVERT: M 443 MET cc_start: 0.8141 (tpp) cc_final: 0.7870 (tpp) REVERT: M 873 SER cc_start: 0.9000 (m) cc_final: 0.8424 (t) REVERT: P 14 ILE cc_start: 0.8882 (mp) cc_final: 0.8622 (mt) REVERT: P 32 LEU cc_start: 0.8734 (tp) cc_final: 0.8507 (tp) REVERT: P 500 MET cc_start: 0.7936 (mmm) cc_final: 0.7734 (mpp) REVERT: P 564 ASP cc_start: 0.8225 (t0) cc_final: 0.7961 (t0) REVERT: P 604 MET cc_start: 0.8450 (tmm) cc_final: 0.7944 (tmm) REVERT: Q 289 MET cc_start: 0.9208 (tpp) cc_final: 0.8913 (tpp) REVERT: Q 539 MET cc_start: 0.8877 (ttm) cc_final: 0.8557 (ttm) REVERT: R 485 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7598 (mm-40) REVERT: R 500 MET cc_start: 0.5567 (mmt) cc_final: 0.5292 (tpp) REVERT: R 535 TYR cc_start: 0.4894 (m-10) cc_final: 0.4450 (m-80) REVERT: A 765 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (mtm) REVERT: B 41 LEU cc_start: 0.8717 (tp) cc_final: 0.8388 (tp) REVERT: B 626 ILE cc_start: 0.8763 (pt) cc_final: 0.8445 (pt) REVERT: B 765 MET cc_start: 0.8129 (ppp) cc_final: 0.7195 (tpp) REVERT: B 844 LEU cc_start: 0.8669 (mp) cc_final: 0.8400 (mp) REVERT: D 256 LEU cc_start: 0.8917 (mt) cc_final: 0.8650 (mt) REVERT: D 289 MET cc_start: 0.8084 (tpt) cc_final: 0.7541 (tpt) REVERT: E 32 LEU cc_start: 0.8653 (tp) cc_final: 0.8420 (tp) REVERT: E 430 TYR cc_start: 0.7285 (m-80) cc_final: 0.6761 (m-80) REVERT: E 444 ASP cc_start: 0.7814 (p0) cc_final: 0.7245 (t0) REVERT: E 564 ASP cc_start: 0.8157 (t0) cc_final: 0.7932 (t0) REVERT: E 604 MET cc_start: 0.8833 (tmm) cc_final: 0.8198 (tmm) REVERT: G 255 ARG cc_start: 0.7607 (ptt90) cc_final: 0.6790 (ptt90) REVERT: G 443 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7240 (mpp) REVERT: G 539 MET cc_start: 0.8766 (ttm) cc_final: 0.8535 (ttm) REVERT: G 855 ILE cc_start: 0.8664 (mm) cc_final: 0.8456 (mm) REVERT: H 481 TYR cc_start: 0.6679 (t80) cc_final: 0.6353 (t80) outliers start: 99 outliers final: 67 residues processed: 1026 average time/residue: 0.8640 time to fit residues: 1532.6043 Evaluate side-chains 946 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 877 time to evaluate : 8.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 850 ILE Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 171 GLU Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain Q residue 201 GLU Chi-restraints excluded: chain Q residue 656 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain H residue 737 VAL Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 594 optimal weight: 0.0670 chunk 332 optimal weight: 20.0000 chunk 890 optimal weight: 0.3980 chunk 728 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 1071 optimal weight: 7.9990 chunk 1157 optimal weight: 20.0000 chunk 954 optimal weight: 6.9990 chunk 1062 optimal weight: 0.1980 chunk 365 optimal weight: 0.1980 chunk 859 optimal weight: 4.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 GLN K 768 GLN ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 592 ASN M 744 ASN ** P 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 575 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D 744 ASN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 98214 Z= 0.144 Angle : 0.468 8.460 132992 Z= 0.246 Chirality : 0.037 0.308 15018 Planarity : 0.003 0.057 16680 Dihedral : 9.637 89.480 14582 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.08 % Allowed : 11.40 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.08), residues: 11606 helix: 0.65 (0.07), residues: 5926 sheet: 0.48 (0.27), residues: 462 loop : -1.19 (0.09), residues: 5218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 738 HIS 0.004 0.001 HIS R 118 PHE 0.025 0.001 PHE H 741 TYR 0.022 0.001 TYR G 436 ARG 0.007 0.000 ARG L 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 988 time to evaluate : 8.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 294 GLU cc_start: 0.7666 (tt0) cc_final: 0.7446 (tt0) REVERT: K 573 MET cc_start: 0.6399 (mmt) cc_final: 0.6185 (mmt) REVERT: K 604 MET cc_start: 0.7211 (tpp) cc_final: 0.6620 (tpt) REVERT: L 359 ARG cc_start: 0.6981 (mpt-90) cc_final: 0.4589 (ptt90) REVERT: M 354 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8867 (tm-30) REVERT: M 443 MET cc_start: 0.7884 (tpp) cc_final: 0.7559 (tpp) REVERT: M 873 SER cc_start: 0.8941 (m) cc_final: 0.8450 (t) REVERT: P 14 ILE cc_start: 0.8847 (mp) cc_final: 0.8598 (mt) REVERT: P 32 LEU cc_start: 0.8737 (tp) cc_final: 0.8436 (tp) REVERT: P 201 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7891 (tp30) REVERT: P 564 ASP cc_start: 0.8259 (t0) cc_final: 0.7909 (t0) REVERT: P 604 MET cc_start: 0.8463 (tmm) cc_final: 0.8111 (tmm) REVERT: Q 289 MET cc_start: 0.9182 (tpp) cc_final: 0.8916 (tpp) REVERT: Q 539 MET cc_start: 0.8626 (ttm) cc_final: 0.8319 (ttm) REVERT: R 222 ASP cc_start: 0.7234 (t0) cc_final: 0.6919 (t0) REVERT: R 227 PHE cc_start: 0.7868 (m-80) cc_final: 0.7438 (m-10) REVERT: R 380 MET cc_start: 0.6647 (mmp) cc_final: 0.6426 (mmp) REVERT: R 485 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7498 (mm-40) REVERT: R 500 MET cc_start: 0.5394 (mmt) cc_final: 0.5153 (tpp) REVERT: R 535 TYR cc_start: 0.4810 (m-10) cc_final: 0.4365 (m-80) REVERT: B 41 LEU cc_start: 0.8589 (tp) cc_final: 0.8274 (tp) REVERT: B 357 ASN cc_start: 0.7837 (m-40) cc_final: 0.7350 (m110) REVERT: B 380 MET cc_start: 0.8484 (mpp) cc_final: 0.8128 (mpp) REVERT: B 443 MET cc_start: 0.6347 (tmm) cc_final: 0.5761 (tmm) REVERT: B 765 MET cc_start: 0.8097 (ppp) cc_final: 0.7071 (mmt) REVERT: B 844 LEU cc_start: 0.8590 (mp) cc_final: 0.8338 (mp) REVERT: C 718 LYS cc_start: 0.7516 (ptmt) cc_final: 0.7248 (ptmm) REVERT: C 836 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8759 (mmtm) REVERT: D 256 LEU cc_start: 0.8751 (mt) cc_final: 0.8466 (mt) REVERT: D 289 MET cc_start: 0.7878 (tpt) cc_final: 0.7594 (tpt) REVERT: D 443 MET cc_start: 0.8370 (tpp) cc_final: 0.8073 (tpp) REVERT: E 32 LEU cc_start: 0.8654 (tp) cc_final: 0.8359 (tp) REVERT: E 430 TYR cc_start: 0.7266 (m-80) cc_final: 0.6865 (m-80) REVERT: E 444 ASP cc_start: 0.7783 (p0) cc_final: 0.7353 (t0) REVERT: E 564 ASP cc_start: 0.8163 (t0) cc_final: 0.7883 (t0) REVERT: E 604 MET cc_start: 0.8783 (tmm) cc_final: 0.8245 (tmm) REVERT: G 255 ARG cc_start: 0.7575 (ptt90) cc_final: 0.6819 (ptt90) REVERT: G 443 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7088 (mpp) REVERT: G 584 MET cc_start: 0.7999 (mmp) cc_final: 0.7793 (mmm) REVERT: H 227 PHE cc_start: 0.7806 (m-80) cc_final: 0.7387 (m-10) REVERT: H 288 TYR cc_start: 0.7680 (t80) cc_final: 0.7462 (t80) outliers start: 112 outliers final: 81 residues processed: 1062 average time/residue: 0.8505 time to fit residues: 1566.7697 Evaluate side-chains 963 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 881 time to evaluate : 8.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 515 VAL Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 863 CYS Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 171 GLU Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 558 VAL Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain P residue 845 LEU Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 560 ASN Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 775 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 380 MET Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 812 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1058 optimal weight: 1.9990 chunk 805 optimal weight: 0.8980 chunk 556 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 511 optimal weight: 6.9990 chunk 719 optimal weight: 10.0000 chunk 1075 optimal weight: 0.9980 chunk 1138 optimal weight: 6.9990 chunk 561 optimal weight: 20.0000 chunk 1019 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 560 ASN M 869 ASN P 295 GLN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 477 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 98214 Z= 0.176 Angle : 0.477 10.923 132992 Z= 0.248 Chirality : 0.038 0.162 15018 Planarity : 0.003 0.055 16680 Dihedral : 9.492 87.289 14582 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.52 % Allowed : 13.46 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.08), residues: 11606 helix: 0.75 (0.07), residues: 5954 sheet: 0.50 (0.27), residues: 472 loop : -1.22 (0.09), residues: 5180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 738 HIS 0.012 0.001 HIS A 839 PHE 0.025 0.001 PHE R 743 TYR 0.021 0.001 TYR G 436 ARG 0.011 0.000 ARG C 666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 924 time to evaluate : 8.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 573 MET cc_start: 0.6471 (mmt) cc_final: 0.6263 (mmt) REVERT: L 359 ARG cc_start: 0.7134 (mpt-90) cc_final: 0.4737 (ptt90) REVERT: M 354 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8819 (tm-30) REVERT: M 443 MET cc_start: 0.7767 (tpp) cc_final: 0.7468 (tpp) REVERT: M 873 SER cc_start: 0.8956 (m) cc_final: 0.8324 (t) REVERT: P 14 ILE cc_start: 0.8807 (mp) cc_final: 0.8561 (mt) REVERT: P 32 LEU cc_start: 0.8719 (tp) cc_final: 0.8460 (tp) REVERT: P 201 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7887 (tp30) REVERT: P 565 GLU cc_start: 0.7313 (pm20) cc_final: 0.7079 (pm20) REVERT: P 604 MET cc_start: 0.8442 (tmm) cc_final: 0.8005 (tmm) REVERT: Q 78 ARG cc_start: 0.6822 (tpp80) cc_final: 0.5952 (mmm160) REVERT: Q 289 MET cc_start: 0.9190 (tpp) cc_final: 0.8966 (tpp) REVERT: R 227 PHE cc_start: 0.7863 (m-80) cc_final: 0.7440 (m-10) REVERT: R 485 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7571 (mm-40) REVERT: R 535 TYR cc_start: 0.4842 (m-10) cc_final: 0.4414 (m-80) REVERT: R 549 HIS cc_start: 0.7150 (m90) cc_final: 0.6862 (m170) REVERT: B 41 LEU cc_start: 0.8584 (tp) cc_final: 0.8318 (tp) REVERT: B 132 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7147 (mtm) REVERT: B 357 ASN cc_start: 0.7838 (m-40) cc_final: 0.7383 (m110) REVERT: B 443 MET cc_start: 0.6320 (tmm) cc_final: 0.5664 (tmm) REVERT: B 573 MET cc_start: 0.6132 (mmt) cc_final: 0.5600 (mmt) REVERT: B 844 LEU cc_start: 0.8565 (mp) cc_final: 0.8263 (mp) REVERT: C 728 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7927 (mmt-90) REVERT: C 836 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8774 (mmtm) REVERT: D 289 MET cc_start: 0.7863 (tpt) cc_final: 0.7616 (tpt) REVERT: D 354 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 443 MET cc_start: 0.8224 (tpp) cc_final: 0.7828 (tpp) REVERT: E 32 LEU cc_start: 0.8657 (tp) cc_final: 0.8361 (tp) REVERT: E 198 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: E 564 ASP cc_start: 0.8180 (t0) cc_final: 0.7842 (t0) REVERT: E 604 MET cc_start: 0.8763 (tmm) cc_final: 0.8118 (tmm) REVERT: G 255 ARG cc_start: 0.7590 (ptt90) cc_final: 0.6786 (ptt90) REVERT: G 513 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7144 (tm-30) REVERT: G 584 MET cc_start: 0.7985 (mmp) cc_final: 0.7767 (mmm) REVERT: H 227 PHE cc_start: 0.7800 (m-80) cc_final: 0.7389 (m-10) REVERT: H 392 HIS cc_start: 0.7400 (m90) cc_final: 0.7187 (m170) REVERT: H 481 TYR cc_start: 0.6879 (t80) cc_final: 0.6525 (t80) REVERT: H 485 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7648 (mm-40) REVERT: H 511 PHE cc_start: 0.6164 (m-80) cc_final: 0.5712 (m-80) outliers start: 158 outliers final: 109 residues processed: 1039 average time/residue: 0.8803 time to fit residues: 1588.6492 Evaluate side-chains 979 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 868 time to evaluate : 8.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 132 MET Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 863 CYS Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 646 PHE Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 501 LEU Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain R residue 930 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 380 MET Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 754 THR Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 948 optimal weight: 3.9990 chunk 646 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 847 optimal weight: 7.9990 chunk 469 optimal weight: 0.9990 chunk 971 optimal weight: 0.0060 chunk 787 optimal weight: 9.9990 chunk 1 optimal weight: 0.0020 chunk 581 optimal weight: 5.9990 chunk 1022 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 918 ASN ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 98214 Z= 0.177 Angle : 0.475 11.360 132992 Z= 0.247 Chirality : 0.038 0.213 15018 Planarity : 0.003 0.059 16680 Dihedral : 9.401 88.406 14582 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.83 % Allowed : 14.41 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.08), residues: 11606 helix: 0.85 (0.07), residues: 5932 sheet: 0.50 (0.27), residues: 472 loop : -1.22 (0.08), residues: 5202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 738 HIS 0.005 0.001 HIS K 549 PHE 0.028 0.001 PHE E 842 TYR 0.024 0.001 TYR P 436 ARG 0.010 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 907 time to evaluate : 8.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 573 MET cc_start: 0.6515 (mmt) cc_final: 0.6254 (mmt) REVERT: K 725 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8798 (tt) REVERT: K 775 MET cc_start: 0.7267 (tmm) cc_final: 0.6779 (tmm) REVERT: K 808 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7527 (mm) REVERT: L 359 ARG cc_start: 0.7172 (mpt-90) cc_final: 0.4760 (ptt90) REVERT: L 669 MET cc_start: 0.7528 (mmp) cc_final: 0.7192 (mmp) REVERT: M 354 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8783 (tm-30) REVERT: M 443 MET cc_start: 0.7701 (tpp) cc_final: 0.7399 (tpp) REVERT: M 873 SER cc_start: 0.8917 (m) cc_final: 0.8310 (t) REVERT: P 14 ILE cc_start: 0.8795 (mp) cc_final: 0.8553 (mt) REVERT: P 32 LEU cc_start: 0.8664 (tp) cc_final: 0.8387 (tp) REVERT: P 201 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7884 (tp30) REVERT: P 363 ASP cc_start: 0.6990 (t0) cc_final: 0.6667 (t0) REVERT: P 604 MET cc_start: 0.8476 (tmm) cc_final: 0.7990 (tmm) REVERT: Q 289 MET cc_start: 0.9184 (tpp) cc_final: 0.8941 (tpp) REVERT: R 227 PHE cc_start: 0.7841 (m-80) cc_final: 0.7455 (m-10) REVERT: R 485 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7534 (mm-40) REVERT: R 549 HIS cc_start: 0.7044 (m90) cc_final: 0.6788 (m170) REVERT: A 93 LEU cc_start: 0.8286 (mt) cc_final: 0.8006 (mt) REVERT: B 41 LEU cc_start: 0.8572 (tp) cc_final: 0.8329 (tp) REVERT: B 357 ASN cc_start: 0.7820 (m-40) cc_final: 0.7365 (m110) REVERT: B 443 MET cc_start: 0.6475 (tmm) cc_final: 0.5785 (tmm) REVERT: B 765 MET cc_start: 0.8119 (ppp) cc_final: 0.6779 (mmt) REVERT: B 808 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7508 (mm) REVERT: B 844 LEU cc_start: 0.8474 (mp) cc_final: 0.8173 (mp) REVERT: C 836 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8781 (mmtm) REVERT: D 354 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 443 MET cc_start: 0.8187 (tpp) cc_final: 0.7727 (tpp) REVERT: E 32 LEU cc_start: 0.8645 (tp) cc_final: 0.8325 (tp) REVERT: E 604 MET cc_start: 0.8774 (tmm) cc_final: 0.8123 (tmm) REVERT: G 584 MET cc_start: 0.7997 (mmp) cc_final: 0.7778 (mmm) REVERT: H 227 PHE cc_start: 0.7796 (m-80) cc_final: 0.7394 (m-10) REVERT: H 539 MET cc_start: 0.4487 (ptp) cc_final: 0.1969 (mtm) REVERT: H 619 PHE cc_start: 0.7522 (m-80) cc_final: 0.7150 (m-10) outliers start: 190 outliers final: 153 residues processed: 1042 average time/residue: 0.8448 time to fit residues: 1531.1565 Evaluate side-chains 1029 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 873 time to evaluate : 8.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 515 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 554 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 863 CYS Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 531 LEU Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 484 SER Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 617 MET Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 501 LEU Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain R residue 930 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 380 MET Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 737 VAL Chi-restraints excluded: chain H residue 754 THR Chi-restraints excluded: chain H residue 812 THR Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 383 optimal weight: 9.9990 chunk 1025 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 668 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 1139 optimal weight: 20.0000 chunk 946 optimal weight: 6.9990 chunk 527 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 598 optimal weight: 0.9980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 ASN ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 ASN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS C 130 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN G 489 ASN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 98214 Z= 0.272 Angle : 0.524 10.234 132992 Z= 0.272 Chirality : 0.039 0.202 15018 Planarity : 0.003 0.054 16680 Dihedral : 9.429 89.294 14582 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.12 % Allowed : 15.50 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.08), residues: 11606 helix: 0.76 (0.07), residues: 5904 sheet: 0.26 (0.26), residues: 462 loop : -1.26 (0.08), residues: 5240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 738 HIS 0.005 0.001 HIS K 549 PHE 0.022 0.002 PHE M 227 TYR 0.024 0.001 TYR G 436 ARG 0.016 0.000 ARG Q 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 892 time to evaluate : 8.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 725 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8803 (tt) REVERT: K 808 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7585 (mm) REVERT: L 359 ARG cc_start: 0.7179 (mpt-90) cc_final: 0.4681 (ptt90) REVERT: M 354 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8744 (tm-30) REVERT: M 443 MET cc_start: 0.7625 (tpp) cc_final: 0.7409 (tpp) REVERT: M 873 SER cc_start: 0.8942 (m) cc_final: 0.8376 (t) REVERT: P 14 ILE cc_start: 0.8795 (mp) cc_final: 0.8565 (mt) REVERT: P 363 ASP cc_start: 0.7045 (t0) cc_final: 0.6778 (t0) REVERT: Q 289 MET cc_start: 0.9197 (tpp) cc_final: 0.8938 (tpp) REVERT: Q 539 MET cc_start: 0.8635 (ttm) cc_final: 0.8393 (ttm) REVERT: R 227 PHE cc_start: 0.7955 (m-80) cc_final: 0.7546 (m-10) REVERT: R 380 MET cc_start: 0.6931 (mmp) cc_final: 0.6581 (mmp) REVERT: R 485 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7561 (mm-40) REVERT: R 535 TYR cc_start: 0.5353 (m-10) cc_final: 0.4985 (m-10) REVERT: R 539 MET cc_start: 0.4002 (ptt) cc_final: 0.2048 (mtm) REVERT: R 549 HIS cc_start: 0.7161 (m90) cc_final: 0.6850 (m170) REVERT: R 742 TYR cc_start: 0.7998 (t80) cc_final: 0.7519 (t80) REVERT: B 41 LEU cc_start: 0.8657 (tp) cc_final: 0.8357 (tp) REVERT: B 357 ASN cc_start: 0.7864 (m-40) cc_final: 0.7252 (m110) REVERT: B 443 MET cc_start: 0.6480 (tmm) cc_final: 0.5737 (tmm) REVERT: B 765 MET cc_start: 0.8147 (ppp) cc_final: 0.6738 (mmt) REVERT: B 808 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7583 (mm) REVERT: B 844 LEU cc_start: 0.8513 (mp) cc_final: 0.8185 (mp) REVERT: C 289 MET cc_start: 0.8946 (tpp) cc_final: 0.8731 (tpt) REVERT: C 824 ILE cc_start: 0.6774 (tt) cc_final: 0.6567 (mt) REVERT: D 256 LEU cc_start: 0.8813 (mt) cc_final: 0.8524 (mt) REVERT: D 354 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8712 (tm-30) REVERT: D 443 MET cc_start: 0.8065 (tpp) cc_final: 0.7587 (tpp) REVERT: E 604 MET cc_start: 0.8816 (tmm) cc_final: 0.8127 (tmm) REVERT: G 255 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7327 (ptt90) REVERT: G 584 MET cc_start: 0.8037 (mmp) cc_final: 0.7808 (mmm) REVERT: H 227 PHE cc_start: 0.7894 (m-80) cc_final: 0.7467 (m-10) REVERT: H 511 PHE cc_start: 0.6132 (m-80) cc_final: 0.5533 (m-80) REVERT: H 539 MET cc_start: 0.4462 (ptp) cc_final: 0.2129 (mtm) REVERT: H 619 PHE cc_start: 0.7595 (m-80) cc_final: 0.7136 (m-10) outliers start: 220 outliers final: 182 residues processed: 1052 average time/residue: 0.8440 time to fit residues: 1547.1401 Evaluate side-chains 1043 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 857 time to evaluate : 8.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 515 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 554 CYS Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 863 CYS Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 531 LEU Chi-restraints excluded: chain L residue 643 THR Chi-restraints excluded: chain L residue 646 PHE Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain L residue 858 VAL Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 443 MET Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 557 VAL Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 301 LEU Chi-restraints excluded: chain Q residue 394 THR Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 480 ILE Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 501 LEU Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain R residue 930 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 737 VAL Chi-restraints excluded: chain H residue 754 THR Chi-restraints excluded: chain H residue 812 THR Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1098 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 649 optimal weight: 8.9990 chunk 832 optimal weight: 0.7980 chunk 644 optimal weight: 5.9990 chunk 959 optimal weight: 6.9990 chunk 636 optimal weight: 0.9980 chunk 1135 optimal weight: 4.9990 chunk 710 optimal weight: 10.0000 chunk 692 optimal weight: 1.9990 chunk 524 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 ASN ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 ASN ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 ASN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 155 ASN B 268 ASN C 130 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 98214 Z= 0.147 Angle : 0.472 12.536 132992 Z= 0.245 Chirality : 0.037 0.219 15018 Planarity : 0.003 0.055 16680 Dihedral : 9.271 89.304 14582 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.93 % Allowed : 16.25 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.08), residues: 11606 helix: 0.96 (0.07), residues: 5918 sheet: 0.43 (0.26), residues: 476 loop : -1.19 (0.09), residues: 5212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 550 HIS 0.005 0.001 HIS K 549 PHE 0.024 0.001 PHE F 227 TYR 0.025 0.001 TYR P 436 ARG 0.018 0.000 ARG Q 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 926 time to evaluate : 8.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 792 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7369 (tt) REVERT: K 725 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (tt) REVERT: K 808 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7537 (mm) REVERT: L 359 ARG cc_start: 0.7173 (mpt-90) cc_final: 0.4682 (ptt90) REVERT: L 669 MET cc_start: 0.7432 (mmp) cc_final: 0.7176 (mmp) REVERT: M 354 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8691 (tm-30) REVERT: M 443 MET cc_start: 0.7565 (tpp) cc_final: 0.7347 (tpp) REVERT: M 494 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8089 (tt) REVERT: M 873 SER cc_start: 0.8929 (m) cc_final: 0.8363 (t) REVERT: P 14 ILE cc_start: 0.8755 (mp) cc_final: 0.8515 (mt) REVERT: P 201 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7766 (tp30) REVERT: P 363 ASP cc_start: 0.7026 (t0) cc_final: 0.6709 (t0) REVERT: Q 289 MET cc_start: 0.9166 (tpp) cc_final: 0.8906 (tpp) REVERT: R 227 PHE cc_start: 0.7838 (m-80) cc_final: 0.7465 (m-10) REVERT: R 380 MET cc_start: 0.6859 (mmp) cc_final: 0.6635 (tpp) REVERT: R 535 TYR cc_start: 0.5370 (m-10) cc_final: 0.4871 (m-10) REVERT: R 539 MET cc_start: 0.4123 (ptt) cc_final: 0.2239 (mtm) REVERT: R 742 TYR cc_start: 0.7914 (t80) cc_final: 0.7461 (t80) REVERT: B 357 ASN cc_start: 0.7747 (m-40) cc_final: 0.7242 (m110) REVERT: B 443 MET cc_start: 0.6363 (tmm) cc_final: 0.5663 (tmm) REVERT: B 765 MET cc_start: 0.8143 (ppp) cc_final: 0.6703 (mmt) REVERT: B 808 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7547 (mm) REVERT: C 824 ILE cc_start: 0.6852 (tt) cc_final: 0.6621 (mt) REVERT: D 256 LEU cc_start: 0.8717 (mt) cc_final: 0.8423 (mt) REVERT: D 354 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8668 (tm-30) REVERT: D 443 MET cc_start: 0.8011 (tpp) cc_final: 0.7564 (tpp) REVERT: D 818 GLU cc_start: 0.8149 (pp20) cc_final: 0.7906 (pp20) REVERT: E 604 MET cc_start: 0.8795 (tmm) cc_final: 0.8156 (tmm) REVERT: G 584 MET cc_start: 0.8001 (mmp) cc_final: 0.7760 (mmm) REVERT: H 227 PHE cc_start: 0.7775 (m-80) cc_final: 0.7380 (m-10) REVERT: H 266 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: H 485 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7552 (mm-40) REVERT: H 539 MET cc_start: 0.4339 (ptp) cc_final: 0.1951 (mtm) outliers start: 201 outliers final: 153 residues processed: 1080 average time/residue: 0.8471 time to fit residues: 1589.7589 Evaluate side-chains 1037 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 878 time to evaluate : 8.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 515 VAL Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 531 LEU Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain L residue 858 VAL Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 494 LEU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 484 SER Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 811 VAL Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 301 LEU Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 565 GLU Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 812 THR Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 702 optimal weight: 7.9990 chunk 453 optimal weight: 8.9990 chunk 678 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 721 optimal weight: 7.9990 chunk 773 optimal weight: 0.6980 chunk 561 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 892 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 ASN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 499 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN C 276 GLN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 98214 Z= 0.182 Angle : 0.489 10.951 132992 Z= 0.253 Chirality : 0.038 0.230 15018 Planarity : 0.003 0.055 16680 Dihedral : 9.215 89.664 14582 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 16.69 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.08), residues: 11606 helix: 0.96 (0.07), residues: 5950 sheet: 0.40 (0.26), residues: 476 loop : -1.21 (0.09), residues: 5180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 550 HIS 0.020 0.001 HIS B 583 PHE 0.025 0.001 PHE F 227 TYR 0.025 0.001 TYR P 436 ARG 0.013 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 895 time to evaluate : 8.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 792 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7469 (tt) REVERT: K 107 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (mt) REVERT: K 725 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8732 (tt) REVERT: K 808 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7753 (mm) REVERT: L 669 MET cc_start: 0.7375 (mmp) cc_final: 0.7099 (mmp) REVERT: M 354 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8667 (tm-30) REVERT: M 443 MET cc_start: 0.7553 (tpp) cc_final: 0.7334 (tpp) REVERT: M 873 SER cc_start: 0.8999 (m) cc_final: 0.8406 (t) REVERT: P 14 ILE cc_start: 0.8762 (mp) cc_final: 0.8518 (mt) REVERT: P 201 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7858 (tp30) REVERT: P 363 ASP cc_start: 0.6993 (t0) cc_final: 0.6684 (t0) REVERT: P 431 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7828 (tpt90) REVERT: Q 289 MET cc_start: 0.9181 (tpp) cc_final: 0.8948 (tpp) REVERT: R 186 GLN cc_start: 0.5168 (tm-30) cc_final: 0.4336 (tt0) REVERT: R 227 PHE cc_start: 0.7871 (m-80) cc_final: 0.7497 (m-10) REVERT: R 535 TYR cc_start: 0.5322 (m-10) cc_final: 0.4818 (m-10) REVERT: R 539 MET cc_start: 0.4334 (ptt) cc_final: 0.2392 (mtm) REVERT: R 742 TYR cc_start: 0.7918 (t80) cc_final: 0.7524 (t80) REVERT: A 774 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 357 ASN cc_start: 0.7775 (m-40) cc_final: 0.7172 (m110) REVERT: B 443 MET cc_start: 0.6258 (tmm) cc_final: 0.5541 (tmm) REVERT: B 765 MET cc_start: 0.8153 (ppp) cc_final: 0.6796 (mmt) REVERT: B 808 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7559 (mm) REVERT: C 571 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.1994 (mm) REVERT: C 824 ILE cc_start: 0.6948 (tt) cc_final: 0.6726 (mt) REVERT: D 256 LEU cc_start: 0.8701 (mt) cc_final: 0.8435 (mt) REVERT: D 354 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 443 MET cc_start: 0.8002 (tpp) cc_final: 0.7508 (tpp) REVERT: D 818 GLU cc_start: 0.8145 (pp20) cc_final: 0.7863 (pp20) REVERT: E 604 MET cc_start: 0.8799 (tmm) cc_final: 0.8144 (tmm) REVERT: G 584 MET cc_start: 0.8000 (mmp) cc_final: 0.7754 (mmm) REVERT: H 227 PHE cc_start: 0.7788 (m-80) cc_final: 0.7406 (m-10) REVERT: H 539 MET cc_start: 0.4241 (ptp) cc_final: 0.1826 (mtm) outliers start: 205 outliers final: 165 residues processed: 1046 average time/residue: 0.8485 time to fit residues: 1543.2721 Evaluate side-chains 1044 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 871 time to evaluate : 8.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 515 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 531 LEU Chi-restraints excluded: chain L residue 643 THR Chi-restraints excluded: chain L residue 707 SER Chi-restraints excluded: chain L residue 858 VAL Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 171 GLU Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 342 ILE Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 431 ARG Chi-restraints excluded: chain P residue 443 MET Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 484 SER Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 643 THR Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 811 VAL Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 281 VAL Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 301 LEU Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 501 LEU Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 VAL Chi-restraints excluded: chain E residue 565 GLU Chi-restraints excluded: chain E residue 643 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 478 CYS Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 812 THR Chi-restraints excluded: chain H residue 930 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 1032 optimal weight: 0.8980 chunk 1087 optimal weight: 6.9990 chunk 992 optimal weight: 4.9990 chunk 1058 optimal weight: 2.9990 chunk 636 optimal weight: 0.9980 chunk 460 optimal weight: 0.6980 chunk 830 optimal weight: 0.7980 chunk 324 optimal weight: 0.9990 chunk 956 optimal weight: 2.9990 chunk 1000 optimal weight: 10.0000 chunk 1054 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 ASN ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 499 GLN R 513 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 98214 Z= 0.130 Angle : 0.473 10.723 132992 Z= 0.244 Chirality : 0.037 0.218 15018 Planarity : 0.003 0.054 16680 Dihedral : 9.065 88.974 14582 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 17.33 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.08), residues: 11606 helix: 1.09 (0.07), residues: 5960 sheet: 0.53 (0.27), residues: 476 loop : -1.17 (0.09), residues: 5170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 550 HIS 0.018 0.001 HIS B 583 PHE 0.025 0.001 PHE F 227 TYR 0.022 0.001 TYR P 436 ARG 0.012 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 945 time to evaluate : 8.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 792 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7428 (tt) REVERT: K 107 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8066 (mt) REVERT: K 725 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8663 (tt) REVERT: K 808 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (mm) REVERT: L 359 ARG cc_start: 0.7268 (mpt-90) cc_final: 0.4747 (ptt90) REVERT: M 354 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8653 (tm-30) REVERT: M 443 MET cc_start: 0.7528 (tpp) cc_final: 0.7310 (tpp) REVERT: M 873 SER cc_start: 0.8975 (m) cc_final: 0.8435 (t) REVERT: P 14 ILE cc_start: 0.8725 (mp) cc_final: 0.8493 (mt) REVERT: P 201 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7811 (tp30) REVERT: P 363 ASP cc_start: 0.6888 (t0) cc_final: 0.6663 (t0) REVERT: Q 289 MET cc_start: 0.9141 (tpp) cc_final: 0.8860 (tpp) REVERT: R 186 GLN cc_start: 0.4978 (tm-30) cc_final: 0.4222 (tt0) REVERT: R 227 PHE cc_start: 0.7798 (m-80) cc_final: 0.7486 (m-10) REVERT: R 535 TYR cc_start: 0.5228 (m-10) cc_final: 0.4805 (m-10) REVERT: R 539 MET cc_start: 0.4210 (ptt) cc_final: 0.2265 (mtm) REVERT: A 255 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7422 (mtt90) REVERT: A 774 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 357 ASN cc_start: 0.7678 (m-40) cc_final: 0.7206 (m110) REVERT: B 380 MET cc_start: 0.8642 (tpp) cc_final: 0.8361 (mpp) REVERT: B 385 ASP cc_start: 0.8313 (t0) cc_final: 0.8103 (t0) REVERT: B 440 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6848 (mtp85) REVERT: B 765 MET cc_start: 0.8120 (ppp) cc_final: 0.6759 (mmt) REVERT: B 808 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7467 (mm) REVERT: C 783 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6571 (mm) REVERT: C 824 ILE cc_start: 0.6951 (tt) cc_final: 0.6600 (mt) REVERT: D 354 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8617 (tm-30) REVERT: D 443 MET cc_start: 0.8030 (tpp) cc_final: 0.7533 (tpp) REVERT: E 564 ASP cc_start: 0.8085 (t0) cc_final: 0.7882 (t0) REVERT: E 604 MET cc_start: 0.8791 (tmm) cc_final: 0.8083 (tmm) REVERT: G 584 MET cc_start: 0.7977 (mmp) cc_final: 0.7736 (mmm) REVERT: H 227 PHE cc_start: 0.7704 (m-80) cc_final: 0.7361 (m-10) REVERT: H 266 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: H 481 TYR cc_start: 0.6746 (t80) cc_final: 0.6522 (t80) REVERT: H 539 MET cc_start: 0.4254 (ptp) cc_final: 0.1880 (mtm) outliers start: 165 outliers final: 138 residues processed: 1067 average time/residue: 0.8507 time to fit residues: 1579.9585 Evaluate side-chains 1035 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 888 time to evaluate : 8.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 366 MET Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 462 THR Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 643 THR Chi-restraints excluded: chain L residue 858 VAL Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 171 GLU Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 392 HIS Chi-restraints excluded: chain P residue 431 ARG Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 811 VAL Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 815 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 812 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 694 optimal weight: 3.9990 chunk 1118 optimal weight: 0.9990 chunk 682 optimal weight: 4.9990 chunk 530 optimal weight: 0.0030 chunk 777 optimal weight: 4.9990 chunk 1173 optimal weight: 30.0000 chunk 1080 optimal weight: 7.9990 chunk 934 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 721 optimal weight: 0.7980 chunk 573 optimal weight: 7.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 499 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 98214 Z= 0.140 Angle : 0.484 11.591 132992 Z= 0.248 Chirality : 0.037 0.448 15018 Planarity : 0.003 0.057 16680 Dihedral : 9.036 89.360 14582 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.50 % Allowed : 17.63 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.08), residues: 11606 helix: 1.14 (0.07), residues: 5952 sheet: 0.59 (0.27), residues: 476 loop : -1.14 (0.09), residues: 5178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 660 HIS 0.018 0.001 HIS B 583 PHE 0.028 0.001 PHE F 227 TYR 0.029 0.001 TYR P 436 ARG 0.014 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23212 Ramachandran restraints generated. 11606 Oldfield, 0 Emsley, 11606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 907 time to evaluate : 9.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 792 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7424 (tt) REVERT: K 107 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8051 (mt) REVERT: K 725 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8650 (tt) REVERT: K 808 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7758 (mm) REVERT: L 359 ARG cc_start: 0.7294 (mpt-90) cc_final: 0.4768 (ptt90) REVERT: M 354 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8659 (tm-30) REVERT: M 443 MET cc_start: 0.7513 (tpp) cc_final: 0.7295 (tpp) REVERT: M 873 SER cc_start: 0.8966 (m) cc_final: 0.8434 (t) REVERT: P 14 ILE cc_start: 0.8731 (mp) cc_final: 0.8495 (mt) REVERT: P 201 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7804 (tp30) REVERT: P 363 ASP cc_start: 0.6940 (t0) cc_final: 0.6657 (t0) REVERT: Q 289 MET cc_start: 0.9159 (tpp) cc_final: 0.8922 (tpp) REVERT: R 227 PHE cc_start: 0.7782 (m-80) cc_final: 0.7483 (m-10) REVERT: R 535 TYR cc_start: 0.5291 (m-10) cc_final: 0.4855 (m-10) REVERT: R 539 MET cc_start: 0.4283 (ptt) cc_final: 0.2243 (mtm) REVERT: A 774 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 357 ASN cc_start: 0.7688 (m-40) cc_final: 0.7188 (m110) REVERT: B 380 MET cc_start: 0.8675 (tpp) cc_final: 0.8388 (mpp) REVERT: B 440 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6747 (mtp85) REVERT: B 765 MET cc_start: 0.8141 (ppp) cc_final: 0.6783 (mmt) REVERT: B 808 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7470 (mm) REVERT: C 544 ILE cc_start: 0.3810 (mm) cc_final: 0.3590 (tp) REVERT: C 571 LEU cc_start: 0.1955 (OUTLIER) cc_final: 0.1568 (mm) REVERT: C 783 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6574 (mm) REVERT: C 824 ILE cc_start: 0.7016 (tt) cc_final: 0.6703 (mt) REVERT: D 354 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8624 (tm-30) REVERT: D 443 MET cc_start: 0.7936 (tpp) cc_final: 0.7494 (tpp) REVERT: E 604 MET cc_start: 0.8771 (tmm) cc_final: 0.8090 (tmm) REVERT: G 291 GLU cc_start: 0.7875 (tp30) cc_final: 0.7628 (tp30) REVERT: H 227 PHE cc_start: 0.7680 (m-80) cc_final: 0.7351 (m-10) REVERT: H 266 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: H 511 PHE cc_start: 0.6202 (m-80) cc_final: 0.5734 (m-80) REVERT: H 539 MET cc_start: 0.4196 (ptp) cc_final: 0.1952 (mtm) outliers start: 156 outliers final: 139 residues processed: 1029 average time/residue: 0.8547 time to fit residues: 1534.0992 Evaluate side-chains 1034 residues out of total 10390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 886 time to evaluate : 8.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 140 TYR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 366 MET Chi-restraints excluded: chain K residue 444 ASP Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 725 ILE Chi-restraints excluded: chain K residue 727 ILE Chi-restraints excluded: chain K residue 795 SER Chi-restraints excluded: chain K residue 808 LEU Chi-restraints excluded: chain K residue 892 TRP Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 472 SER Chi-restraints excluded: chain L residue 643 THR Chi-restraints excluded: chain L residue 858 VAL Chi-restraints excluded: chain L residue 923 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 294 GLU Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 869 ASN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 358 LEU Chi-restraints excluded: chain P residue 392 HIS Chi-restraints excluded: chain P residue 431 ARG Chi-restraints excluded: chain P residue 445 SER Chi-restraints excluded: chain P residue 597 ASN Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 811 VAL Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 283 LEU Chi-restraints excluded: chain Q residue 446 LEU Chi-restraints excluded: chain Q residue 797 SER Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 386 PHE Chi-restraints excluded: chain R residue 443 MET Chi-restraints excluded: chain R residue 478 CYS Chi-restraints excluded: chain R residue 508 VAL Chi-restraints excluded: chain R residue 574 VAL Chi-restraints excluded: chain R residue 649 VAL Chi-restraints excluded: chain R residue 846 ILE Chi-restraints excluded: chain R residue 914 ILE Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 795 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 863 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 554 CYS Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 386 PHE Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 574 VAL Chi-restraints excluded: chain H residue 812 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1178 random chunks: chunk 742 optimal weight: 10.0000 chunk 995 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 861 optimal weight: 0.0980 chunk 137 optimal weight: 0.0470 chunk 259 optimal weight: 8.9990 chunk 936 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 961 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 898 ASN K 118 HIS ** K 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 768 GLN ** K 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN R 499 GLN ** R 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 118 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 HIS ** G 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111888 restraints weight = 206913.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114719 restraints weight = 133760.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115835 restraints weight = 99609.363| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 98214 Z= 0.132 Angle : 0.479 11.877 132992 Z= 0.245 Chirality : 0.037 0.305 15018 Planarity : 0.003 0.057 16680 Dihedral : 8.966 89.443 14582 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.55 % Allowed : 17.74 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.08), residues: 11606 helix: 1.19 (0.07), residues: 5960 sheet: 0.68 (0.27), residues: 476 loop : -1.12 (0.09), residues: 5170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 550 HIS 0.017 0.001 HIS B 583 PHE 0.027 0.001 PHE F 227 TYR 0.030 0.001 TYR P 436 ARG 0.014 0.000 ARG B 78 =============================================================================== Job complete usr+sys time: 22783.84 seconds wall clock time: 402 minutes 24.25 seconds (24144.25 seconds total)