Starting phenix.real_space_refine on Tue Mar 19 11:31:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr9_34964/03_2024/8hr9_34964_neut_updated.pdb" } resolution = 3.03 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 30 5.49 5 S 434 5.16 5 C 59164 2.51 5 N 16046 2.21 5 O 17720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E GLU 818": "OE1" <-> "OE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F GLU 761": "OE1" <-> "OE2" Residue "F GLU 818": "OE1" <-> "OE2" Residue "G GLU 790": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 359": "NH1" <-> "NH2" Residue "H GLU 488": "OE1" <-> "OE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I GLU 473": "OE1" <-> "OE2" Residue "J GLU 333": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "K GLU 565": "OE1" <-> "OE2" Residue "L PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 327": "OE1" <-> "OE2" Residue "L GLU 818": "OE1" <-> "OE2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "M PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 326": "OE1" <-> "OE2" Residue "M GLU 471": "OE1" <-> "OE2" Residue "M GLU 488": "OE1" <-> "OE2" Residue "M GLU 529": "OE1" <-> "OE2" Residue "M GLU 761": "OE1" <-> "OE2" Residue "M GLU 818": "OE1" <-> "OE2" Residue "N GLU 789": "OE1" <-> "OE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93394 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "C" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6655 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "D" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "E" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6633 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 809} Chain breaks: 5 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: "F" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6658 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "G" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6617 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 23, 'TRANS': 806} Chain breaks: 5 Chain: "H" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6653 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 5 Chain: "I" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "J" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6655 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "K" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "L" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6633 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 809} Chain breaks: 5 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: "M" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6658 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "N" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6617 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 23, 'TRANS': 806} Chain breaks: 5 Chain: "O" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6653 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" 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} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "O" 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: 35.44, per 1000 atoms: 0.38 Number of scatterers: 93394 At special positions: 0 Unit cell: (250.64, 167.44, 161.2, 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 434 16.00 P 30 15.00 O 17720 8.00 N 16046 7.00 C 59164 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=0, symmetry=0 Time building additional restraints: 29.07 Conformation dependent library (CDL) restraints added in 12.9 seconds 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 546 helices and 42 sheets defined 54.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.80 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.544A pdb=" N SER A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.623A pdb=" N GLU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.666A pdb=" N SER A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.666A pdb=" N ASP A 232 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 235 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 240 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.517A pdb=" N GLN A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.503A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 4.031A pdb=" N GLU A 285 " --> pdb=" O VAL A 281 " (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 317 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 376 through 394 removed outlier: 3.516A pdb=" N ASP A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.638A pdb=" N GLY A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.624A pdb=" N PHE A 451 " --> pdb=" O CYS A 447 " (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 474 through 489 removed outlier: 4.130A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 504 through 514 removed outlier: 3.724A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.826A pdb=" N ALA A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 4.207A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 639 through 647 removed outlier: 4.142A pdb=" N THR A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 removed outlier: 4.191A pdb=" N LYS A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 731 through 751 removed outlier: 3.615A pdb=" N ASP A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 771 through 793 removed outlier: 3.617A pdb=" N MET A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 830 removed outlier: 3.614A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 removed outlier: 3.647A pdb=" N LEU A 844 " --> pdb=" O PRO A 840 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) 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: 3.962A pdb=" N SER A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.704A pdb=" N ASN C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 121 through 139 removed outlier: 4.131A pdb=" N LYS C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 3.632A pdb=" N GLU C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 174 through 180 removed outlier: 4.237A pdb=" N SER C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.589A pdb=" N TRP C 231 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 232 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 235 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 239 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE C 240 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 269 removed outlier: 3.979A pdb=" N TYR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 276 No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.944A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 314 through 317 No H-bonds generated for 'chain 'C' and resid 314 through 317' Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.559A pdb=" N TYR C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 413 through 432 removed outlier: 3.772A pdb=" N GLY C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 429 " --> pdb=" O MET C 425 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 457 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 489 removed outlier: 3.579A pdb=" N ILE C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.610A pdb=" N LEU C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 499 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 514 removed outlier: 4.113A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 509 " --> pdb=" O CYS C 505 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 514 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 539 removed outlier: 3.894A pdb=" N ILE C 532 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 removed outlier: 3.853A pdb=" N CYS C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' 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 598 through 605 removed outlier: 3.538A pdb=" N ALA C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 632 removed outlier: 3.546A pdb=" N ALA C 628 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 3.816A pdb=" N ALA C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL C 649 " --> pdb=" O ALA C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 721 removed outlier: 3.614A pdb=" N THR C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS C 712 " --> pdb=" O ASP C 708 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 731 through 751 Processing helix chain 'C' and resid 771 through 793 removed outlier: 3.952A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 830 Processing helix chain 'C' and resid 835 through 838 No H-bonds generated for 'chain 'C' and resid 835 through 838' Processing helix chain 'C' and resid 840 through 846 Processing helix chain 'C' and resid 852 through 855 No H-bonds generated for 'chain 'C' and resid 852 through 855' Processing helix chain 'C' and resid 865 through 882 removed outlier: 3.929A pdb=" N ASN C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS C 870 " --> pdb=" O LYS C 866 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 880 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 896 No H-bonds generated for 'chain 'C' and resid 893 through 896' Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.982A pdb=" N ASP D 39 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 48 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.585A pdb=" N SER D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 3.698A pdb=" N LYS D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 168 removed outlier: 3.775A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.657A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP D 231 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D 232 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 235 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 239 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.565A pdb=" N ASN D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.983A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS D 292 " --> pdb=" O TYR D 288 " (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 344 through 356 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 376 through 394 Processing helix chain 'D' and resid 413 through 431 removed outlier: 3.929A pdb=" N SER D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 457 removed outlier: 3.629A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.527A pdb=" N SER D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.640A pdb=" N MET D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.531A pdb=" N ILE D 510 " --> pdb=" O GLY D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 518 No H-bonds generated for 'chain 'D' and resid 515 through 518' Processing helix chain 'D' and resid 527 through 539 removed outlier: 3.593A pdb=" N SER D 533 " --> pdb=" O GLU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 558 removed outlier: 4.207A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 557 " --> pdb=" O ARG D 553 " (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 602 through 607 Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 639 through 650 removed outlier: 3.904A pdb=" N THR D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASN D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA D 645 " --> pdb=" O ALA D 641 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.985A pdb=" N ASP D 708 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D 711 " --> pdb=" O ASP D 708 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP D 716 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 717 " --> pdb=" O GLU D 714 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 721 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 722 " --> pdb=" O ASN D 719 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 724 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 725 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 751 Processing helix chain 'D' and resid 771 through 793 removed outlier: 3.746A pdb=" N PHE D 777 " --> pdb=" O LYS D 773 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 779 " --> pdb=" O MET D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 830 removed outlier: 3.554A pdb=" N LYS D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 846 Processing helix chain 'D' and resid 852 through 855 No H-bonds generated for 'chain 'D' and resid 852 through 855' Processing helix chain 'D' and resid 858 through 860 No H-bonds generated for 'chain 'D' and resid 858 through 860' Processing helix chain 'D' and resid 865 through 882 removed outlier: 3.863A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 871 " --> pdb=" O ALA D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 896 removed outlier: 4.063A pdb=" N TYR D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 919 No H-bonds generated for 'chain 'D' and resid 916 through 919' 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 34 through 47 removed outlier: 3.977A pdb=" N ASP E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 42 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 43 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.760A pdb=" N VAL E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 137 Processing helix chain 'E' and resid 143 through 167 removed outlier: 3.689A pdb=" N GLN E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 180 removed outlier: 4.081A pdb=" N SER E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 227 through 240 removed outlier: 3.521A pdb=" N GLY E 230 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP E 232 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 235 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 238 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE E 240 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 267 removed outlier: 3.527A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 301 removed outlier: 3.589A pdb=" N GLN E 296 " --> pdb=" O HIS E 292 " (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 344 through 355 removed outlier: 3.508A pdb=" N GLY E 349 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 354 " --> pdb=" O ASP E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 376 through 394 removed outlier: 4.349A pdb=" N LYS E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 445 through 457 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 490 removed outlier: 3.715A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'E' and resid 504 through 514 removed outlier: 3.943A pdb=" N VAL E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 509 " --> pdb=" O CYS E 505 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 539 removed outlier: 3.525A pdb=" N GLU E 534 " --> pdb=" O GLN E 530 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET E 539 " --> pdb=" O TYR E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 558 removed outlier: 3.892A 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 600 through 606 removed outlier: 3.612A pdb=" N SER E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 633 removed outlier: 3.516A pdb=" N ALA E 630 " --> pdb=" O ILE E 626 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP E 631 " --> pdb=" O GLY E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 648 removed outlier: 4.088A pdb=" N ASN E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 726 removed outlier: 3.734A pdb=" N LYS E 712 " --> pdb=" O ASP E 708 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU E 722 " --> pdb=" O LYS E 718 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE E 725 " --> pdb=" O ASN E 721 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY E 726 " --> pdb=" O GLU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 752 Processing helix chain 'E' and resid 771 through 793 Processing helix chain 'E' and resid 815 through 830 removed outlier: 3.504A pdb=" N LYS E 820 " --> pdb=" O GLU E 816 " (cutoff:3.500A) 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 858 through 860 No H-bonds generated for 'chain 'E' and resid 858 through 860' Processing helix chain 'E' and resid 865 through 882 removed outlier: 3.872A pdb=" N ASN E 869 " --> pdb=" O VAL E 865 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 870 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 896 removed outlier: 3.685A pdb=" N THR E 896 " --> pdb=" O TRP E 892 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 919 No H-bonds generated for 'chain 'E' and resid 917 through 919' Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.578A pdb=" N ILE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 121 through 139 removed outlier: 3.568A pdb=" N LYS F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 167 removed outlier: 3.775A pdb=" N HIS F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 166 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.950A 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: 3.906A pdb=" N TRP F 231 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 235 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 238 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 239 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 301 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 317 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 362 through 372 removed outlier: 4.568A pdb=" N TYR F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 394 removed outlier: 3.752A pdb=" N THR F 388 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 432 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 443 through 457 removed outlier: 3.504A pdb=" N PHE F 451 " --> pdb=" O CYS F 447 " (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 489 removed outlier: 3.793A pdb=" N ILE F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR F 481 " --> pdb=" O ASN F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 502 removed outlier: 3.662A pdb=" N MET F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 515 removed outlier: 4.020A pdb=" N VAL F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 514 " --> pdb=" O ILE F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 539 Processing helix chain 'F' and resid 547 through 560 removed outlier: 3.562A pdb=" N VAL F 558 " --> pdb=" O CYS F 554 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 559 " --> pdb=" O CYS F 555 " (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 599 through 606 Processing helix chain 'F' and resid 622 through 634 Processing helix chain 'F' and resid 639 through 645 removed outlier: 3.960A pdb=" N ASN F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 726 removed outlier: 3.543A pdb=" N GLU F 722 " --> pdb=" O LYS F 718 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE F 725 " --> pdb=" O ASN F 721 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY F 726 " --> pdb=" O GLU F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 748 Processing helix chain 'F' and resid 771 through 792 removed outlier: 3.784A pdb=" N PHE F 777 " --> pdb=" O LYS F 773 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 791 " --> pdb=" O LEU F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 830 removed outlier: 4.204A pdb=" N LYS F 820 " --> pdb=" O GLU F 816 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE F 821 " --> pdb=" O PHE F 817 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 826 " --> pdb=" O LYS F 822 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 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 869 through 882 removed outlier: 3.618A pdb=" N ILE F 878 " --> pdb=" O PHE F 874 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU F 880 " --> pdb=" O LYS F 876 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 881 " --> pdb=" O LEU F 877 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 895 removed outlier: 3.902A pdb=" N LEU F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.729A pdb=" N VAL G 42 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU G 43 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 49 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.577A pdb=" N SER G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 139 removed outlier: 3.523A pdb=" N MET G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 167 removed outlier: 3.535A pdb=" N GLN G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 180 removed outlier: 3.631A pdb=" N SER G 178 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.558A pdb=" N ASP G 232 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU G 235 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG G 238 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS G 239 " --> pdb=" O SER G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.512A pdb=" N GLY G 263 " --> pdb=" O GLN G 259 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 267 " --> pdb=" O GLY G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 276 removed outlier: 3.989A pdb=" N GLU G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 301 removed outlier: 3.629A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR G 288 " --> pdb=" O ALA G 284 " (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 316 No H-bonds generated for 'chain 'G' and resid 313 through 316' Processing helix chain 'G' and resid 344 through 355 Processing helix chain 'G' and resid 362 through 372 removed outlier: 3.927A pdb=" N VAL G 368 " --> pdb=" O ALA G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 394 removed outlier: 3.670A pdb=" N TYR G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 394 " --> pdb=" O LYS G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 422 Processing helix chain 'G' and resid 426 through 432 Processing helix chain 'G' and resid 443 through 457 removed outlier: 3.606A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 450 " --> pdb=" O LEU G 446 " (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 removed outlier: 3.964A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 481 " --> pdb=" O ASN G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 506 through 514 Processing helix chain 'G' and resid 527 through 538 Processing helix chain 'G' and resid 547 through 558 removed outlier: 3.821A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 607 removed outlier: 3.794A pdb=" N MET G 604 " --> pdb=" O ALA G 600 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER G 606 " --> pdb=" O ALA G 602 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 632 Processing helix chain 'G' and resid 639 through 650 removed outlier: 4.090A pdb=" N ASN G 647 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS G 648 " --> pdb=" O ASN G 644 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL G 649 " --> pdb=" O ALA G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 726 removed outlier: 3.652A pdb=" N THR G 711 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN G 721 " --> pdb=" O LEU G 717 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU G 722 " --> pdb=" O LYS G 718 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE G 725 " --> pdb=" O ASN G 721 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY G 726 " --> pdb=" O GLU G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 751 removed outlier: 3.627A pdb=" N GLY G 735 " --> pdb=" O ALA G 731 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN G 746 " --> pdb=" O TYR G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 755 No H-bonds generated for 'chain 'G' and resid 753 through 755' Processing helix chain 'G' and resid 771 through 792 removed outlier: 4.204A pdb=" N MET G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE G 777 " --> pdb=" O LYS G 773 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 779 " --> pdb=" O MET G 775 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU G 789 " --> pdb=" O ALA G 785 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 790 " --> pdb=" O VAL G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 831 removed outlier: 3.934A pdb=" N LYS G 820 " --> pdb=" O GLU G 816 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE G 821 " --> pdb=" O PHE G 817 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU G 826 " --> pdb=" O LYS G 822 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 830 " --> pdb=" O GLU G 826 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP G 831 " --> pdb=" O LYS G 827 " (cutoff:3.500A) Processing helix chain 'G' and resid 840 through 843 No H-bonds generated for 'chain 'G' and resid 840 through 843' 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 868 through 882 removed outlier: 3.700A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 877 " --> pdb=" O SER G 873 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE G 878 " --> pdb=" O PHE G 874 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU G 880 " --> pdb=" O LYS G 876 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE G 881 " --> pdb=" O LEU G 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 889 through 896 removed outlier: 4.080A pdb=" N LEU G 895 " --> pdb=" O GLU G 891 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR G 896 " --> pdb=" O TRP G 892 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.735A pdb=" N ILE H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.525A pdb=" N SER H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 139 removed outlier: 3.678A pdb=" N LYS H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 168 removed outlier: 3.535A pdb=" N ARG H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.690A pdb=" N GLU H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 239 Processing helix chain 'H' and resid 254 through 267 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 280 through 301 removed outlier: 3.566A pdb=" N GLU H 285 " --> pdb=" O VAL H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 313 through 317 Processing helix chain 'H' and resid 344 through 356 Processing helix chain 'H' and resid 362 through 373 Processing helix chain 'H' and resid 376 through 393 removed outlier: 3.549A pdb=" N GLN H 381 " --> pdb=" O ARG H 377 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR H 391 " --> pdb=" O TYR H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 424 removed outlier: 3.658A pdb=" N GLY H 423 " --> pdb=" O ASN H 419 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 432 removed outlier: 3.543A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 456 removed outlier: 3.789A pdb=" N LYS H 448 " --> pdb=" O ASP H 444 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 456 " --> pdb=" O THR H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 465 Processing helix chain 'H' and resid 473 through 489 removed outlier: 3.684A pdb=" N ILE H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 513 removed outlier: 3.726A pdb=" N CYS H 505 " --> pdb=" O LEU H 501 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER H 509 " --> pdb=" O CYS H 505 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN H 512 " --> pdb=" O VAL H 508 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN H 513 " --> pdb=" O SER H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 518 No H-bonds generated for 'chain 'H' and resid 515 through 518' Processing helix chain 'H' and resid 527 through 539 removed outlier: 4.091A pdb=" N LEU H 531 " --> pdb=" O LYS H 527 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE H 532 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU H 534 " --> pdb=" O GLN H 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA H 537 " --> pdb=" O SER H 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR H 538 " --> pdb=" O GLU H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.596A pdb=" N ASN H 552 " --> pdb=" O SER H 548 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG H 553 " --> pdb=" O HIS H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 566 No H-bonds generated for 'chain 'H' and resid 564 through 566' Processing helix chain 'H' and resid 593 through 595 No H-bonds generated for 'chain 'H' and resid 593 through 595' Processing helix chain 'H' and resid 598 through 607 removed outlier: 3.765A pdb=" N ALA H 602 " --> pdb=" O GLY H 598 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 606 " --> pdb=" O ALA H 602 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER H 607 " --> pdb=" O ALA H 603 " (cutoff:3.500A) Processing helix chain 'H' and resid 622 through 632 removed outlier: 3.568A pdb=" N ILE H 629 " --> pdb=" O LEU H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 650 removed outlier: 3.715A pdb=" N ILE H 650 " --> pdb=" O PHE H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 707 through 720 removed outlier: 3.867A pdb=" N THR H 711 " --> pdb=" O SER H 707 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS H 712 " --> pdb=" O ASP H 708 " (cutoff:3.500A) Processing helix chain 'H' and resid 724 through 726 No H-bonds generated for 'chain 'H' and resid 724 through 726' Processing helix chain 'H' and resid 731 through 751 removed outlier: 3.857A pdb=" N GLY H 735 " --> pdb=" O ALA H 731 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 747 " --> pdb=" O PHE H 743 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP H 750 " --> pdb=" O ASN H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 773 through 788 removed outlier: 3.772A pdb=" N PHE H 777 " --> pdb=" O LYS H 773 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN H 778 " --> pdb=" O ILE H 774 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H 779 " --> pdb=" O MET H 775 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA H 781 " --> pdb=" O PHE H 777 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 787 " --> pdb=" O LEU H 783 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 831 removed outlier: 4.037A pdb=" N LYS H 820 " --> pdb=" O GLU H 816 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 821 " --> pdb=" O PHE H 817 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS H 822 " --> pdb=" O GLU H 818 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS H 829 " --> pdb=" O GLY H 825 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 830 " --> pdb=" O GLU H 826 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP H 831 " --> pdb=" O LYS H 827 " (cutoff:3.500A) Processing helix chain 'H' and resid 840 through 845 Processing helix chain 'H' and resid 852 through 854 No H-bonds generated for 'chain 'H' and resid 852 through 854' Processing helix chain 'H' and resid 865 through 871 removed outlier: 3.897A pdb=" N ASN H 869 " --> pdb=" O VAL H 865 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS H 870 " --> pdb=" O LYS H 866 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU H 871 " --> pdb=" O ALA H 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 865 through 871' Processing helix chain 'H' and resid 877 through 882 Processing helix chain 'H' and resid 889 through 896 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.579A pdb=" N SER I 88 " --> pdb=" O THR I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 139 removed outlier: 3.547A pdb=" N GLY I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 166 removed outlier: 3.582A pdb=" N ARG I 147 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU I 151 " --> pdb=" O ARG I 147 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N HIS I 165 " --> pdb=" O GLN I 161 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU I 166 " --> pdb=" O ARG I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 180 removed outlier: 3.513A pdb=" N SER I 178 " --> pdb=" O GLU I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 211 Processing helix chain 'I' and resid 227 through 240 removed outlier: 3.666A pdb=" N ASP I 232 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU I 235 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG I 238 " --> pdb=" O GLU I 235 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE I 240 " --> pdb=" O ILE I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 268 removed outlier: 3.706A pdb=" N GLN I 259 " --> pdb=" O ARG I 255 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU I 267 " --> pdb=" O GLY I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 removed outlier: 3.517A pdb=" N GLU I 275 " --> pdb=" O LYS I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 301 removed outlier: 4.046A pdb=" N GLU I 285 " --> pdb=" O VAL I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 306 No H-bonds generated for 'chain 'I' and resid 304 through 306' Processing helix chain 'I' and resid 313 through 317 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 344 through 353 Processing helix chain 'I' and resid 365 through 372 Processing helix chain 'I' and resid 376 through 394 removed outlier: 3.848A pdb=" N TYR I 387 " --> pdb=" O LEU I 383 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS I 389 " --> pdb=" O ASP I 385 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA I 393 " --> pdb=" O LYS I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 424 removed outlier: 3.631A pdb=" N GLY I 423 " --> pdb=" O ASN I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 432 Processing helix chain 'I' and resid 438 through 440 No H-bonds generated for 'chain 'I' and resid 438 through 440' Processing helix chain 'I' and resid 443 through 457 removed outlier: 3.523A pdb=" N LYS I 448 " --> pdb=" O ASP I 444 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE I 451 " --> pdb=" O CYS I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 465 No H-bonds generated for 'chain 'I' and resid 463 through 465' Processing helix chain 'I' and resid 474 through 489 removed outlier: 4.143A pdb=" N ILE I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 481 " --> pdb=" O ASN I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 502 Processing helix chain 'I' and resid 504 through 514 removed outlier: 3.742A pdb=" N VAL I 508 " --> pdb=" O GLY I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 516 through 518 No H-bonds generated for 'chain 'I' and resid 516 through 518' Processing helix chain 'I' and resid 527 through 539 removed outlier: 3.890A pdb=" N ALA I 537 " --> pdb=" O SER I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 560 removed outlier: 4.274A pdb=" N ALA I 556 " --> pdb=" O ASN I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 607 Processing helix chain 'I' and resid 623 through 634 Processing helix chain 'I' and resid 642 through 647 Processing helix chain 'I' and resid 707 through 721 removed outlier: 4.080A pdb=" N LYS I 712 " --> pdb=" O ASP I 708 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN I 719 " --> pdb=" O GLN I 715 " (cutoff:3.500A) Processing helix chain 'I' and resid 724 through 726 No H-bonds generated for 'chain 'I' and resid 724 through 726' Processing helix chain 'I' and resid 731 through 751 removed outlier: 3.643A pdb=" N ASP I 750 " --> pdb=" O ASN I 746 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 760 No H-bonds generated for 'chain 'I' and resid 758 through 760' Processing helix chain 'I' and resid 771 through 793 removed outlier: 3.571A pdb=" N MET I 775 " --> pdb=" O ALA I 771 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG I 776 " --> pdb=" O ALA I 772 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU I 790 " --> pdb=" O VAL I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 830 removed outlier: 3.553A pdb=" N ILE I 821 " --> pdb=" O PHE I 817 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 830 " --> pdb=" O GLU I 826 " (cutoff:3.500A) Processing helix chain 'I' and resid 840 through 846 removed outlier: 3.636A pdb=" N LEU I 844 " --> pdb=" O PRO I 840 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU I 845 " --> pdb=" O LEU I 841 " (cutoff:3.500A) Processing helix chain 'I' and resid 849 through 855 Proline residue: I 853 - end of helix No H-bonds generated for 'chain 'I' and resid 849 through 855' Processing helix chain 'I' and resid 865 through 882 removed outlier: 3.914A pdb=" N SER I 873 " --> pdb=" O ASN I 869 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 896 Processing helix chain 'I' and resid 916 through 919 No H-bonds generated for 'chain 'I' and resid 916 through 919' Processing helix chain 'J' and resid 35 through 50 removed outlier: 3.701A pdb=" N ASN J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE J 49 " --> pdb=" O ILE J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 112 through 114 No H-bonds generated for 'chain 'J' and resid 112 through 114' Processing helix chain 'J' and resid 121 through 139 removed outlier: 4.108A pdb=" N LYS J 138 " --> pdb=" O SER J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 162 Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'J' and resid 174 through 180 removed outlier: 4.224A pdb=" N SER J 178 " --> pdb=" O GLU J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 210 Processing helix chain 'J' and resid 227 through 240 removed outlier: 3.559A pdb=" N TRP J 231 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP J 232 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU J 235 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG J 238 " --> pdb=" O GLU J 235 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS J 239 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE J 240 " --> pdb=" O ILE J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 267 Processing helix chain 'J' and resid 273 through 276 No H-bonds generated for 'chain 'J' and resid 273 through 276' Processing helix chain 'J' and resid 280 through 301 removed outlier: 3.904A pdb=" N GLU J 285 " --> pdb=" O VAL J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing helix chain 'J' and resid 314 through 317 No H-bonds generated for 'chain 'J' and resid 314 through 317' Processing helix chain 'J' and resid 344 through 356 Processing helix chain 'J' and resid 362 through 372 removed outlier: 3.582A pdb=" N TYR J 367 " --> pdb=" O ASP J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 394 removed outlier: 3.502A pdb=" N HIS J 392 " --> pdb=" O THR J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 424 removed outlier: 3.815A pdb=" N GLY J 423 " --> pdb=" O ASN J 419 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER J 424 " --> pdb=" O ALA J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 432 removed outlier: 3.668A pdb=" N TYR J 430 " --> pdb=" O LEU J 426 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG J 431 " --> pdb=" O SER J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 457 Processing helix chain 'J' and resid 463 through 465 No H-bonds generated for 'chain 'J' and resid 463 through 465' Processing helix chain 'J' and resid 473 through 489 removed outlier: 3.695A pdb=" N ILE J 480 " --> pdb=" O ARG J 476 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR J 481 " --> pdb=" O ASN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 502 removed outlier: 3.623A pdb=" N GLN J 499 " --> pdb=" O SER J 495 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET J 500 " --> pdb=" O LYS J 496 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 514 removed outlier: 3.657A pdb=" N SER J 509 " --> pdb=" O CYS J 505 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN J 513 " --> pdb=" O SER J 509 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE J 514 " --> pdb=" O ILE J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 527 through 539 removed outlier: 3.868A pdb=" N ILE J 532 " --> pdb=" O PHE J 528 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER J 533 " --> pdb=" O GLU J 529 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU J 534 " --> pdb=" O GLN J 530 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA J 537 " --> pdb=" O SER J 533 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR J 538 " --> pdb=" O GLU J 534 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET J 539 " --> pdb=" O TYR J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 557 removed outlier: 4.007A pdb=" N CYS J 555 " --> pdb=" O ALA J 551 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA J 556 " --> pdb=" O ASN J 552 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 566 No H-bonds generated for 'chain 'J' and resid 564 through 566' Processing helix chain 'J' and resid 593 through 595 No H-bonds generated for 'chain 'J' and resid 593 through 595' Processing helix chain 'J' and resid 598 through 606 Processing helix chain 'J' and resid 622 through 632 removed outlier: 3.545A pdb=" N ALA J 628 " --> pdb=" O ASN J 624 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP J 631 " --> pdb=" O GLY J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 648 removed outlier: 3.724A pdb=" N ALA J 645 " --> pdb=" O ALA J 641 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN J 647 " --> pdb=" O THR J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 707 through 721 removed outlier: 3.624A pdb=" N THR J 711 " --> pdb=" O SER J 707 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS J 712 " --> pdb=" O ASP J 708 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU J 717 " --> pdb=" O VAL J 713 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN J 719 " --> pdb=" O GLN J 715 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN J 721 " --> pdb=" O LEU J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 724 through 726 No H-bonds generated for 'chain 'J' and resid 724 through 726' Processing helix chain 'J' and resid 731 through 751 removed outlier: 3.510A pdb=" N GLY J 735 " --> pdb=" O ALA J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 771 through 792 removed outlier: 3.793A pdb=" N MET J 775 " --> pdb=" O ALA J 771 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J 789 " --> pdb=" O ALA J 785 " (cutoff:3.500A) Processing helix chain 'J' and resid 815 through 830 removed outlier: 3.567A pdb=" N LYS J 820 " --> pdb=" O GLU J 816 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS J 827 " --> pdb=" O ILE J 823 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 840 through 846 Processing helix chain 'J' and resid 852 through 855 No H-bonds generated for 'chain 'J' and resid 852 through 855' Processing helix chain 'J' and resid 865 through 882 removed outlier: 3.912A pdb=" N ASN J 869 " --> pdb=" O VAL J 865 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS J 870 " --> pdb=" O LYS J 866 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU J 880 " --> pdb=" O LYS J 876 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 881 " --> pdb=" O LEU J 877 " (cutoff:3.500A) Processing helix chain 'J' and resid 893 through 896 No H-bonds generated for 'chain 'J' and resid 893 through 896' Processing helix chain 'K' and resid 34 through 49 removed outlier: 3.951A pdb=" N ASP K 39 " --> pdb=" O SER K 36 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER K 48 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 95 removed outlier: 3.569A pdb=" N SER K 95 " --> pdb=" O LYS K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 138 removed outlier: 3.709A pdb=" N LYS K 131 " --> pdb=" O ALA K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 168 removed outlier: 3.597A pdb=" N LYS K 148 " --> pdb=" O ASN K 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY K 163 " --> pdb=" O GLN K 159 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS K 165 " --> pdb=" O GLN K 161 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU K 166 " --> pdb=" O ARG K 162 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU K 167 " --> pdb=" O GLY K 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 180 Processing helix chain 'K' and resid 196 through 211 Processing helix chain 'K' and resid 227 through 239 removed outlier: 3.658A pdb=" N GLY K 230 " --> pdb=" O PHE K 227 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP K 231 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP K 232 " --> pdb=" O ALA K 229 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU K 235 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS K 239 " --> pdb=" O SER K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 268 removed outlier: 3.579A pdb=" N ASN K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 280 through 301 removed outlier: 3.977A pdb=" N GLU K 285 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS K 292 " --> pdb=" O TYR K 288 " (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 Processing helix chain 'K' and resid 363 through 373 removed outlier: 3.963A pdb=" N TYR K 367 " --> pdb=" O ASP K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 394 Processing helix chain 'K' and resid 413 through 431 removed outlier: 3.888A pdb=" N SER K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER K 427 " --> pdb=" O GLY K 423 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER K 428 " --> pdb=" O SER K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 457 removed outlier: 3.763A pdb=" N LYS K 448 " --> pdb=" O ASP K 444 " (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 489 removed outlier: 3.697A pdb=" N SER K 479 " --> pdb=" O LEU K 475 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE K 480 " --> pdb=" O ARG K 476 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR K 481 " --> pdb=" O ASN K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 501 removed outlier: 3.724A pdb=" N MET K 500 " --> pdb=" O LYS K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 512 removed outlier: 3.533A pdb=" N ILE K 510 " --> pdb=" O GLY K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 518 No H-bonds generated for 'chain 'K' and resid 515 through 518' Processing helix chain 'K' and resid 527 through 539 Processing helix chain 'K' and resid 547 through 558 removed outlier: 4.172A pdb=" N ALA K 556 " --> pdb=" O ASN K 552 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL K 557 " --> pdb=" O ARG K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 593 through 595 No H-bonds generated for 'chain 'K' and resid 593 through 595' Processing helix chain 'K' and resid 602 through 607 Processing helix chain 'K' and resid 622 through 634 Processing helix chain 'K' and resid 639 through 650 removed outlier: 3.864A pdb=" N THR K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN K 644 " --> pdb=" O SER K 640 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA K 645 " --> pdb=" O ALA K 641 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE K 650 " --> pdb=" O PHE K 646 " (cutoff:3.500A) Processing helix chain 'K' and resid 705 through 726 removed outlier: 3.963A pdb=" N ASP K 708 " --> pdb=" O GLU K 705 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR K 711 " --> pdb=" O ASP K 708 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU K 714 " --> pdb=" O THR K 711 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU K 717 " --> pdb=" O GLU K 714 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN K 721 " --> pdb=" O LYS K 718 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU K 722 " --> pdb=" O ASN K 719 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU K 724 " --> pdb=" O ASN K 721 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K 725 " --> pdb=" O GLU K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 731 through 751 Processing helix chain 'K' and resid 771 through 793 removed outlier: 3.745A pdb=" N MET K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE K 777 " --> pdb=" O LYS K 773 " (cutoff:3.500A) Processing helix chain 'K' and resid 815 through 830 removed outlier: 3.720A 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 Processing helix chain 'K' and resid 852 through 855 No H-bonds generated for 'chain 'K' and resid 852 through 855' Processing helix chain 'K' and resid 858 through 860 No H-bonds generated for 'chain 'K' and resid 858 through 860' Processing helix chain 'K' and resid 865 through 882 removed outlier: 3.914A pdb=" N ASN K 869 " --> pdb=" O VAL K 865 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS K 870 " --> pdb=" O LYS K 866 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU K 871 " --> pdb=" O ALA K 867 " (cutoff:3.500A) Processing helix chain 'K' and resid 889 through 896 removed outlier: 4.057A pdb=" N TYR K 894 " --> pdb=" O GLU K 890 " (cutoff:3.500A) Processing helix chain 'K' and resid 916 through 919 No H-bonds generated for 'chain 'K' and resid 916 through 919' Processing helix chain 'L' and resid 24 through 26 No H-bonds generated for 'chain 'L' and resid 24 through 26' Processing helix chain 'L' and resid 34 through 47 removed outlier: 3.976A pdb=" N ASP L 39 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL L 42 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU L 43 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 removed outlier: 3.756A pdb=" N VAL L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 139 Processing helix chain 'L' and resid 143 through 166 removed outlier: 4.056A pdb=" N GLU L 151 " --> pdb=" O ARG L 147 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN L 152 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS L 165 " --> pdb=" O GLN L 161 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU L 166 " --> pdb=" O ARG L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 180 removed outlier: 4.051A pdb=" N SER L 178 " --> pdb=" O PRO L 174 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP L 179 " --> pdb=" O GLU L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 211 Processing helix chain 'L' and resid 230 through 240 Processing helix chain 'L' and resid 254 through 267 removed outlier: 3.544A pdb=" N GLU L 267 " --> pdb=" O GLY L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 removed outlier: 3.526A pdb=" N GLU L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 301 removed outlier: 3.558A 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 344 through 355 removed outlier: 4.327A pdb=" N GLU L 354 " --> pdb=" O ASP L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 373 Processing helix chain 'L' and resid 376 through 394 removed outlier: 4.367A pdb=" N LYS L 389 " --> pdb=" O ASP L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 422 Processing helix chain 'L' and resid 426 through 432 Processing helix chain 'L' and resid 445 through 457 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 473 through 489 removed outlier: 3.709A pdb=" N ILE L 480 " --> pdb=" O ARG L 476 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR L 481 " --> pdb=" O ASN L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 502 Processing helix chain 'L' and resid 504 through 514 removed outlier: 4.000A pdb=" N VAL L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 509 " --> pdb=" O CYS L 505 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN L 512 " --> pdb=" O VAL L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 539 removed outlier: 3.678A pdb=" N MET L 539 " --> pdb=" O TYR L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 547 through 558 removed outlier: 3.913A pdb=" N ALA L 556 " --> pdb=" O ASN L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 566 No H-bonds generated for 'chain 'L' and resid 564 through 566' Processing helix chain 'L' and resid 598 through 604 Processing helix chain 'L' and resid 622 through 633 removed outlier: 3.582A pdb=" N ASP L 631 " --> pdb=" O GLY L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 648 removed outlier: 4.201A pdb=" N ASN L 644 " --> pdb=" O SER L 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 707 through 726 removed outlier: 3.724A pdb=" N LYS L 712 " --> pdb=" O ASP L 708 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU L 722 " --> pdb=" O LYS L 718 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE L 725 " --> pdb=" O ASN L 721 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY L 726 " --> pdb=" O GLU L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 731 through 752 Processing helix chain 'L' and resid 771 through 793 Processing helix chain 'L' and resid 815 through 830 removed outlier: 3.510A pdb=" N LYS L 820 " --> pdb=" O GLU L 816 " (cutoff:3.500A) Processing helix chain 'L' and resid 835 through 838 No H-bonds generated for 'chain 'L' and resid 835 through 838' 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 865 through 882 removed outlier: 3.829A pdb=" N ASN L 869 " --> pdb=" O VAL L 865 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE L 881 " --> pdb=" O LEU L 877 " (cutoff:3.500A) Processing helix chain 'L' and resid 889 through 896 removed outlier: 3.771A pdb=" N LEU L 895 " --> pdb=" O GLU L 891 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR L 896 " --> pdb=" O TRP L 892 " (cutoff:3.500A) Processing helix chain 'L' and resid 917 through 919 No H-bonds generated for 'chain 'L' and resid 917 through 919' Processing helix chain 'M' and resid 38 through 50 removed outlier: 3.590A pdb=" N ILE M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 94 Processing helix chain 'M' and resid 121 through 139 removed outlier: 3.519A pdb=" N LYS M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 167 removed outlier: 3.738A pdb=" N HIS M 156 " --> pdb=" O GLN M 152 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS M 165 " --> pdb=" O GLN M 161 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU M 166 " --> pdb=" O ARG M 162 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU M 167 " --> pdb=" O GLY M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 181 removed outlier: 3.884A pdb=" N SER M 178 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 211 Processing helix chain 'M' and resid 227 through 240 removed outlier: 3.666A pdb=" N TRP M 231 " --> pdb=" O ASP M 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP M 232 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU M 235 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 238 " --> pdb=" O GLU M 235 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS M 239 " --> pdb=" O SER M 236 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE M 240 " --> pdb=" O ILE M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 265 Processing helix chain 'M' and resid 271 through 276 Processing helix chain 'M' and resid 280 through 301 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 344 through 356 Processing helix chain 'M' and resid 362 through 372 removed outlier: 4.559A pdb=" N TYR M 367 " --> pdb=" O ASP M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 384 Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 413 through 424 Processing helix chain 'M' and resid 426 through 432 Processing helix chain 'M' and resid 438 through 440 No H-bonds generated for 'chain 'M' and resid 438 through 440' Processing helix chain 'M' and resid 443 through 457 Processing helix chain 'M' and resid 463 through 465 No H-bonds generated for 'chain 'M' and resid 463 through 465' Processing helix chain 'M' and resid 473 through 489 removed outlier: 3.849A pdb=" N ILE M 480 " --> pdb=" O ARG M 476 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR M 481 " --> pdb=" O ASN M 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 495 through 502 removed outlier: 3.575A pdb=" N MET M 500 " --> pdb=" O LYS M 496 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 515 removed outlier: 4.043A pdb=" N VAL M 508 " --> pdb=" O GLY M 504 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN M 513 " --> pdb=" O SER M 509 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE M 514 " --> pdb=" O ILE M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 527 through 539 Processing helix chain 'M' and resid 547 through 560 removed outlier: 3.575A pdb=" N VAL M 558 " --> pdb=" O CYS M 554 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA M 559 " --> pdb=" O CYS M 555 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 607 Processing helix chain 'M' and resid 622 through 634 Processing helix chain 'M' and resid 639 through 645 removed outlier: 4.010A pdb=" N ASN M 644 " --> pdb=" O SER M 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 705 through 726 removed outlier: 3.582A pdb=" N GLU M 722 " --> pdb=" O LYS M 718 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE M 725 " --> pdb=" O ASN M 721 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY M 726 " --> pdb=" O GLU M 722 " (cutoff:3.500A) Processing helix chain 'M' and resid 731 through 748 removed outlier: 3.510A pdb=" N ASN M 747 " --> pdb=" O PHE M 743 " (cutoff:3.500A) Processing helix chain 'M' and resid 771 through 792 removed outlier: 3.775A pdb=" N PHE M 777 " --> pdb=" O LYS M 773 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 790 " --> pdb=" O VAL M 786 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU M 792 " --> pdb=" O VAL M 788 " (cutoff:3.500A) Processing helix chain 'M' and resid 815 through 830 removed outlier: 3.992A pdb=" N LYS M 820 " --> pdb=" O GLU M 816 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE M 821 " --> pdb=" O PHE M 817 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU M 826 " --> pdb=" O LYS M 822 " (cutoff:3.500A) Processing helix chain 'M' and resid 840 through 846 Processing helix chain 'M' and resid 849 through 855 Proline residue: M 853 - end of helix No H-bonds generated for 'chain 'M' and resid 849 through 855' Processing helix chain 'M' and resid 869 through 882 removed outlier: 3.583A pdb=" N ILE M 878 " --> pdb=" O PHE M 874 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU M 880 " --> pdb=" O LYS M 876 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE M 881 " --> pdb=" O LEU M 877 " (cutoff:3.500A) Processing helix chain 'M' and resid 889 through 895 removed outlier: 3.994A pdb=" N LEU M 895 " --> pdb=" O GLU M 891 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 50 removed outlier: 3.596A pdb=" N ILE N 49 " --> pdb=" O ILE N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 removed outlier: 3.615A pdb=" N SER N 88 " --> pdb=" O THR N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 139 removed outlier: 3.591A pdb=" N GLY N 139 " --> pdb=" O ASP N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 167 removed outlier: 3.531A pdb=" N GLN N 159 " --> pdb=" O ASN N 155 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N HIS N 165 " --> pdb=" O GLN N 161 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU N 166 " --> pdb=" O ARG N 162 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU N 167 " --> pdb=" O GLY N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 180 removed outlier: 3.655A pdb=" N SER N 178 " --> pdb=" O GLU N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 211 Processing helix chain 'N' and resid 227 through 239 removed outlier: 3.500A pdb=" N TRP N 231 " --> pdb=" O ASP N 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP N 232 " --> pdb=" O ALA N 229 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU N 235 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG N 238 " --> pdb=" O GLU N 235 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS N 239 " --> pdb=" O SER N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 268 Processing helix chain 'N' and resid 273 through 276 No H-bonds generated for 'chain 'N' and resid 273 through 276' Processing helix chain 'N' and resid 280 through 301 removed outlier: 4.061A pdb=" N GLU N 285 " --> pdb=" O VAL N 281 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 306 No H-bonds generated for 'chain 'N' and resid 304 through 306' Processing helix chain 'N' and resid 313 through 316 No H-bonds generated for 'chain 'N' and resid 313 through 316' Processing helix chain 'N' and resid 344 through 355 Processing helix chain 'N' and resid 362 through 372 removed outlier: 3.506A pdb=" N TYR N 367 " --> pdb=" O ASP N 363 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL N 368 " --> pdb=" O ALA N 364 " (cutoff:3.500A) Processing helix chain 'N' and resid 376 through 394 removed outlier: 3.709A pdb=" N TYR N 391 " --> pdb=" O TYR N 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR N 394 " --> pdb=" O LYS N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 413 through 424 Processing helix chain 'N' and resid 426 through 432 Processing helix chain 'N' and resid 443 through 457 removed outlier: 3.739A pdb=" N ILE N 450 " --> pdb=" O LEU N 446 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE N 451 " --> pdb=" O CYS N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 465 No H-bonds generated for 'chain 'N' and resid 463 through 465' Processing helix chain 'N' and resid 473 through 489 removed outlier: 3.528A pdb=" N CYS N 478 " --> pdb=" O ALA N 474 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 479 " --> pdb=" O LEU N 475 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE N 480 " --> pdb=" O ARG N 476 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR N 481 " --> pdb=" O ASN N 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 496 through 514 removed outlier: 3.535A pdb=" N GLY N 506 " --> pdb=" O LEU N 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL N 508 " --> pdb=" O GLY N 504 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN N 513 " --> pdb=" O SER N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 527 through 538 Processing helix chain 'N' and resid 547 through 558 removed outlier: 3.576A pdb=" N CYS N 555 " --> pdb=" O ALA N 551 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA N 556 " --> pdb=" O ASN N 552 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL N 557 " --> pdb=" O ARG N 553 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 566 No H-bonds generated for 'chain 'N' and resid 564 through 566' Processing helix chain 'N' and resid 600 through 607 removed outlier: 3.589A pdb=" N MET N 604 " --> pdb=" O ALA N 600 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER N 606 " --> pdb=" O ALA N 602 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER N 607 " --> pdb=" O ALA N 603 " (cutoff:3.500A) Processing helix chain 'N' and resid 622 through 632 Processing helix chain 'N' and resid 639 through 650 removed outlier: 4.028A pdb=" N ASN N 647 " --> pdb=" O THR N 643 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS N 648 " --> pdb=" O ASN N 644 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL N 649 " --> pdb=" O ALA N 645 " (cutoff:3.500A) Processing helix chain 'N' and resid 707 through 726 removed outlier: 3.796A pdb=" N THR N 711 " --> pdb=" O SER N 707 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN N 721 " --> pdb=" O LEU N 717 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU N 722 " --> pdb=" O LYS N 718 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE N 725 " --> pdb=" O ASN N 721 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY N 726 " --> pdb=" O GLU N 722 " (cutoff:3.500A) Processing helix chain 'N' and resid 731 through 751 removed outlier: 3.504A pdb=" N ASN N 746 " --> pdb=" O TYR N 742 " (cutoff:3.500A) Processing helix chain 'N' and resid 753 through 755 No H-bonds generated for 'chain 'N' and resid 753 through 755' Processing helix chain 'N' and resid 771 through 793 removed outlier: 4.024A pdb=" N MET N 775 " --> pdb=" O ALA N 771 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 779 " --> pdb=" O MET N 775 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU N 789 " --> pdb=" O ALA N 785 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER N 791 " --> pdb=" O LEU N 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 814 through 829 removed outlier: 5.138A pdb=" N LYS N 819 " --> pdb=" O GLU N 816 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS N 820 " --> pdb=" O PHE N 817 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY N 825 " --> pdb=" O LYS N 822 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU N 828 " --> pdb=" O GLY N 825 " (cutoff:3.500A) Processing helix chain 'N' and resid 840 through 843 No H-bonds generated for 'chain 'N' and resid 840 through 843' Processing helix chain 'N' and resid 849 through 855 Proline residue: N 853 - end of helix No H-bonds generated for 'chain 'N' and resid 849 through 855' Processing helix chain 'N' and resid 865 through 882 removed outlier: 4.339A pdb=" N ASN N 869 " --> pdb=" O VAL N 865 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS N 870 " --> pdb=" O LYS N 866 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER N 873 " --> pdb=" O ASN N 869 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU N 877 " --> pdb=" O SER N 873 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE N 878 " --> pdb=" O PHE N 874 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU N 880 " --> pdb=" O LYS N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 889 through 896 removed outlier: 4.037A pdb=" N LEU N 895 " --> pdb=" O GLU N 891 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR N 896 " --> pdb=" O TRP N 892 " (cutoff:3.500A) Processing helix chain 'N' and resid 917 through 919 No H-bonds generated for 'chain 'N' and resid 917 through 919' Processing helix chain 'O' and resid 24 through 26 No H-bonds generated for 'chain 'O' and resid 24 through 26' Processing helix chain 'O' and resid 35 through 50 removed outlier: 3.729A pdb=" N ILE O 49 " --> pdb=" O ILE O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 94 Processing helix chain 'O' and resid 121 through 139 removed outlier: 3.637A pdb=" N LYS O 131 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 168 removed outlier: 4.564A pdb=" N HIS O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU O 167 " --> pdb=" O GLY O 163 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR O 168 " --> pdb=" O LEU O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 177 Processing helix chain 'O' and resid 196 through 211 Processing helix chain 'O' and resid 227 through 239 removed outlier: 3.503A pdb=" N GLY O 230 " --> pdb=" O PHE O 227 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP O 232 " --> pdb=" O ALA O 229 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG O 238 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS O 239 " --> pdb=" O SER O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 254 through 267 Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 280 through 301 removed outlier: 3.550A pdb=" N GLU O 285 " --> pdb=" O VAL O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 306 No H-bonds generated for 'chain 'O' and resid 304 through 306' Processing helix chain 'O' and resid 313 through 316 No H-bonds generated for 'chain 'O' and resid 313 through 316' Processing helix chain 'O' and resid 344 through 355 removed outlier: 3.703A pdb=" N GLU O 354 " --> pdb=" O ASP O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 373 removed outlier: 3.520A pdb=" N TYR O 367 " --> pdb=" O ASP O 363 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU O 371 " --> pdb=" O TYR O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 393 removed outlier: 4.040A pdb=" N TYR O 391 " --> pdb=" O TYR O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 424 removed outlier: 3.545A pdb=" N GLY O 423 " --> pdb=" O ASN O 419 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER O 424 " --> pdb=" O ALA O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 432 removed outlier: 3.535A pdb=" N ARG O 431 " --> pdb=" O SER O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 457 removed outlier: 3.803A pdb=" N ASP O 449 " --> pdb=" O SER O 445 " (cutoff:3.500A) Processing helix chain 'O' and resid 463 through 465 No H-bonds generated for 'chain 'O' and resid 463 through 465' Processing helix chain 'O' and resid 473 through 489 removed outlier: 3.841A pdb=" N ILE O 480 " --> pdb=" O ARG O 476 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR O 481 " --> pdb=" O ASN O 477 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 513 removed outlier: 3.804A pdb=" N LEU O 498 " --> pdb=" O LEU O 494 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS O 505 " --> pdb=" O LEU O 501 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER O 507 " --> pdb=" O VAL O 503 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL O 508 " --> pdb=" O GLY O 504 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER O 509 " --> pdb=" O CYS O 505 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE O 511 " --> pdb=" O SER O 507 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN O 512 " --> pdb=" O VAL O 508 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN O 513 " --> pdb=" O SER O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 518 No H-bonds generated for 'chain 'O' and resid 515 through 518' Processing helix chain 'O' and resid 527 through 539 removed outlier: 4.105A pdb=" N LEU O 531 " --> pdb=" O LYS O 527 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE O 532 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU O 534 " --> pdb=" O GLN O 530 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA O 537 " --> pdb=" O SER O 533 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR O 538 " --> pdb=" O GLU O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 547 through 559 removed outlier: 3.956A pdb=" N ARG O 553 " --> pdb=" O HIS O 549 " (cutoff:3.500A) Processing helix chain 'O' and resid 564 through 566 No H-bonds generated for 'chain 'O' and resid 564 through 566' Processing helix chain 'O' and resid 593 through 595 No H-bonds generated for 'chain 'O' and resid 593 through 595' Processing helix chain 'O' and resid 598 through 607 removed outlier: 4.103A pdb=" N ALA O 602 " --> pdb=" O GLY O 598 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER O 607 " --> pdb=" O ALA O 603 " (cutoff:3.500A) Processing helix chain 'O' and resid 622 through 632 removed outlier: 3.985A pdb=" N ILE O 629 " --> pdb=" O LEU O 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 646 removed outlier: 3.519A pdb=" N PHE O 646 " --> pdb=" O THR O 643 " (cutoff:3.500A) Processing helix chain 'O' and resid 705 through 719 removed outlier: 3.572A pdb=" N ILE O 710 " --> pdb=" O PHE O 706 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS O 712 " --> pdb=" O ASP O 708 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL O 713 " --> pdb=" O ALA O 709 " (cutoff:3.500A) Processing helix chain 'O' and resid 722 through 725 No H-bonds generated for 'chain 'O' and resid 722 through 725' Processing helix chain 'O' and resid 731 through 751 removed outlier: 3.664A pdb=" N GLY O 735 " --> pdb=" O ALA O 731 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN O 747 " --> pdb=" O PHE O 743 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP O 750 " --> pdb=" O ASN O 746 " (cutoff:3.500A) Processing helix chain 'O' and resid 771 through 791 removed outlier: 3.881A pdb=" N MET O 775 " --> pdb=" O ALA O 771 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN O 778 " --> pdb=" O ILE O 774 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL O 779 " --> pdb=" O MET O 775 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA O 781 " --> pdb=" O PHE O 777 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE O 782 " --> pdb=" O ASN O 778 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU O 787 " --> pdb=" O LEU O 783 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU O 789 " --> pdb=" O ALA O 785 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU O 790 " --> pdb=" O VAL O 786 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER O 791 " --> pdb=" O LEU O 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 815 through 831 removed outlier: 3.987A pdb=" N LYS O 820 " --> pdb=" O GLU O 816 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE O 821 " --> pdb=" O PHE O 817 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS O 829 " --> pdb=" O GLY O 825 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA O 830 " --> pdb=" O GLU O 826 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP O 831 " --> pdb=" O LYS O 827 " (cutoff:3.500A) Processing helix chain 'O' and resid 835 through 838 No H-bonds generated for 'chain 'O' and resid 835 through 838' Processing helix chain 'O' and resid 840 through 846 Processing helix chain 'O' and resid 849 through 854 Proline residue: O 853 - end of helix No H-bonds generated for 'chain 'O' and resid 849 through 854' Processing helix chain 'O' and resid 865 through 871 removed outlier: 3.697A pdb=" N ASN O 869 " --> pdb=" O VAL O 865 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS O 870 " --> pdb=" O LYS O 866 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU O 871 " --> pdb=" O ALA O 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 865 through 871' Processing helix chain 'O' and resid 873 through 875 No H-bonds generated for 'chain 'O' and resid 873 through 875' Processing helix chain 'O' and resid 877 through 882 Processing helix chain 'O' and resid 889 through 896 Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 307 through 309 removed outlier: 8.363A pdb=" N ILE A 308 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 73 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE A 72 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 248 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL A 74 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 250 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 220 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 608 through 611 Processing sheet with id= D, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= E, first strand: chain 'C' and resid 307 through 309 removed outlier: 8.155A pdb=" N ILE C 308 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 73 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE C 72 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 248 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 74 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 250 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 573 through 575 Processing sheet with id= G, first strand: chain 'D' and resid 14 through 17 Processing sheet with id= H, first strand: chain 'D' and resid 307 through 310 removed outlier: 7.713A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 310 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASP D 75 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN D 70 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE D 216 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL D 249 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 218 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR D 251 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 573 through 576 Processing sheet with id= J, first strand: chain 'E' and resid 14 through 17 Processing sheet with id= K, first strand: chain 'E' and resid 307 through 309 removed outlier: 7.812A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 70 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY E 252 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 616 through 620 removed outlier: 3.717A pdb=" N ALA E 612 " --> pdb=" O CYS E 655 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 14 through 17 Processing sheet with id= N, first strand: chain 'F' and resid 307 through 309 removed outlier: 8.170A pdb=" N ILE F 308 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE F 73 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE F 72 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 248 " --> pdb=" O PHE F 72 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL F 74 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA F 250 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 216 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL F 249 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 218 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR F 251 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE F 220 " --> pdb=" O THR F 251 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 573 through 575 removed outlier: 3.545A pdb=" N VAL F 611 " --> pdb=" O MET F 617 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 14 through 17 Processing sheet with id= Q, first strand: chain 'G' and resid 307 through 309 removed outlier: 8.256A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE G 72 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL G 248 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL G 74 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA G 250 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 610 through 612 removed outlier: 3.518A pdb=" N CYS G 655 " --> pdb=" O THR G 610 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= T, first strand: chain 'H' and resid 307 through 309 removed outlier: 8.144A pdb=" N ILE H 308 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE H 73 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE H 72 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL H 248 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL H 74 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA H 250 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL H 249 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE H 218 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE H 220 " --> pdb=" O THR H 251 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 573 through 575 Processing sheet with id= V, first strand: chain 'I' and resid 14 through 17 Processing sheet with id= W, first strand: chain 'I' and resid 307 through 309 removed outlier: 8.370A pdb=" N ILE I 308 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE I 73 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N PHE I 72 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL I 248 " --> pdb=" O PHE I 72 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL I 74 " --> pdb=" O VAL I 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA I 250 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE I 216 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL I 249 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE I 218 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR I 251 " --> pdb=" O ILE I 218 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE I 220 " --> pdb=" O THR I 251 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 608 through 611 Processing sheet with id= Y, first strand: chain 'J' and resid 14 through 17 Processing sheet with id= Z, first strand: chain 'J' and resid 307 through 309 removed outlier: 8.143A pdb=" N ILE J 308 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE J 73 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE J 72 " --> pdb=" O LEU J 246 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL J 248 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL J 74 " --> pdb=" O VAL J 248 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA J 250 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE J 216 " --> pdb=" O VAL J 247 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL J 249 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE J 218 " --> pdb=" O VAL J 249 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR J 251 " --> pdb=" O ILE J 218 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE J 220 " --> pdb=" O THR J 251 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 573 through 576 removed outlier: 4.364A pdb=" N ASP J 618 " --> pdb=" O LEU J 576 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 14 through 17 Processing sheet with id= AC, first strand: chain 'K' and resid 307 through 310 removed outlier: 7.695A pdb=" N ILE K 308 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE K 73 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU K 310 " --> pdb=" O PHE K 73 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP K 75 " --> pdb=" O LEU K 310 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN K 70 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE K 216 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL K 249 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE K 218 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR K 251 " --> pdb=" O ILE K 218 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 573 through 576 removed outlier: 3.714A pdb=" N ASP K 618 " --> pdb=" O LEU K 576 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 14 through 17 Processing sheet with id= AF, first strand: chain 'L' and resid 307 through 309 removed outlier: 7.841A pdb=" N ILE L 308 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE L 73 " --> pdb=" O ILE L 308 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN L 70 " --> pdb=" O LEU L 246 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY L 252 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE L 216 " --> pdb=" O VAL L 247 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL L 249 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE L 218 " --> pdb=" O VAL L 249 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR L 251 " --> pdb=" O ILE L 218 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 573 through 576 removed outlier: 3.832A pdb=" N VAL L 574 " --> pdb=" O CYS L 620 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS L 620 " --> pdb=" O VAL L 574 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP L 618 " --> pdb=" O LEU L 576 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA L 612 " --> pdb=" O CYS L 655 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'M' and resid 307 through 309 removed outlier: 8.166A pdb=" N ILE M 308 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE M 73 " --> pdb=" O ILE M 308 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE M 72 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL M 248 " --> pdb=" O PHE M 72 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL M 74 " --> pdb=" O VAL M 248 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA M 250 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE M 216 " --> pdb=" O VAL M 247 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL M 249 " --> pdb=" O ILE M 216 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE M 218 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR M 251 " --> pdb=" O ILE M 218 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE M 220 " --> pdb=" O THR M 251 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 573 through 575 removed outlier: 3.541A pdb=" N VAL M 574 " --> pdb=" O CYS M 620 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 14 through 17 Processing sheet with id= AL, first strand: chain 'N' and resid 307 through 309 removed outlier: 8.241A pdb=" N ILE N 308 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE N 73 " --> pdb=" O ILE N 308 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE N 72 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL N 248 " --> pdb=" O PHE N 72 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL N 74 " --> pdb=" O VAL N 248 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA N 250 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE N 216 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL N 249 " --> pdb=" O ILE N 216 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE N 218 " --> pdb=" O VAL N 249 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR N 251 " --> pdb=" O ILE N 218 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 610 through 612 Processing sheet with id= AN, first strand: chain 'O' and resid 14 through 17 Processing sheet with id= AO, first strand: chain 'O' and resid 307 through 309 removed outlier: 8.139A pdb=" N ILE O 308 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE O 73 " --> pdb=" O ILE O 308 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N PHE O 72 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL O 248 " --> pdb=" O PHE O 72 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL O 74 " --> pdb=" O VAL O 248 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA O 250 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE O 216 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL O 249 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE O 218 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR O 251 " --> pdb=" O ILE O 218 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE O 220 " --> pdb=" O THR O 251 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 573 through 575 3684 hydrogen bonds defined for protein. 10506 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: 40.77 Time building geometry restraints manager: 31.94 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: 29314 1.34 - 1.46: 12923 1.46 - 1.58: 52079 1.58 - 1.70: 50 1.70 - 1.82: 658 Bond restraints: 95024 Sorted by residual: bond pdb=" N VAL F 814 " pdb=" CA VAL F 814 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.50e+01 bond pdb=" N GLU H 333 " pdb=" CA GLU H 333 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.49e+01 bond pdb=" N LEU M 599 " pdb=" CA LEU M 599 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" N VAL H 330 " pdb=" CA VAL H 330 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N ILE M 656 " pdb=" CA ILE M 656 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 ... (remaining 95019 not shown) Histogram of bond angle deviations from ideal: 97.93 - 106.34: 1828 106.34 - 114.75: 57546 114.75 - 123.16: 65381 123.16 - 131.57: 3340 131.57 - 139.98: 159 Bond angle restraints: 128254 Sorted by residual: angle pdb=" PB ATP O1001 " pdb=" O3B ATP O1001 " pdb=" PG ATP O1001 " ideal model delta sigma weight residual 139.87 133.42 6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" N LYS J 271 " pdb=" CA LYS J 271 " pdb=" C LYS J 271 " ideal model delta sigma weight residual 113.97 107.13 6.84 1.28e+00 6.10e-01 2.86e+01 angle pdb=" N VAL O 786 " pdb=" CA VAL O 786 " pdb=" C VAL O 786 " ideal model delta sigma weight residual 112.29 107.32 4.97 9.40e-01 1.13e+00 2.79e+01 angle pdb=" C GLY M 598 " pdb=" N LEU M 599 " pdb=" CA LEU M 599 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 angle pdb=" PB ATP J1001 " pdb=" O3B ATP J1001 " pdb=" PG ATP J1001 " ideal model delta sigma weight residual 139.87 135.64 4.23 1.00e+00 1.00e+00 1.79e+01 ... (remaining 128249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 51177 17.95 - 35.91: 5486 35.91 - 53.86: 1000 53.86 - 71.82: 217 71.82 - 89.77: 100 Dihedral angle restraints: 57980 sinusoidal: 23852 harmonic: 34128 Sorted by residual: dihedral pdb=" CA ARG O 440 " pdb=" C ARG O 440 " pdb=" N PHE O 441 " pdb=" CA PHE O 441 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET L 313 " pdb=" C MET L 313 " pdb=" N LEU L 314 " pdb=" CA LEU L 314 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN F 226 " pdb=" C GLN F 226 " pdb=" N PHE F 227 " pdb=" CA PHE F 227 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 57977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 11829 0.049 - 0.097: 2164 0.097 - 0.146: 387 0.146 - 0.194: 24 0.194 - 0.243: 12 Chirality restraints: 14416 Sorted by residual: chirality pdb=" CA ARG G 467 " pdb=" N ARG G 467 " pdb=" C ARG G 467 " pdb=" CB ARG G 467 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU O 733 " pdb=" CB LEU O 733 " pdb=" CD1 LEU O 733 " pdb=" CD2 LEU O 733 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL H 786 " pdb=" CA VAL H 786 " pdb=" CG1 VAL H 786 " pdb=" CG2 VAL H 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 14413 not shown) Planarity restraints: 16406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 270 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C SER J 270 " -0.043 2.00e-02 2.50e+03 pdb=" O SER J 270 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS J 271 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 173 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO I 174 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO I 174 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 174 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 597 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C ASN M 597 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN M 597 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY M 598 " 0.014 2.00e-02 2.50e+03 ... (remaining 16403 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 929 2.57 - 3.15: 76962 3.15 - 3.74: 151316 3.74 - 4.32: 216121 4.32 - 4.90: 345862 Nonbonded interactions: 791190 Sorted by model distance: nonbonded pdb=" OD1 ASP H 798 " pdb=" N ARG H 799 " model vdw 1.989 2.520 nonbonded pdb=" OG1 THR C 83 " pdb=" O2G ATP C1001 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR E 538 " pdb=" O ILE E 656 " model vdw 2.197 2.440 nonbonded pdb=" OG SER H 546 " pdb=" OD2 ASP H 631 " model vdw 2.201 2.440 nonbonded pdb=" NE2 GLN F 226 " pdb=" OD1 ASP F 228 " model vdw 2.203 2.520 ... (remaining 791185 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 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'C' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'D' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'E' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or resid 908 through 932) \ ) selection = (chain 'F' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'G' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 897 or (resid 907 and (name N or name CA or name C or name O or name CB )) or r \ esid 909 through 932)) selection = (chain 'H' and (resid 13 through 394 or resid 412 through 517 or resid 527 throu \ gh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C o \ r name O or name CB )) or resid 909 through 932)) selection = (chain 'I' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'J' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'K' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'L' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or resid 908 through 932) \ ) selection = (chain 'M' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'N' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 897 or (resid 907 and (name N or name CA or name C or name O or name CB )) or r \ esid 909 through 932)) selection = (chain 'O' and (resid 13 through 394 or resid 412 through 517 or resid 527 throu \ gh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C o \ r name O or name CB )) or resid 909 through 932)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 20.400 Check model and map are aligned: 1.040 Set scattering table: 0.630 Process input model: 199.050 Find NCS groups from input model: 6.940 Set up NCS constraints: 0.310 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 235.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 0.042 95024 Z= 0.156 Angle : 0.475 8.587 128254 Z= 0.270 Chirality : 0.039 0.243 14416 Planarity : 0.003 0.058 16406 Dihedral : 15.460 89.771 35852 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % 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: -0.66 (0.08), residues: 11510 helix: -0.25 (0.06), residues: 6140 sheet: 0.59 (0.24), residues: 538 loop : -0.63 (0.09), residues: 4832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 660 HIS 0.008 0.001 HIS I 292 PHE 0.032 0.001 PHE O 741 TYR 0.024 0.001 TYR I 793 ARG 0.011 0.000 ARG M 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1241 time to evaluate : 8.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.7756 (mt) cc_final: 0.7537 (mt) REVERT: A 765 MET cc_start: 0.5705 (mmp) cc_final: 0.5251 (ptt) REVERT: D 913 THR cc_start: 0.7124 (m) cc_final: 0.6911 (p) REVERT: E 500 MET cc_start: 0.6126 (tpt) cc_final: 0.5773 (tpt) REVERT: E 534 GLU cc_start: 0.7530 (mp0) cc_final: 0.7100 (mp0) REVERT: E 646 PHE cc_start: 0.8506 (t80) cc_final: 0.8233 (t80) REVERT: F 166 LEU cc_start: 0.8455 (pp) cc_final: 0.8166 (mt) REVERT: F 656 ILE cc_start: 0.8041 (mt) cc_final: 0.7510 (mt) REVERT: F 827 LYS cc_start: 0.7325 (mmmt) cc_final: 0.7015 (mmmt) REVERT: G 328 ILE cc_start: 0.7172 (mp) cc_final: 0.6917 (mp) REVERT: G 451 PHE cc_start: 0.5824 (t80) cc_final: 0.5588 (t80) REVERT: G 617 MET cc_start: 0.7308 (ptt) cc_final: 0.7105 (ptp) REVERT: G 741 PHE cc_start: 0.6156 (t80) cc_final: 0.4700 (t80) REVERT: H 338 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6203 (m-30) REVERT: H 388 THR cc_start: 0.7968 (p) cc_final: 0.7692 (p) REVERT: H 418 ARG cc_start: 0.7387 (tmm-80) cc_final: 0.6998 (tmm-80) REVERT: H 435 ASN cc_start: 0.7252 (t0) cc_final: 0.6976 (p0) REVERT: K 380 MET cc_start: 0.2811 (tmm) cc_final: 0.2602 (ttp) REVERT: K 913 THR cc_start: 0.7050 (m) cc_final: 0.6781 (p) REVERT: L 599 LEU cc_start: 0.6982 (tp) cc_final: 0.6701 (tp) REVERT: L 646 PHE cc_start: 0.8519 (t80) cc_final: 0.8260 (t80) REVERT: L 850 ILE cc_start: 0.8418 (mm) cc_final: 0.8217 (mm) REVERT: L 893 ASP cc_start: 0.7495 (m-30) cc_final: 0.7295 (t0) REVERT: M 538 TYR cc_start: 0.8020 (t80) cc_final: 0.7675 (t80) REVERT: M 798 ASP cc_start: 0.6180 (p0) cc_final: 0.5808 (p0) REVERT: N 19 PHE cc_start: 0.6756 (m-80) cc_final: 0.6388 (m-80) REVERT: N 328 ILE cc_start: 0.7150 (mp) cc_final: 0.6905 (mp) REVERT: N 741 PHE cc_start: 0.6280 (t80) cc_final: 0.4890 (t80) outliers start: 5 outliers final: 1 residues processed: 1246 average time/residue: 0.9149 time to fit residues: 1939.7161 Evaluate side-chains 999 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 997 time to evaluate : 7.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain M residue 611 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 981 optimal weight: 9.9990 chunk 880 optimal weight: 9.9990 chunk 488 optimal weight: 9.9990 chunk 300 optimal weight: 1.9990 chunk 594 optimal weight: 3.9990 chunk 470 optimal weight: 10.0000 chunk 910 optimal weight: 30.0000 chunk 352 optimal weight: 0.6980 chunk 553 optimal weight: 20.0000 chunk 677 optimal weight: 5.9990 chunk 1055 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 583 HIS D 908 GLN ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 862 ASN ** H 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 839 HIS ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 752 HIS ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN L 346 GLN ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 647 ASN ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 862 ASN M 357 ASN M 392 HIS ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 552 ASN O 624 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 95024 Z= 0.449 Angle : 0.632 11.274 128254 Z= 0.331 Chirality : 0.045 0.203 14416 Planarity : 0.005 0.064 16406 Dihedral : 6.690 81.079 12903 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.95 % Allowed : 9.12 % Favored : 89.93 % 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: -0.87 (0.08), residues: 11510 helix: -0.31 (0.06), residues: 6338 sheet: 0.12 (0.22), residues: 594 loop : -0.88 (0.09), residues: 4578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 738 HIS 0.011 0.001 HIS I 292 PHE 0.030 0.002 PHE O 464 TYR 0.027 0.002 TYR F 465 ARG 0.006 0.001 ARG N 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1058 time to evaluate : 8.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: C 336 MET cc_start: 0.6947 (mtt) cc_final: 0.6680 (mtp) REVERT: C 370 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6490 (mm-30) REVERT: C 531 LEU cc_start: 0.7576 (tt) cc_final: 0.7335 (tp) REVERT: C 534 GLU cc_start: 0.7298 (pt0) cc_final: 0.7046 (tt0) REVERT: D 140 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: D 429 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6824 (mp) REVERT: D 527 LYS cc_start: 0.5526 (tptt) cc_final: 0.4551 (mmtp) REVERT: E 425 MET cc_start: 0.7904 (ttp) cc_final: 0.7671 (ttm) REVERT: E 500 MET cc_start: 0.6018 (tpt) cc_final: 0.5698 (tpt) REVERT: E 646 PHE cc_start: 0.8480 (t80) cc_final: 0.8147 (t80) REVERT: F 510 ILE cc_start: 0.8561 (mm) cc_final: 0.8352 (mm) REVERT: G 328 ILE cc_start: 0.7288 (mp) cc_final: 0.7038 (mp) REVERT: G 741 PHE cc_start: 0.6171 (t80) cc_final: 0.4803 (t80) REVERT: H 435 ASN cc_start: 0.7423 (t0) cc_final: 0.7060 (p0) REVERT: H 573 MET cc_start: 0.5145 (mtt) cc_final: 0.4672 (tpp) REVERT: H 604 MET cc_start: 0.7319 (tpt) cc_final: 0.7041 (tpt) REVERT: H 794 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6289 (m-70) REVERT: I 275 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: I 647 ASN cc_start: 0.6957 (m-40) cc_final: 0.6699 (m110) REVERT: I 802 ILE cc_start: 0.7675 (mm) cc_final: 0.7468 (mm) REVERT: J 313 MET cc_start: 0.6855 (mmt) cc_final: 0.6494 (mmp) REVERT: K 380 MET cc_start: 0.2743 (tmm) cc_final: 0.2496 (ttp) REVERT: K 429 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6769 (mp) REVERT: L 599 LEU cc_start: 0.6473 (tp) cc_final: 0.6222 (tp) REVERT: L 617 MET cc_start: 0.6266 (mtt) cc_final: 0.6058 (mtm) REVERT: L 646 PHE cc_start: 0.8492 (t80) cc_final: 0.8179 (t80) REVERT: L 850 ILE cc_start: 0.8446 (mm) cc_final: 0.8234 (mm) REVERT: L 894 TYR cc_start: 0.5690 (t80) cc_final: 0.5396 (t80) REVERT: M 454 VAL cc_start: 0.8860 (m) cc_final: 0.8597 (t) REVERT: M 510 ILE cc_start: 0.8544 (mm) cc_final: 0.8329 (mm) REVERT: M 538 TYR cc_start: 0.8202 (t80) cc_final: 0.7871 (t80) REVERT: M 798 ASP cc_start: 0.6276 (p0) cc_final: 0.5862 (p0) REVERT: M 818 GLU cc_start: 0.6426 (tt0) cc_final: 0.6087 (tt0) REVERT: N 19 PHE cc_start: 0.7067 (m-80) cc_final: 0.6767 (m-80) REVERT: N 328 ILE cc_start: 0.7242 (mp) cc_final: 0.7001 (mp) REVERT: N 617 MET cc_start: 0.6065 (ptp) cc_final: 0.5588 (ptp) REVERT: N 624 ASN cc_start: 0.6085 (m-40) cc_final: 0.5864 (m110) REVERT: N 741 PHE cc_start: 0.6323 (t80) cc_final: 0.4886 (t80) REVERT: O 202 GLU cc_start: 0.7730 (mp0) cc_final: 0.7452 (mp0) REVERT: O 573 MET cc_start: 0.5148 (mtt) cc_final: 0.4768 (tpp) REVERT: O 794 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6757 (m-70) outliers start: 98 outliers final: 66 residues processed: 1118 average time/residue: 0.8789 time to fit residues: 1670.8660 Evaluate side-chains 1030 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 957 time to evaluate : 7.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 173 LYS Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 811 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 843 PHE Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 413 VAL Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 795 SER Chi-restraints excluded: chain H residue 796 VAL Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 191 ILE Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 173 LYS Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 416 LEU Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 811 VAL Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 794 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 586 optimal weight: 0.9980 chunk 327 optimal weight: 10.0000 chunk 878 optimal weight: 0.9990 chunk 718 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 1057 optimal weight: 9.9990 chunk 1141 optimal weight: 6.9990 chunk 941 optimal weight: 0.9990 chunk 1048 optimal weight: 7.9990 chunk 360 optimal weight: 0.9980 chunk 848 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN G 87 ASN G 469 GLN G 747 ASN ** H 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 HIS ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 469 GLN I 549 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 GLN ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 ASN ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 624 ASN ** O 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 95024 Z= 0.160 Angle : 0.475 10.288 128254 Z= 0.253 Chirality : 0.038 0.225 14416 Planarity : 0.003 0.056 16406 Dihedral : 6.406 81.917 12903 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.01 % Allowed : 11.73 % Favored : 87.26 % 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: -0.44 (0.08), residues: 11510 helix: 0.07 (0.06), residues: 6362 sheet: 0.29 (0.24), residues: 522 loop : -0.72 (0.09), residues: 4626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 738 HIS 0.005 0.001 HIS H 794 PHE 0.029 0.001 PHE O 464 TYR 0.019 0.001 TYR L 288 ARG 0.005 0.000 ARG M 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1098 time to evaluate : 8.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 845 LEU cc_start: 0.8178 (mm) cc_final: 0.7791 (mm) REVERT: C 336 MET cc_start: 0.6682 (mtt) cc_final: 0.6422 (mtp) REVERT: C 370 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6276 (mm-30) REVERT: C 531 LEU cc_start: 0.7526 (tt) cc_final: 0.7268 (tp) REVERT: C 534 GLU cc_start: 0.7266 (pt0) cc_final: 0.7011 (tt0) REVERT: D 429 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6777 (mp) REVERT: D 527 LYS cc_start: 0.5565 (tptt) cc_final: 0.4716 (mptt) REVERT: D 827 LYS cc_start: 0.7431 (mmtm) cc_final: 0.7022 (mttp) REVERT: D 835 TRP cc_start: 0.7097 (m100) cc_final: 0.6879 (t60) REVERT: E 380 MET cc_start: 0.6853 (mmt) cc_final: 0.5109 (ttm) REVERT: E 425 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7427 (ttm) REVERT: E 441 PHE cc_start: 0.2901 (m-80) cc_final: 0.2616 (m-80) REVERT: E 485 GLN cc_start: 0.6610 (tp-100) cc_final: 0.6342 (mm-40) REVERT: E 500 MET cc_start: 0.5916 (tpt) cc_final: 0.5550 (tpt) REVERT: E 560 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6448 (t0) REVERT: E 646 PHE cc_start: 0.8326 (t80) cc_final: 0.8035 (t80) REVERT: F 176 TYR cc_start: 0.8155 (m-80) cc_final: 0.7893 (m-80) REVERT: F 454 VAL cc_start: 0.8805 (m) cc_final: 0.8497 (t) REVERT: F 538 TYR cc_start: 0.7886 (t80) cc_final: 0.7428 (t80) REVERT: G 328 ILE cc_start: 0.7212 (mp) cc_final: 0.6962 (mp) REVERT: G 741 PHE cc_start: 0.6163 (t80) cc_final: 0.4723 (t80) REVERT: H 794 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6208 (m90) REVERT: I 275 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: I 647 ASN cc_start: 0.6946 (m-40) cc_final: 0.6664 (m110) REVERT: I 845 LEU cc_start: 0.8151 (mm) cc_final: 0.7789 (mm) REVERT: J 370 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6533 (mm-30) REVERT: K 14 ILE cc_start: 0.7847 (mp) cc_final: 0.7420 (mm) REVERT: K 380 MET cc_start: 0.2596 (tmm) cc_final: 0.2338 (ttp) REVERT: K 429 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6777 (mp) REVERT: K 836 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7595 (ptmt) REVERT: L 346 GLN cc_start: 0.6877 (mm110) cc_final: 0.6665 (mm-40) REVERT: L 599 LEU cc_start: 0.6705 (tp) cc_final: 0.6464 (tp) REVERT: L 646 PHE cc_start: 0.8395 (t80) cc_final: 0.8100 (t80) REVERT: L 894 TYR cc_start: 0.5673 (t80) cc_final: 0.5187 (t80) REVERT: M 538 TYR cc_start: 0.8229 (t80) cc_final: 0.7931 (t80) REVERT: M 798 ASP cc_start: 0.6202 (p0) cc_final: 0.5788 (p0) REVERT: N 19 PHE cc_start: 0.7341 (m-80) cc_final: 0.7123 (m-80) REVERT: N 328 ILE cc_start: 0.7134 (mp) cc_final: 0.6855 (mp) REVERT: N 617 MET cc_start: 0.5964 (ptp) cc_final: 0.5566 (ptp) REVERT: N 741 PHE cc_start: 0.6216 (t80) cc_final: 0.4757 (t80) REVERT: O 336 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4191 (tpt) REVERT: O 573 MET cc_start: 0.4966 (mtt) cc_final: 0.4740 (tpp) REVERT: O 794 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6365 (m-70) outliers start: 104 outliers final: 56 residues processed: 1164 average time/residue: 0.8614 time to fit residues: 1718.7820 Evaluate side-chains 1069 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1004 time to evaluate : 7.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 560 ASN Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 794 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1044 optimal weight: 0.6980 chunk 794 optimal weight: 9.9990 chunk 548 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 504 optimal weight: 5.9990 chunk 709 optimal weight: 20.0000 chunk 1060 optimal weight: 8.9990 chunk 1123 optimal weight: 10.0000 chunk 554 optimal weight: 1.9990 chunk 1005 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 GLN E 40 GLN ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 ASN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 862 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 ASN G 747 ASN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 HIS ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 435 ASN ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 744 ASN ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 GLN K 575 GLN K 908 GLN L 40 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 624 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 95024 Z= 0.383 Angle : 0.568 9.820 128254 Z= 0.297 Chirality : 0.042 0.186 14416 Planarity : 0.004 0.061 16406 Dihedral : 6.575 87.735 12902 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.86 % Allowed : 13.67 % Favored : 84.47 % 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: -0.63 (0.08), residues: 11510 helix: -0.05 (0.06), residues: 6374 sheet: -0.05 (0.22), residues: 584 loop : -0.83 (0.09), residues: 4552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 835 HIS 0.016 0.001 HIS I 549 PHE 0.038 0.002 PHE O 464 TYR 0.020 0.002 TYR F 465 ARG 0.006 0.000 ARG M 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1016 time to evaluate : 8.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7772 (mm) REVERT: C 336 MET cc_start: 0.6716 (mtt) cc_final: 0.6483 (mtp) REVERT: C 370 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6329 (mm-30) REVERT: C 531 LEU cc_start: 0.7584 (tt) cc_final: 0.7319 (tp) REVERT: C 534 GLU cc_start: 0.7322 (pt0) cc_final: 0.7081 (tt0) REVERT: D 140 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: D 429 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6872 (mp) REVERT: D 527 LYS cc_start: 0.5575 (tptt) cc_final: 0.4754 (mptt) REVERT: D 827 LYS cc_start: 0.7464 (mmtm) cc_final: 0.7118 (mttp) REVERT: E 441 PHE cc_start: 0.3022 (m-80) cc_final: 0.2778 (m-80) REVERT: E 500 MET cc_start: 0.6008 (tpt) cc_final: 0.5697 (tpt) REVERT: F 176 TYR cc_start: 0.8303 (m-10) cc_final: 0.8095 (m-80) REVERT: F 454 VAL cc_start: 0.8904 (m) cc_final: 0.8614 (t) REVERT: F 510 ILE cc_start: 0.8466 (mm) cc_final: 0.8216 (mm) REVERT: F 538 TYR cc_start: 0.7967 (t80) cc_final: 0.7548 (t80) REVERT: G 426 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7930 (mp) REVERT: G 741 PHE cc_start: 0.6248 (t80) cc_final: 0.4916 (t80) REVERT: H 435 ASN cc_start: 0.6952 (t0) cc_final: 0.6739 (p0) REVERT: H 604 MET cc_start: 0.7339 (tpt) cc_final: 0.6657 (tpt) REVERT: H 822 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6583 (mmtt) REVERT: J 534 GLU cc_start: 0.7697 (pt0) cc_final: 0.7313 (tt0) REVERT: K 429 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6806 (mp) REVERT: K 836 LYS cc_start: 0.7761 (ptmt) cc_final: 0.7509 (ptmt) REVERT: L 366 MET cc_start: 0.8068 (ptm) cc_final: 0.7764 (ptp) REVERT: L 380 MET cc_start: 0.6842 (mmt) cc_final: 0.5075 (ttm) REVERT: L 599 LEU cc_start: 0.6670 (tp) cc_final: 0.6379 (tp) REVERT: L 646 PHE cc_start: 0.8407 (t80) cc_final: 0.8115 (t80) REVERT: L 894 TYR cc_start: 0.5699 (t80) cc_final: 0.5110 (t80) REVERT: M 510 ILE cc_start: 0.8516 (mm) cc_final: 0.8263 (mm) REVERT: M 538 TYR cc_start: 0.8280 (t80) cc_final: 0.7996 (t80) REVERT: M 798 ASP cc_start: 0.6089 (p0) cc_final: 0.5654 (p0) REVERT: N 19 PHE cc_start: 0.7284 (m-80) cc_final: 0.7029 (m-80) REVERT: N 328 ILE cc_start: 0.7273 (mp) cc_final: 0.7071 (mp) REVERT: N 336 MET cc_start: 0.4762 (mmm) cc_final: 0.4479 (mmm) REVERT: N 617 MET cc_start: 0.5802 (ptp) cc_final: 0.5547 (ptp) REVERT: N 741 PHE cc_start: 0.6300 (t80) cc_final: 0.4806 (t80) REVERT: O 573 MET cc_start: 0.5037 (mtt) cc_final: 0.4696 (tpp) REVERT: O 794 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6402 (m-70) REVERT: O 822 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6756 (mmtt) outliers start: 192 outliers final: 129 residues processed: 1150 average time/residue: 0.8725 time to fit residues: 1712.9316 Evaluate side-chains 1106 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 971 time to evaluate : 8.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 491 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 413 VAL Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 727 ILE Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 466 LEU Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 727 ILE Chi-restraints excluded: chain M residue 770 ASN Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 452 THR Chi-restraints excluded: chain O residue 544 ILE Chi-restraints excluded: chain O residue 794 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 935 optimal weight: 1.9990 chunk 637 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 836 optimal weight: 3.9990 chunk 463 optimal weight: 10.0000 chunk 958 optimal weight: 5.9990 chunk 776 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 573 optimal weight: 0.0170 chunk 1008 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 549 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 GLN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 624 ASN ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 GLN O 624 ASN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 95024 Z= 0.214 Angle : 0.488 9.357 128254 Z= 0.258 Chirality : 0.039 0.183 14416 Planarity : 0.004 0.059 16406 Dihedral : 6.421 89.090 12902 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.73 % Allowed : 14.90 % Favored : 83.38 % 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: -0.38 (0.08), residues: 11510 helix: 0.17 (0.06), residues: 6388 sheet: 0.11 (0.23), residues: 542 loop : -0.75 (0.09), residues: 4580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 892 HIS 0.005 0.001 HIS F 392 PHE 0.036 0.002 PHE O 741 TYR 0.019 0.001 TYR N 288 ARG 0.011 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1025 time to evaluate : 8.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 336 MET cc_start: 0.6615 (mtt) cc_final: 0.6396 (mtp) REVERT: C 370 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6282 (mm-30) REVERT: C 425 MET cc_start: 0.6459 (mpp) cc_final: 0.6090 (mmt) REVERT: C 531 LEU cc_start: 0.7555 (tt) cc_final: 0.7288 (tp) REVERT: C 534 GLU cc_start: 0.7362 (pt0) cc_final: 0.7123 (tt0) REVERT: D 140 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: D 429 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6805 (mp) REVERT: D 527 LYS cc_start: 0.5593 (tptt) cc_final: 0.4729 (mptt) REVERT: D 827 LYS cc_start: 0.7449 (mmtm) cc_final: 0.7082 (mttp) REVERT: D 835 TRP cc_start: 0.7156 (m100) cc_final: 0.6941 (t60) REVERT: E 380 MET cc_start: 0.6907 (mmt) cc_final: 0.5136 (ttm) REVERT: E 441 PHE cc_start: 0.2953 (m-80) cc_final: 0.2734 (m-80) REVERT: E 500 MET cc_start: 0.5867 (tpt) cc_final: 0.5519 (tpt) REVERT: E 765 MET cc_start: 0.7085 (mtp) cc_final: 0.6811 (tmm) REVERT: F 454 VAL cc_start: 0.8853 (m) cc_final: 0.8578 (t) REVERT: F 538 TYR cc_start: 0.8003 (t80) cc_final: 0.7627 (t80) REVERT: G 328 ILE cc_start: 0.7390 (mp) cc_final: 0.7190 (mp) REVERT: G 426 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7839 (mp) REVERT: G 715 GLN cc_start: 0.6743 (tp40) cc_final: 0.6425 (mp10) REVERT: G 716 TRP cc_start: 0.5543 (t60) cc_final: 0.5274 (t60) REVERT: G 741 PHE cc_start: 0.6204 (t80) cc_final: 0.4857 (t80) REVERT: H 435 ASN cc_start: 0.6939 (t0) cc_final: 0.6654 (p0) REVERT: H 604 MET cc_start: 0.7451 (tpt) cc_final: 0.6800 (tpt) REVERT: H 822 LYS cc_start: 0.6918 (mmtt) cc_final: 0.6622 (mmtt) REVERT: I 275 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: J 534 GLU cc_start: 0.7652 (pt0) cc_final: 0.7319 (tt0) REVERT: K 429 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6761 (mp) REVERT: K 836 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7536 (ptmt) REVERT: L 366 MET cc_start: 0.8034 (ptm) cc_final: 0.7810 (ptp) REVERT: L 380 MET cc_start: 0.6849 (mmt) cc_final: 0.5134 (ttm) REVERT: L 599 LEU cc_start: 0.6670 (tp) cc_final: 0.6385 (tp) REVERT: M 538 TYR cc_start: 0.8170 (t80) cc_final: 0.7909 (t80) REVERT: M 798 ASP cc_start: 0.6053 (p0) cc_final: 0.5616 (p0) REVERT: N 19 PHE cc_start: 0.7347 (m-80) cc_final: 0.7099 (m-80) REVERT: N 328 ILE cc_start: 0.7214 (mp) cc_final: 0.7007 (mp) REVERT: N 336 MET cc_start: 0.4770 (mmm) cc_final: 0.4527 (mtp) REVERT: N 741 PHE cc_start: 0.6205 (t80) cc_final: 0.4713 (t80) REVERT: O 336 MET cc_start: 0.4831 (OUTLIER) cc_final: 0.4324 (tpt) REVERT: O 418 ARG cc_start: 0.7469 (tmm-80) cc_final: 0.6982 (tmm-80) REVERT: O 822 LYS cc_start: 0.6918 (mmtt) cc_final: 0.6674 (mmtt) outliers start: 178 outliers final: 123 residues processed: 1148 average time/residue: 0.8785 time to fit residues: 1721.6260 Evaluate side-chains 1107 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 977 time to evaluate : 8.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 441 PHE Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 796 VAL Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 816 GLU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 452 THR Chi-restraints excluded: chain O residue 654 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 377 optimal weight: 7.9990 chunk 1011 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 659 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 1124 optimal weight: 10.0000 chunk 933 optimal weight: 0.5980 chunk 520 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 590 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN K 477 ASN ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 560 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 GLN ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 95024 Z= 0.191 Angle : 0.477 9.646 128254 Z= 0.252 Chirality : 0.039 0.174 14416 Planarity : 0.003 0.056 16406 Dihedral : 6.341 89.849 12902 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.96 % Allowed : 15.32 % Favored : 82.73 % 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: -0.22 (0.08), residues: 11510 helix: 0.33 (0.06), residues: 6396 sheet: 0.17 (0.23), residues: 542 loop : -0.73 (0.09), residues: 4572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 892 HIS 0.012 0.001 HIS A 549 PHE 0.036 0.001 PHE O 741 TYR 0.022 0.001 TYR D 288 ARG 0.007 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1033 time to evaluate : 8.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 845 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7732 (mm) REVERT: C 336 MET cc_start: 0.6699 (mtt) cc_final: 0.6490 (mtp) REVERT: C 370 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6256 (mm-30) REVERT: C 425 MET cc_start: 0.6360 (mpp) cc_final: 0.6033 (mmt) REVERT: C 531 LEU cc_start: 0.7543 (tt) cc_final: 0.7277 (tp) REVERT: C 534 GLU cc_start: 0.7363 (pt0) cc_final: 0.7119 (tt0) REVERT: D 140 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: D 416 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 429 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6787 (mp) REVERT: D 527 LYS cc_start: 0.5562 (tptt) cc_final: 0.4718 (mptt) REVERT: D 827 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6891 (mtmm) REVERT: D 928 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5742 (t0) REVERT: E 380 MET cc_start: 0.6902 (mmt) cc_final: 0.5127 (ttm) REVERT: E 441 PHE cc_start: 0.2910 (m-80) cc_final: 0.2693 (m-80) REVERT: E 765 MET cc_start: 0.7010 (mtp) cc_final: 0.6800 (tmm) REVERT: F 454 VAL cc_start: 0.8821 (m) cc_final: 0.8550 (t) REVERT: F 499 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: F 538 TYR cc_start: 0.8035 (t80) cc_final: 0.7657 (t80) REVERT: F 790 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6819 (mt-10) REVERT: G 426 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7815 (mp) REVERT: G 741 PHE cc_start: 0.6200 (t80) cc_final: 0.4847 (t80) REVERT: H 435 ASN cc_start: 0.6959 (t0) cc_final: 0.6643 (p0) REVERT: H 604 MET cc_start: 0.7443 (tpt) cc_final: 0.7001 (mmm) REVERT: H 794 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.5916 (m-70) REVERT: H 822 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6688 (mmtt) REVERT: I 275 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: I 647 ASN cc_start: 0.7092 (m-40) cc_final: 0.6862 (m110) REVERT: J 534 GLU cc_start: 0.7627 (pt0) cc_final: 0.7320 (tt0) REVERT: K 425 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6787 (mmp) REVERT: K 429 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6763 (mp) REVERT: K 928 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5790 (t0) REVERT: L 380 MET cc_start: 0.6807 (mmt) cc_final: 0.5091 (ttm) REVERT: L 560 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6401 (t0) REVERT: L 599 LEU cc_start: 0.6682 (tp) cc_final: 0.6398 (tp) REVERT: L 894 TYR cc_start: 0.5605 (t80) cc_final: 0.5123 (t80) REVERT: M 538 TYR cc_start: 0.8152 (t80) cc_final: 0.7832 (t80) REVERT: M 798 ASP cc_start: 0.6042 (p0) cc_final: 0.5656 (p0) REVERT: N 19 PHE cc_start: 0.7414 (m-80) cc_final: 0.7169 (m-80) REVERT: N 741 PHE cc_start: 0.6175 (t80) cc_final: 0.4685 (t80) REVERT: O 336 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4404 (tpt) REVERT: O 488 GLU cc_start: 0.6228 (tt0) cc_final: 0.6015 (tt0) REVERT: O 822 LYS cc_start: 0.6885 (mmtt) cc_final: 0.6636 (mmtt) outliers start: 202 outliers final: 147 residues processed: 1179 average time/residue: 0.9321 time to fit residues: 1893.1212 Evaluate side-chains 1137 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 975 time to evaluate : 8.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 499 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 649 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain G residue 918 ASN Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 851 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 554 CYS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 544 ILE Chi-restraints excluded: chain J residue 592 ASN Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 425 MET Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 466 LEU Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 560 ASN Chi-restraints excluded: chain L residue 655 CYS Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 787 LEU Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1083 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 640 optimal weight: 5.9990 chunk 821 optimal weight: 7.9990 chunk 636 optimal weight: 20.0000 chunk 946 optimal weight: 8.9990 chunk 627 optimal weight: 1.9990 chunk 1119 optimal weight: 1.9990 chunk 700 optimal weight: 9.9990 chunk 682 optimal weight: 0.4980 chunk 517 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 GLN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN H 439 HIS ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 GLN I 549 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN O 624 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 95024 Z= 0.235 Angle : 0.494 10.723 128254 Z= 0.259 Chirality : 0.040 0.160 14416 Planarity : 0.004 0.068 16406 Dihedral : 6.321 87.164 12902 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.22 % Allowed : 15.75 % Favored : 82.03 % 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: -0.22 (0.08), residues: 11510 helix: 0.35 (0.06), residues: 6398 sheet: 0.17 (0.23), residues: 562 loop : -0.77 (0.09), residues: 4550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 716 HIS 0.006 0.001 HIS H 439 PHE 0.038 0.002 PHE O 741 TYR 0.015 0.001 TYR J 391 ARG 0.008 0.000 ARG M 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1009 time to evaluate : 8.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 425 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6882 (mmt) REVERT: A 799 ARG cc_start: 0.7185 (ppt170) cc_final: 0.6931 (ppt170) REVERT: A 845 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7743 (mm) REVERT: C 336 MET cc_start: 0.6689 (mtt) cc_final: 0.6464 (mtp) REVERT: C 370 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6224 (mm-30) REVERT: C 425 MET cc_start: 0.6408 (mpp) cc_final: 0.5974 (mmt) REVERT: C 531 LEU cc_start: 0.7550 (tt) cc_final: 0.7289 (tp) REVERT: C 534 GLU cc_start: 0.7350 (pt0) cc_final: 0.7084 (tt0) REVERT: D 140 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: D 416 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8043 (tp) REVERT: D 429 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6787 (mp) REVERT: D 527 LYS cc_start: 0.5565 (tptt) cc_final: 0.4715 (mptt) REVERT: D 827 LYS cc_start: 0.7477 (mmtm) cc_final: 0.7008 (mtmm) REVERT: D 928 ASP cc_start: 0.5956 (OUTLIER) cc_final: 0.5751 (t0) REVERT: E 380 MET cc_start: 0.6900 (mmt) cc_final: 0.5127 (ttm) REVERT: E 441 PHE cc_start: 0.2942 (m-80) cc_final: 0.2716 (m-80) REVERT: E 711 THR cc_start: 0.7781 (m) cc_final: 0.7461 (p) REVERT: E 765 MET cc_start: 0.7081 (mtp) cc_final: 0.6869 (tmm) REVERT: F 454 VAL cc_start: 0.8807 (m) cc_final: 0.8551 (t) REVERT: F 499 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: F 538 TYR cc_start: 0.8052 (t80) cc_final: 0.7671 (t80) REVERT: G 426 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7782 (mp) REVERT: G 715 GLN cc_start: 0.6716 (tp40) cc_final: 0.6373 (mp10) REVERT: G 741 PHE cc_start: 0.6214 (t80) cc_final: 0.4858 (t80) REVERT: H 604 MET cc_start: 0.7434 (tpt) cc_final: 0.7003 (mmm) REVERT: H 794 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6314 (m-70) REVERT: H 822 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6697 (mmtt) REVERT: I 275 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: I 647 ASN cc_start: 0.7174 (m-40) cc_final: 0.6924 (m110) REVERT: J 534 GLU cc_start: 0.7627 (pt0) cc_final: 0.7321 (tt0) REVERT: K 416 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8041 (tp) REVERT: K 429 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6778 (mp) REVERT: K 928 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5793 (t0) REVERT: L 380 MET cc_start: 0.6835 (mmt) cc_final: 0.5116 (ttm) REVERT: L 599 LEU cc_start: 0.6691 (tp) cc_final: 0.6399 (tp) REVERT: L 850 ILE cc_start: 0.8491 (mm) cc_final: 0.8275 (mm) REVERT: M 176 TYR cc_start: 0.8156 (m-80) cc_final: 0.7922 (m-80) REVERT: M 499 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: M 538 TYR cc_start: 0.8141 (t80) cc_final: 0.7834 (t80) REVERT: M 798 ASP cc_start: 0.6018 (p0) cc_final: 0.5641 (p0) REVERT: N 19 PHE cc_start: 0.7265 (m-80) cc_final: 0.7009 (m-80) REVERT: N 617 MET cc_start: 0.5832 (ptp) cc_final: 0.5408 (ptp) REVERT: N 741 PHE cc_start: 0.6177 (t80) cc_final: 0.4676 (t80) REVERT: O 822 LYS cc_start: 0.6880 (mmtt) cc_final: 0.6610 (mmtt) outliers start: 229 outliers final: 175 residues processed: 1175 average time/residue: 0.8726 time to fit residues: 1758.0315 Evaluate side-chains 1160 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 970 time to evaluate : 8.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 499 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain F residue 811 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 558 VAL Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 441 PHE Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 851 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain I residue 808 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 544 ILE Chi-restraints excluded: chain J residue 592 ASN Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 727 ILE Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 416 LEU Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 466 LEU Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 499 GLN Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 609 SER Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 770 ASN Chi-restraints excluded: chain M residue 787 LEU Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 811 VAL Chi-restraints excluded: chain M residue 816 GLU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 272 THR Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 140 TYR Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 251 THR Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 452 THR Chi-restraints excluded: chain O residue 654 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 692 optimal weight: 0.0980 chunk 447 optimal weight: 9.9990 chunk 668 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 712 optimal weight: 6.9990 chunk 763 optimal weight: 5.9990 chunk 553 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 880 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 560 ASN ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 530 GLN O 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 95024 Z= 0.270 Angle : 0.514 10.355 128254 Z= 0.268 Chirality : 0.040 0.177 14416 Planarity : 0.004 0.061 16406 Dihedral : 6.335 89.238 12902 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.34 % Allowed : 15.99 % Favored : 81.67 % 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: -0.29 (0.08), residues: 11510 helix: 0.31 (0.06), residues: 6420 sheet: -0.02 (0.22), residues: 592 loop : -0.81 (0.09), residues: 4498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 716 HIS 0.010 0.001 HIS I 549 PHE 0.043 0.002 PHE D 842 TYR 0.016 0.001 TYR M 176 ARG 0.008 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1004 time to evaluate : 8.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6856 (mmt) REVERT: A 799 ARG cc_start: 0.7228 (ppt170) cc_final: 0.6966 (ppt170) REVERT: A 845 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7764 (mm) REVERT: C 336 MET cc_start: 0.6600 (mtt) cc_final: 0.6379 (mtp) REVERT: C 370 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6235 (mm-30) REVERT: C 425 MET cc_start: 0.6424 (mpp) cc_final: 0.5997 (mmt) REVERT: C 531 LEU cc_start: 0.7584 (tt) cc_final: 0.7329 (tp) REVERT: C 534 GLU cc_start: 0.7353 (pt0) cc_final: 0.7089 (tt0) REVERT: D 140 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: D 416 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8006 (tp) REVERT: D 429 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6779 (mp) REVERT: D 527 LYS cc_start: 0.5582 (tptt) cc_final: 0.4743 (mptt) REVERT: D 827 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7030 (mtmm) REVERT: D 844 LEU cc_start: 0.8298 (mt) cc_final: 0.7969 (mt) REVERT: D 928 ASP cc_start: 0.5944 (OUTLIER) cc_final: 0.5739 (t0) REVERT: E 380 MET cc_start: 0.6913 (mmt) cc_final: 0.5135 (ttm) REVERT: E 437 GLU cc_start: 0.6072 (pt0) cc_final: 0.5780 (pt0) REVERT: E 765 MET cc_start: 0.7099 (mtp) cc_final: 0.6877 (tmm) REVERT: F 454 VAL cc_start: 0.8832 (m) cc_final: 0.8571 (t) REVERT: F 499 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6516 (mp10) REVERT: F 538 TYR cc_start: 0.8062 (t80) cc_final: 0.7684 (t80) REVERT: G 426 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7765 (mp) REVERT: G 443 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.3730 (mmt) REVERT: G 741 PHE cc_start: 0.6271 (t80) cc_final: 0.4943 (t80) REVERT: G 756 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4593 (mm) REVERT: H 604 MET cc_start: 0.7453 (tpt) cc_final: 0.7027 (mmm) REVERT: H 794 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: J 534 GLU cc_start: 0.7628 (pt0) cc_final: 0.7329 (tt0) REVERT: K 416 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8033 (tp) REVERT: K 429 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6786 (mp) REVERT: K 928 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5797 (t0) REVERT: L 380 MET cc_start: 0.6850 (mmt) cc_final: 0.5116 (ttm) REVERT: L 599 LEU cc_start: 0.6671 (tp) cc_final: 0.6371 (tp) REVERT: L 850 ILE cc_start: 0.8494 (mm) cc_final: 0.8277 (mm) REVERT: M 499 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: M 538 TYR cc_start: 0.8109 (t80) cc_final: 0.7735 (t80) REVERT: M 798 ASP cc_start: 0.6007 (p0) cc_final: 0.5639 (p0) REVERT: N 19 PHE cc_start: 0.7266 (m-80) cc_final: 0.7011 (m-80) REVERT: N 617 MET cc_start: 0.5788 (ptp) cc_final: 0.5382 (ptp) REVERT: N 741 PHE cc_start: 0.6184 (t80) cc_final: 0.4691 (t80) REVERT: N 790 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6439 (tm-30) REVERT: O 822 LYS cc_start: 0.6876 (mmtt) cc_final: 0.6618 (mmtt) outliers start: 241 outliers final: 191 residues processed: 1178 average time/residue: 0.8866 time to fit residues: 1791.5586 Evaluate side-chains 1182 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 976 time to evaluate : 8.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain D residue 775 MET Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain D residue 928 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 499 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 649 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 811 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 608 LEU Chi-restraints excluded: chain G residue 756 LEU Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 441 PHE Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 851 LEU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain I residue 808 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 544 ILE Chi-restraints excluded: chain J residue 592 ASN Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 657 VAL Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 416 LEU Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 466 LEU Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain K residue 928 ASP Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 332 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 499 GLN Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 609 SER Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 727 ILE Chi-restraints excluded: chain M residue 770 ASN Chi-restraints excluded: chain M residue 775 MET Chi-restraints excluded: chain M residue 787 LEU Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 793 TYR Chi-restraints excluded: chain M residue 811 VAL Chi-restraints excluded: chain M residue 816 GLU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 272 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 385 ASP Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 732 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 140 TYR Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 251 THR Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 452 THR Chi-restraints excluded: chain O residue 544 ILE Chi-restraints excluded: chain O residue 654 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1018 optimal weight: 2.9990 chunk 1072 optimal weight: 9.9990 chunk 978 optimal weight: 3.9990 chunk 1043 optimal weight: 3.9990 chunk 628 optimal weight: 0.0980 chunk 454 optimal weight: 10.0000 chunk 819 optimal weight: 5.9990 chunk 320 optimal weight: 0.6980 chunk 943 optimal weight: 3.9990 chunk 987 optimal weight: 0.6980 chunk 1040 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 862 ASN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 HIS ** I 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 95024 Z= 0.207 Angle : 0.495 9.344 128254 Z= 0.259 Chirality : 0.039 0.223 14416 Planarity : 0.003 0.063 16406 Dihedral : 6.253 88.253 12902 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.15 % Allowed : 16.32 % Favored : 81.52 % 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: -0.17 (0.08), residues: 11510 helix: 0.40 (0.06), residues: 6436 sheet: 0.16 (0.23), residues: 572 loop : -0.78 (0.09), residues: 4502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP N 716 HIS 0.006 0.001 HIS A 549 PHE 0.043 0.002 PHE O 741 TYR 0.025 0.001 TYR I 430 ARG 0.008 0.000 ARG F 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1000 time to evaluate : 8.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 425 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6889 (mmt) REVERT: A 550 TRP cc_start: 0.7824 (t60) cc_final: 0.7615 (t60) REVERT: A 845 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7747 (mm) REVERT: C 336 MET cc_start: 0.6676 (mtt) cc_final: 0.6444 (mtp) REVERT: C 370 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6214 (mm-30) REVERT: C 425 MET cc_start: 0.6361 (mpp) cc_final: 0.5883 (mmt) REVERT: C 531 LEU cc_start: 0.7568 (tt) cc_final: 0.7311 (tp) REVERT: C 534 GLU cc_start: 0.7340 (pt0) cc_final: 0.7073 (tt0) REVERT: D 140 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: D 416 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7997 (tp) REVERT: D 429 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6762 (mp) REVERT: D 527 LYS cc_start: 0.5552 (tptt) cc_final: 0.4869 (mmtp) REVERT: D 844 LEU cc_start: 0.8326 (mt) cc_final: 0.7853 (mt) REVERT: E 380 MET cc_start: 0.6894 (mmt) cc_final: 0.5125 (ttm) REVERT: E 437 GLU cc_start: 0.6081 (pt0) cc_final: 0.5763 (pt0) REVERT: E 711 THR cc_start: 0.7753 (m) cc_final: 0.7431 (p) REVERT: E 765 MET cc_start: 0.7087 (mtp) cc_final: 0.6880 (tmm) REVERT: F 176 TYR cc_start: 0.8228 (m-80) cc_final: 0.8013 (m-80) REVERT: F 454 VAL cc_start: 0.8804 (m) cc_final: 0.8553 (t) REVERT: F 499 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: F 538 TYR cc_start: 0.8046 (t80) cc_final: 0.7670 (t80) REVERT: G 426 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7756 (mp) REVERT: G 443 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3704 (mmt) REVERT: G 617 MET cc_start: 0.6233 (ptp) cc_final: 0.5685 (ptp) REVERT: G 741 PHE cc_start: 0.6242 (t80) cc_final: 0.4903 (t80) REVERT: H 604 MET cc_start: 0.7467 (tpt) cc_final: 0.7066 (mmm) REVERT: H 794 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6445 (m-70) REVERT: I 275 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: I 647 ASN cc_start: 0.7175 (m-40) cc_final: 0.6930 (m110) REVERT: J 534 GLU cc_start: 0.7618 (pt0) cc_final: 0.7325 (tt0) REVERT: K 429 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6737 (mp) REVERT: K 861 ILE cc_start: 0.6309 (mp) cc_final: 0.6012 (mp) REVERT: L 380 MET cc_start: 0.6828 (mmt) cc_final: 0.5104 (ttm) REVERT: L 599 LEU cc_start: 0.6696 (tp) cc_final: 0.6399 (tp) REVERT: M 499 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6557 (mt0) REVERT: M 538 TYR cc_start: 0.8095 (t80) cc_final: 0.7758 (t80) REVERT: M 798 ASP cc_start: 0.6051 (p0) cc_final: 0.5637 (p0) REVERT: N 19 PHE cc_start: 0.7251 (m-80) cc_final: 0.6952 (m-80) REVERT: N 336 MET cc_start: 0.4473 (mmm) cc_final: 0.4239 (mmm) REVERT: N 443 MET cc_start: 0.5651 (mmt) cc_final: 0.4727 (mmt) REVERT: N 617 MET cc_start: 0.5790 (ptp) cc_final: 0.5396 (ptp) REVERT: N 741 PHE cc_start: 0.6157 (t80) cc_final: 0.4665 (t80) REVERT: N 790 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6445 (tm-30) REVERT: O 336 MET cc_start: 0.4859 (OUTLIER) cc_final: 0.4325 (tpt) REVERT: O 822 LYS cc_start: 0.6847 (mmtt) cc_final: 0.6580 (mmtt) outliers start: 222 outliers final: 186 residues processed: 1158 average time/residue: 0.9724 time to fit residues: 1953.9545 Evaluate side-chains 1173 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 973 time to evaluate : 8.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 499 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 649 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain F residue 775 MET Chi-restraints excluded: chain F residue 811 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 608 LEU Chi-restraints excluded: chain G residue 797 SER Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 338 ASP Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 441 PHE Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 851 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain I residue 808 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 544 ILE Chi-restraints excluded: chain J residue 592 ASN Chi-restraints excluded: chain J residue 609 SER Chi-restraints excluded: chain J residue 657 VAL Chi-restraints excluded: chain J residue 721 ASN Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain M residue 366 MET Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 499 GLN Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 609 SER Chi-restraints excluded: chain M residue 611 VAL Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 727 ILE Chi-restraints excluded: chain M residue 770 ASN Chi-restraints excluded: chain M residue 775 MET Chi-restraints excluded: chain M residue 787 LEU Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 811 VAL Chi-restraints excluded: chain M residue 816 GLU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 272 THR Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 385 ASP Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 558 VAL Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 797 SER Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 140 TYR Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 209 GLU Chi-restraints excluded: chain O residue 212 ASP Chi-restraints excluded: chain O residue 251 THR Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 452 THR Chi-restraints excluded: chain O residue 544 ILE Chi-restraints excluded: chain O residue 654 THR Chi-restraints excluded: chain O residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 685 optimal weight: 0.5980 chunk 1103 optimal weight: 3.9990 chunk 673 optimal weight: 2.9990 chunk 523 optimal weight: 8.9990 chunk 767 optimal weight: 0.7980 chunk 1157 optimal weight: 0.7980 chunk 1065 optimal weight: 5.9990 chunk 921 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 712 optimal weight: 5.9990 chunk 565 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 GLN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 469 GLN ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN K 477 ASN ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 95024 Z= 0.148 Angle : 0.472 9.818 128254 Z= 0.247 Chirality : 0.038 0.199 14416 Planarity : 0.003 0.060 16406 Dihedral : 6.112 88.636 12902 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.68 % Allowed : 16.92 % Favored : 81.41 % 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: 0.01 (0.08), residues: 11510 helix: 0.56 (0.06), residues: 6462 sheet: 0.26 (0.24), residues: 532 loop : -0.72 (0.09), residues: 4516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP N 716 HIS 0.026 0.001 HIS A 549 PHE 0.042 0.001 PHE O 741 TYR 0.028 0.001 TYR A 430 ARG 0.007 0.000 ARG A 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23020 Ramachandran restraints generated. 11510 Oldfield, 0 Emsley, 11510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1040 time to evaluate : 8.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 425 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6716 (mmt) REVERT: A 647 ASN cc_start: 0.7202 (m-40) cc_final: 0.6934 (m110) REVERT: A 845 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7714 (mm) REVERT: C 336 MET cc_start: 0.6690 (mtt) cc_final: 0.6450 (mtp) REVERT: C 370 GLU cc_start: 0.6382 (mm-30) cc_final: 0.6117 (mm-30) REVERT: C 425 MET cc_start: 0.6340 (mpp) cc_final: 0.5751 (mmt) REVERT: C 531 LEU cc_start: 0.7501 (tt) cc_final: 0.7246 (tp) REVERT: C 534 GLU cc_start: 0.7335 (pt0) cc_final: 0.7059 (tt0) REVERT: C 799 ARG cc_start: 0.5784 (tmt170) cc_final: 0.5579 (tmm160) REVERT: D 140 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: D 429 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6791 (mp) REVERT: D 527 LYS cc_start: 0.5544 (tptt) cc_final: 0.4867 (mmtp) REVERT: D 827 LYS cc_start: 0.7523 (mmtm) cc_final: 0.6977 (mtmm) REVERT: E 380 MET cc_start: 0.6908 (mmt) cc_final: 0.5137 (ttm) REVERT: E 437 GLU cc_start: 0.6066 (pt0) cc_final: 0.5746 (pt0) REVERT: E 711 THR cc_start: 0.7789 (m) cc_final: 0.7461 (p) REVERT: F 454 VAL cc_start: 0.8761 (m) cc_final: 0.8517 (t) REVERT: F 499 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: F 538 TYR cc_start: 0.8017 (t80) cc_final: 0.7644 (t80) REVERT: G 426 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7777 (mp) REVERT: G 443 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.3679 (mmt) REVERT: G 617 MET cc_start: 0.6156 (ptp) cc_final: 0.5614 (ptp) REVERT: G 741 PHE cc_start: 0.6215 (t80) cc_final: 0.4871 (t80) REVERT: G 756 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4655 (mm) REVERT: H 391 TYR cc_start: 0.7244 (t80) cc_final: 0.7025 (t80) REVERT: H 604 MET cc_start: 0.7446 (tpt) cc_final: 0.7050 (mmm) REVERT: H 782 PHE cc_start: 0.6604 (t80) cc_final: 0.6395 (t80) REVERT: H 794 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6559 (m-70) REVERT: I 647 ASN cc_start: 0.7224 (m-40) cc_final: 0.6946 (m110) REVERT: J 799 ARG cc_start: 0.5847 (tmt170) cc_final: 0.5643 (tmm160) REVERT: K 429 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6679 (mp) REVERT: K 861 ILE cc_start: 0.6200 (mp) cc_final: 0.5947 (mp) REVERT: L 380 MET cc_start: 0.6941 (mmt) cc_final: 0.5203 (ttm) REVERT: L 599 LEU cc_start: 0.6652 (tp) cc_final: 0.6366 (tp) REVERT: L 718 LYS cc_start: 0.8120 (tptp) cc_final: 0.7840 (mttm) REVERT: M 499 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: M 538 TYR cc_start: 0.8069 (t80) cc_final: 0.7736 (t80) REVERT: M 798 ASP cc_start: 0.6058 (p0) cc_final: 0.5632 (p0) REVERT: N 19 PHE cc_start: 0.7258 (m-80) cc_final: 0.6910 (m-80) REVERT: N 336 MET cc_start: 0.4462 (mmm) cc_final: 0.4260 (mmm) REVERT: N 443 MET cc_start: 0.5641 (mmt) cc_final: 0.4771 (mmt) REVERT: N 617 MET cc_start: 0.5733 (ptp) cc_final: 0.5351 (ptp) REVERT: N 741 PHE cc_start: 0.6118 (t80) cc_final: 0.4636 (t80) REVERT: O 336 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.4104 (tpt) REVERT: O 370 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6722 (tp30) outliers start: 173 outliers final: 143 residues processed: 1158 average time/residue: 0.8594 time to fit residues: 1713.1647 Evaluate side-chains 1153 residues out of total 10312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 996 time to evaluate : 7.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 392 HIS Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 577 ASN Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 657 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 594 ASP Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 914 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 499 GLN Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain F residue 649 VAL Chi-restraints excluded: chain F residue 765 MET Chi-restraints excluded: chain F residue 770 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 384 GLN Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain G residue 756 LEU Chi-restraints excluded: chain G residue 865 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 441 PHE Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 720 VAL Chi-restraints excluded: chain H residue 794 HIS Chi-restraints excluded: chain H residue 851 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 549 HIS Chi-restraints excluded: chain I residue 706 PHE Chi-restraints excluded: chain I residue 808 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 278 LYS Chi-restraints excluded: chain J residue 281 VAL Chi-restraints excluded: chain J residue 340 ASP Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 508 VAL Chi-restraints excluded: chain J residue 544 ILE Chi-restraints excluded: chain J residue 592 ASN Chi-restraints excluded: chain J residue 657 VAL Chi-restraints excluded: chain J residue 811 VAL Chi-restraints excluded: chain J residue 846 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 429 ILE Chi-restraints excluded: chain K residue 466 LEU Chi-restraints excluded: chain K residue 616 LEU Chi-restraints excluded: chain K residue 657 VAL Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 301 LEU Chi-restraints excluded: chain L residue 532 ILE Chi-restraints excluded: chain L residue 657 VAL Chi-restraints excluded: chain L residue 868 LEU Chi-restraints excluded: chain L residue 914 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 462 THR Chi-restraints excluded: chain M residue 499 GLN Chi-restraints excluded: chain M residue 574 VAL Chi-restraints excluded: chain M residue 609 SER Chi-restraints excluded: chain M residue 652 GLN Chi-restraints excluded: chain M residue 727 ILE Chi-restraints excluded: chain M residue 770 ASN Chi-restraints excluded: chain M residue 775 MET Chi-restraints excluded: chain M residue 787 LEU Chi-restraints excluded: chain M residue 792 LEU Chi-restraints excluded: chain M residue 811 VAL Chi-restraints excluded: chain M residue 816 GLU Chi-restraints excluded: chain M residue 930 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 171 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 272 THR Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 384 GLN Chi-restraints excluded: chain N residue 475 LEU Chi-restraints excluded: chain N residue 608 LEU Chi-restraints excluded: chain N residue 745 LEU Chi-restraints excluded: chain N residue 831 ASP Chi-restraints excluded: chain O residue 140 TYR Chi-restraints excluded: chain O residue 205 LYS Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 MET Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain O residue 654 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 732 optimal weight: 7.9990 chunk 981 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 chunk 849 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 256 optimal weight: 0.9990 chunk 923 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 948 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 GLN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 575 GLN ** N 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.188224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143990 restraints weight = 137702.759| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.17 r_work: 0.3606 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 95024 Z= 0.153 Angle : 0.471 9.871 128254 Z= 0.246 Chirality : 0.038 0.202 14416 Planarity : 0.003 0.073 16406 Dihedral : 6.029 87.469 12900 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.72 % Allowed : 17.00 % Favored : 81.28 % 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: 0.16 (0.08), residues: 11510 helix: 0.70 (0.07), residues: 6420 sheet: 0.38 (0.24), residues: 530 loop : -0.70 (0.09), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 716 HIS 0.005 0.001 HIS A 549 PHE 0.042 0.001 PHE O 741 TYR 0.018 0.001 TYR F 176 ARG 0.008 0.000 ARG A 431 =============================================================================== Job complete usr+sys time: 27455.33 seconds wall clock time: 483 minutes 7.04 seconds (28987.04 seconds total)