Starting phenix.real_space_refine on Wed Apr 10 01:03:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppd_20433/04_2024/6ppd_20433.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 457 5.16 5 C 43739 2.51 5 N 11944 2.21 5 O 12629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 106": "NH1" <-> "NH2" Residue "W PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 702": "NH1" <-> "NH2" Residue "W ARG 753": "NH1" <-> "NH2" Residue "W TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 106": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "S PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 572": "NH1" <-> "NH2" Residue "S ARG 702": "NH1" <-> "NH2" Residue "S ARG 753": "NH1" <-> "NH2" Residue "S ARG 1070": "NH1" <-> "NH2" Residue "S TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 106": "NH1" <-> "NH2" Residue "T PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 702": "NH1" <-> "NH2" Residue "T ARG 753": "NH1" <-> "NH2" Residue "T TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 106": "NH1" <-> "NH2" Residue "4 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 702": "NH1" <-> "NH2" Residue "4 ARG 753": "NH1" <-> "NH2" Residue "4 TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 66": "NH1" <-> "NH2" Residue "5 ARG 188": "NH1" <-> "NH2" Residue "5 ARG 238": "NH1" <-> "NH2" Residue "6 TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 267": "NH1" <-> "NH2" Residue "7 ARG 285": "NH1" <-> "NH2" Residue "7 ARG 305": "NH1" <-> "NH2" Residue "b ARG 238": "NH1" <-> "NH2" Residue "c TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 305": "NH1" <-> "NH2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "d ARG 231": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X ARG 106": "NH1" <-> "NH2" Residue "X ARG 112": "NH1" <-> "NH2" Residue "X TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 309": "NH1" <-> "NH2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 572": "NH1" <-> "NH2" Residue "X ARG 702": "NH1" <-> "NH2" Residue "X ARG 753": "NH1" <-> "NH2" Residue "X PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 68769 Number of models: 1 Model: "" Number of chains: 16 Chain: "0" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "W" Number of atoms: 10622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1354, 10622 Classifications: {'peptide': 1354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "2" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "S" Number of atoms: 10061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 10061 Classifications: {'peptide': 1281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 73, 'TRANS': 1207} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 10667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10667 Classifications: {'peptide': 1360} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1283} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "4" Number of atoms: 9634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1222, 9634 Classifications: {'peptide': 1222} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 68, 'TRANS': 1152} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 380 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2425 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 292} Chain breaks: 3 Chain: "6" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2330 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "7" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2294 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 274} Chain breaks: 2 Chain: "b" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2478 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 297} Chain breaks: 2 Chain: "c" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2330 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain breaks: 1 Chain: "d" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2365 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Chain: "1" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 10519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10519 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 1265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 26.12, per 1000 atoms: 0.38 Number of scatterers: 68769 At special positions: 0 Unit cell: (216.3, 207.03, 222.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 457 16.00 O 12629 8.00 N 11944 7.00 C 43739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 6 212 " - pdb=" SG CYS 7 222 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 222 " - pdb=" SG CYS 7 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 212 " - pdb=" SG CYS d 222 " distance=2.02 Simple disulfide: pdb=" SG CYS c 222 " - pdb=" SG CYS d 212 " distance=2.04 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: 18.22 Conformation dependent library (CDL) restraints added in 9.2 seconds 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16548 Finding SS restraints... Secondary structure from input PDB file: 375 helices and 97 sheets defined 39.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain '0' and resid 22 through 30 removed outlier: 4.023A pdb=" N ALA 0 26 " --> pdb=" O HIS 0 22 " (cutoff:3.500A) Processing helix chain '0' and resid 37 through 65 removed outlier: 3.713A pdb=" N VAL 0 43 " --> pdb=" O ALA 0 39 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 0 63 " --> pdb=" O GLU 0 59 " (cutoff:3.500A) Processing helix chain '0' and resid 69 through 77 removed outlier: 3.663A pdb=" N HIS 0 73 " --> pdb=" O GLN 0 69 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 29 removed outlier: 4.001A pdb=" N ALA W 28 " --> pdb=" O LYS W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 43 removed outlier: 3.691A pdb=" N ALA W 43 " --> pdb=" O GLY W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 73 removed outlier: 3.573A pdb=" N ALA W 72 " --> pdb=" O THR W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 138 Processing helix chain 'W' and resid 145 through 153 removed outlier: 3.892A pdb=" N THR W 150 " --> pdb=" O PRO W 146 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU W 151 " --> pdb=" O LEU W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 162 Processing helix chain 'W' and resid 163 through 169 removed outlier: 3.654A pdb=" N MET W 167 " --> pdb=" O LEU W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 185 removed outlier: 3.587A pdb=" N LEU W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL W 175 " --> pdb=" O GLU W 171 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 197 removed outlier: 4.654A pdb=" N THR W 194 " --> pdb=" O PHE W 190 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU W 195 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP W 197 " --> pdb=" O LYS W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 225 removed outlier: 3.628A pdb=" N SER W 215 " --> pdb=" O SER W 211 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET W 216 " --> pdb=" O ASP W 212 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER W 225 " --> pdb=" O LEU W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 231 Processing helix chain 'W' and resid 237 through 250 Processing helix chain 'W' and resid 266 through 270 removed outlier: 3.903A pdb=" N GLY W 269 " --> pdb=" O THR W 266 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN W 270 " --> pdb=" O ALA W 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 266 through 270' Processing helix chain 'W' and resid 279 through 290 removed outlier: 3.614A pdb=" N ARG W 284 " --> pdb=" O ASP W 280 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG W 285 " --> pdb=" O SER W 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN W 288 " --> pdb=" O ARG W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 318 Processing helix chain 'W' and resid 325 through 334 removed outlier: 3.643A pdb=" N ALA W 331 " --> pdb=" O GLU W 327 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG W 332 " --> pdb=" O GLN W 328 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE W 333 " --> pdb=" O PHE W 329 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 351 removed outlier: 5.131A pdb=" N ALA W 348 " --> pdb=" O GLU W 344 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA W 349 " --> pdb=" O GLY W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 Processing helix chain 'W' and resid 461 through 472 removed outlier: 3.605A pdb=" N ALA W 471 " --> pdb=" O ALA W 467 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 502 removed outlier: 3.846A pdb=" N THR W 496 " --> pdb=" O ASN W 492 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN W 499 " --> pdb=" O ARG W 495 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR W 500 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR W 501 " --> pdb=" O PHE W 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 519 through 525 removed outlier: 3.783A pdb=" N LEU W 524 " --> pdb=" O THR W 520 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS W 525 " --> pdb=" O GLU W 521 " (cutoff:3.500A) Processing helix chain 'W' and resid 529 through 534 removed outlier: 3.920A pdb=" N LEU W 534 " --> pdb=" O ARG W 530 " (cutoff:3.500A) Processing helix chain 'W' and resid 571 through 587 removed outlier: 3.552A pdb=" N ALA W 584 " --> pdb=" O ALA W 580 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL W 585 " --> pdb=" O GLN W 581 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR W 586 " --> pdb=" O PHE W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 593 through 595 No H-bonds generated for 'chain 'W' and resid 593 through 595' Processing helix chain 'W' and resid 596 through 605 removed outlier: 3.665A pdb=" N ILE W 600 " --> pdb=" O THR W 596 " (cutoff:3.500A) Processing helix chain 'W' and resid 610 through 621 removed outlier: 3.723A pdb=" N TYR W 614 " --> pdb=" O PRO W 610 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA W 618 " --> pdb=" O TYR W 614 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS W 621 " --> pdb=" O GLU W 617 " (cutoff:3.500A) Processing helix chain 'W' and resid 623 through 630 removed outlier: 3.502A pdb=" N VAL W 628 " --> pdb=" O GLU W 624 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET W 629 " --> pdb=" O GLU W 625 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN W 630 " --> pdb=" O LYS W 626 " (cutoff:3.500A) Processing helix chain 'W' and resid 630 through 645 removed outlier: 3.740A pdb=" N VAL W 643 " --> pdb=" O GLN W 639 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN W 644 " --> pdb=" O THR W 640 " (cutoff:3.500A) Processing helix chain 'W' and resid 653 through 663 removed outlier: 3.522A pdb=" N VAL W 657 " --> pdb=" O SER W 653 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS W 661 " --> pdb=" O VAL W 657 " (cutoff:3.500A) Processing helix chain 'W' and resid 670 through 695 removed outlier: 3.501A pdb=" N GLY W 675 " --> pdb=" O LYS W 671 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS W 676 " --> pdb=" O GLU W 672 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR W 677 " --> pdb=" O ALA W 673 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA W 686 " --> pdb=" O GLY W 682 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU W 688 " --> pdb=" O LEU W 684 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN W 689 " --> pdb=" O ILE W 685 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA W 690 " --> pdb=" O ALA W 686 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU W 694 " --> pdb=" O ALA W 690 " (cutoff:3.500A) Processing helix chain 'W' and resid 705 through 710 removed outlier: 4.537A pdb=" N SER W 710 " --> pdb=" O THR W 706 " (cutoff:3.500A) Processing helix chain 'W' and resid 726 through 734 removed outlier: 3.529A pdb=" N GLN W 732 " --> pdb=" O THR W 728 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS W 733 " --> pdb=" O ASP W 729 " (cutoff:3.500A) Processing helix chain 'W' and resid 749 through 753 Processing helix chain 'W' and resid 769 through 779 removed outlier: 3.695A pdb=" N ILE W 773 " --> pdb=" O ASN W 769 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR W 774 " --> pdb=" O LEU W 770 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR W 776 " --> pdb=" O ASN W 772 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG W 777 " --> pdb=" O ILE W 773 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL W 778 " --> pdb=" O TYR W 774 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN W 779 " --> pdb=" O GLN W 775 " (cutoff:3.500A) Processing helix chain 'W' and resid 799 through 808 removed outlier: 3.694A pdb=" N GLU W 803 " --> pdb=" O ASN W 799 " (cutoff:3.500A) Processing helix chain 'W' and resid 809 through 815 removed outlier: 3.720A pdb=" N VAL W 813 " --> pdb=" O VAL W 809 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 834 removed outlier: 3.798A pdb=" N LEU W 831 " --> pdb=" O GLN W 827 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR W 832 " --> pdb=" O ASN W 828 " (cutoff:3.500A) Processing helix chain 'W' and resid 836 through 840 removed outlier: 3.654A pdb=" N VAL W 839 " --> pdb=" O ASN W 836 " (cutoff:3.500A) Processing helix chain 'W' and resid 849 through 853 Processing helix chain 'W' and resid 858 through 864 Processing helix chain 'W' and resid 871 through 881 removed outlier: 3.659A pdb=" N ILE W 875 " --> pdb=" O THR W 871 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU W 878 " --> pdb=" O MET W 874 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR W 880 " --> pdb=" O ARG W 876 " (cutoff:3.500A) Processing helix chain 'W' and resid 882 through 885 Processing helix chain 'W' and resid 899 through 903 removed outlier: 4.012A pdb=" N SER W 903 " --> pdb=" O PRO W 900 " (cutoff:3.500A) Processing helix chain 'W' and resid 908 through 910 No H-bonds generated for 'chain 'W' and resid 908 through 910' Processing helix chain 'W' and resid 935 through 937 No H-bonds generated for 'chain 'W' and resid 935 through 937' Processing helix chain 'W' and resid 950 through 958 removed outlier: 3.946A pdb=" N THR W 956 " --> pdb=" O LEU W 952 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU W 957 " --> pdb=" O VAL W 953 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS W 958 " --> pdb=" O ALA W 954 " (cutoff:3.500A) Processing helix chain 'W' and resid 958 through 968 removed outlier: 4.032A pdb=" N TYR W 964 " --> pdb=" O LEU W 960 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR W 966 " --> pdb=" O ALA W 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU W 968 " --> pdb=" O TYR W 964 " (cutoff:3.500A) Processing helix chain 'W' and resid 969 through 973 removed outlier: 3.640A pdb=" N ARG W 972 " --> pdb=" O PRO W 969 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN W 973 " --> pdb=" O ASN W 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 969 through 973' Processing helix chain 'W' and resid 992 through 1000 removed outlier: 4.226A pdb=" N ALA W 996 " --> pdb=" O LYS W 992 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA W1000 " --> pdb=" O ALA W 996 " (cutoff:3.500A) Processing helix chain 'W' and resid 1005 through 1007 No H-bonds generated for 'chain 'W' and resid 1005 through 1007' Processing helix chain 'W' and resid 1008 through 1014 removed outlier: 3.559A pdb=" N MET W1012 " --> pdb=" O ALA W1008 " (cutoff:3.500A) Processing helix chain 'W' and resid 1015 through 1017 No H-bonds generated for 'chain 'W' and resid 1015 through 1017' Processing helix chain 'W' and resid 1020 through 1030 removed outlier: 3.657A pdb=" N PHE W1024 " --> pdb=" O SER W1020 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE W1025 " --> pdb=" O ALA W1021 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS W1026 " --> pdb=" O PRO W1022 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS W1030 " --> pdb=" O CYS W1026 " (cutoff:3.500A) Processing helix chain 'W' and resid 1117 through 1122 removed outlier: 3.773A pdb=" N ILE W1121 " --> pdb=" O ASP W1117 " (cutoff:3.500A) Processing helix chain 'W' and resid 1132 through 1141 removed outlier: 3.516A pdb=" N LYS W1137 " --> pdb=" O HIS W1133 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET W1138 " --> pdb=" O ASP W1134 " (cutoff:3.500A) Processing helix chain 'W' and resid 1211 through 1221 removed outlier: 3.575A pdb=" N LEU W1219 " --> pdb=" O ALA W1215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP W1221 " --> pdb=" O ARG W1217 " (cutoff:3.500A) Processing helix chain 'W' and resid 1244 through 1251 removed outlier: 3.595A pdb=" N ASN W1251 " --> pdb=" O ASP W1247 " (cutoff:3.500A) Processing helix chain 'W' and resid 1264 through 1269 Processing helix chain 'W' and resid 1271 through 1276 removed outlier: 3.693A pdb=" N ILE W1275 " --> pdb=" O HIS W1271 " (cutoff:3.500A) Processing helix chain 'W' and resid 1277 through 1279 No H-bonds generated for 'chain 'W' and resid 1277 through 1279' Processing helix chain 'W' and resid 1281 through 1292 removed outlier: 4.074A pdb=" N SER W1290 " --> pdb=" O VAL W1286 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA W1291 " --> pdb=" O ASN W1287 " (cutoff:3.500A) Processing helix chain 'W' and resid 1334 through 1344 removed outlier: 4.262A pdb=" N LEU W1338 " --> pdb=" O HIS W1334 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP W1339 " --> pdb=" O ARG W1335 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET W1342 " --> pdb=" O LEU W1338 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN W1344 " --> pdb=" O GLU W1340 " (cutoff:3.500A) Processing helix chain '2' and resid 22 through 30 removed outlier: 4.023A pdb=" N ALA 2 26 " --> pdb=" O HIS 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 65 removed outlier: 3.712A pdb=" N VAL 2 43 " --> pdb=" O ALA 2 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 2 63 " --> pdb=" O GLU 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 77 removed outlier: 3.664A pdb=" N HIS 2 73 " --> pdb=" O GLN 2 69 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 2 76 " --> pdb=" O ASP 2 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 65 through 75 removed outlier: 3.559A pdb=" N THR S 69 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA S 70 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU S 71 " --> pdb=" O GLU S 68 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA S 72 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 86 removed outlier: 3.543A pdb=" N MET S 86 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 138 removed outlier: 3.604A pdb=" N ILE S 136 " --> pdb=" O ALA S 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU S 138 " --> pdb=" O ALA S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 184 removed outlier: 3.649A pdb=" N THR S 150 " --> pdb=" O PRO S 146 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY S 154 " --> pdb=" O THR S 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 155 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR S 158 " --> pdb=" O GLY S 154 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER S 161 " --> pdb=" O LYS S 157 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY S 166 " --> pdb=" O ALA S 162 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU S 170 " --> pdb=" O GLY S 166 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU S 171 " --> pdb=" O MET S 167 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL S 175 " --> pdb=" O GLU S 171 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL S 181 " --> pdb=" O THR S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 197 removed outlier: 4.684A pdb=" N THR S 194 " --> pdb=" O PHE S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 204 removed outlier: 4.250A pdb=" N ARG S 203 " --> pdb=" O TYR S 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY S 204 " --> pdb=" O SER S 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 200 through 204' Processing helix chain 'S' and resid 206 through 215 removed outlier: 3.549A pdb=" N SER S 211 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP S 212 " --> pdb=" O ALA S 208 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 224 removed outlier: 3.506A pdb=" N ILE S 222 " --> pdb=" O LYS S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 Processing helix chain 'S' and resid 232 through 234 No H-bonds generated for 'chain 'S' and resid 232 through 234' Processing helix chain 'S' and resid 237 through 252 removed outlier: 3.640A pdb=" N ASP S 247 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA S 250 " --> pdb=" O SER S 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA S 251 " --> pdb=" O ASP S 247 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL S 252 " --> pdb=" O MET S 248 " (cutoff:3.500A) Processing helix chain 'S' and resid 279 through 290 removed outlier: 4.266A pdb=" N ARG S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN S 288 " --> pdb=" O ARG S 284 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU S 289 " --> pdb=" O ARG S 285 " (cutoff:3.500A) Processing helix chain 'S' and resid 379 through 386 removed outlier: 3.820A pdb=" N TYR S 383 " --> pdb=" O LEU S 379 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR S 386 " --> pdb=" O MET S 382 " (cutoff:3.500A) Processing helix chain 'S' and resid 466 through 472 removed outlier: 3.685A pdb=" N PHE S 472 " --> pdb=" O LEU S 468 " (cutoff:3.500A) Processing helix chain 'S' and resid 492 through 501 removed outlier: 3.891A pdb=" N TYR S 500 " --> pdb=" O THR S 496 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR S 501 " --> pdb=" O PHE S 497 " (cutoff:3.500A) Processing helix chain 'S' and resid 529 through 534 removed outlier: 4.288A pdb=" N LEU S 534 " --> pdb=" O ARG S 530 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 587 removed outlier: 4.138A pdb=" N GLN S 581 " --> pdb=" O SER S 577 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA S 584 " --> pdb=" O ALA S 580 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR S 586 " --> pdb=" O PHE S 582 " (cutoff:3.500A) Processing helix chain 'S' and resid 593 through 605 removed outlier: 3.880A pdb=" N VAL S 599 " --> pdb=" O LEU S 595 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE S 600 " --> pdb=" O THR S 596 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR S 603 " --> pdb=" O VAL S 599 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA S 604 " --> pdb=" O ILE S 600 " (cutoff:3.500A) Processing helix chain 'S' and resid 611 through 621 removed outlier: 3.960A pdb=" N GLU S 617 " --> pdb=" O CYS S 613 " (cutoff:3.500A) Processing helix chain 'S' and resid 623 through 643 removed outlier: 3.623A pdb=" N ASN S 630 " --> pdb=" O LYS S 626 " (cutoff:3.500A) Proline residue: S 632 - end of helix removed outlier: 3.679A pdb=" N ALA S 635 " --> pdb=" O MET S 631 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU S 636 " --> pdb=" O PRO S 632 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN S 639 " --> pdb=" O ALA S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 653 through 664 removed outlier: 3.718A pdb=" N VAL S 657 " --> pdb=" O SER S 653 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET S 664 " --> pdb=" O ILE S 660 " (cutoff:3.500A) Processing helix chain 'S' and resid 670 through 695 removed outlier: 3.820A pdb=" N HIS S 676 " --> pdb=" O GLU S 672 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR S 677 " --> pdb=" O ALA S 673 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE S 680 " --> pdb=" O HIS S 676 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU S 681 " --> pdb=" O TYR S 677 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE S 685 " --> pdb=" O LEU S 681 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA S 686 " --> pdb=" O GLY S 682 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS S 693 " --> pdb=" O GLN S 689 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA S 695 " --> pdb=" O LEU S 691 " (cutoff:3.500A) Processing helix chain 'S' and resid 705 through 710 removed outlier: 4.673A pdb=" N SER S 710 " --> pdb=" O THR S 706 " (cutoff:3.500A) Processing helix chain 'S' and resid 725 through 732 removed outlier: 3.886A pdb=" N ASP S 729 " --> pdb=" O ASP S 725 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET S 731 " --> pdb=" O PHE S 727 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN S 732 " --> pdb=" O THR S 728 " (cutoff:3.500A) Processing helix chain 'S' and resid 770 through 780 removed outlier: 3.701A pdb=" N TYR S 774 " --> pdb=" O LEU S 770 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR S 776 " --> pdb=" O ASN S 772 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG S 777 " --> pdb=" O ILE S 773 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL S 778 " --> pdb=" O TYR S 774 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU S 780 " --> pdb=" O THR S 776 " (cutoff:3.500A) Processing helix chain 'S' and resid 799 through 808 removed outlier: 3.708A pdb=" N GLU S 803 " --> pdb=" O ASN S 799 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR S 807 " --> pdb=" O GLU S 803 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR S 808 " --> pdb=" O LYS S 804 " (cutoff:3.500A) Processing helix chain 'S' and resid 810 through 815 Processing helix chain 'S' and resid 825 through 830 Processing helix chain 'S' and resid 831 through 833 No H-bonds generated for 'chain 'S' and resid 831 through 833' Processing helix chain 'S' and resid 858 through 863 Processing helix chain 'S' and resid 871 through 880 removed outlier: 3.594A pdb=" N ILE S 875 " --> pdb=" O THR S 871 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL S 877 " --> pdb=" O ASP S 873 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR S 880 " --> pdb=" O ARG S 876 " (cutoff:3.500A) Processing helix chain 'S' and resid 881 through 883 No H-bonds generated for 'chain 'S' and resid 881 through 883' Processing helix chain 'S' and resid 907 through 910 Processing helix chain 'S' and resid 928 through 930 No H-bonds generated for 'chain 'S' and resid 928 through 930' Processing helix chain 'S' and resid 931 through 936 Processing helix chain 'S' and resid 950 through 955 Processing helix chain 'S' and resid 960 through 968 removed outlier: 3.511A pdb=" N THR S 966 " --> pdb=" O ALA S 962 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU S 968 " --> pdb=" O TYR S 964 " (cutoff:3.500A) Processing helix chain 'S' and resid 969 through 972 removed outlier: 3.807A pdb=" N ARG S 972 " --> pdb=" O PRO S 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 969 through 972' Processing helix chain 'S' and resid 992 through 994 No H-bonds generated for 'chain 'S' and resid 992 through 994' Processing helix chain 'S' and resid 995 through 1000 removed outlier: 3.506A pdb=" N ALA S 999 " --> pdb=" O VAL S 995 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA S1000 " --> pdb=" O ALA S 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 995 through 1000' Processing helix chain 'S' and resid 1005 through 1014 removed outlier: 3.715A pdb=" N SER S1010 " --> pdb=" O PRO S1006 " (cutoff:3.500A) Processing helix chain 'S' and resid 1020 through 1030 removed outlier: 3.741A pdb=" N PHE S1024 " --> pdb=" O SER S1020 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE S1025 " --> pdb=" O ALA S1021 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS S1026 " --> pdb=" O PRO S1022 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS S1030 " --> pdb=" O CYS S1026 " (cutoff:3.500A) Processing helix chain 'S' and resid 1129 through 1141 removed outlier: 3.633A pdb=" N HIS S1133 " --> pdb=" O ASP S1129 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR S1135 " --> pdb=" O GLN S1131 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET S1138 " --> pdb=" O ASP S1134 " (cutoff:3.500A) Processing helix chain 'S' and resid 1211 through 1220 removed outlier: 4.362A pdb=" N ARG S1217 " --> pdb=" O GLU S1213 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU S1218 " --> pdb=" O SER S1214 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU S1219 " --> pdb=" O ALA S1215 " (cutoff:3.500A) Processing helix chain 'S' and resid 1236 through 1241 removed outlier: 3.547A pdb=" N SER S1240 " --> pdb=" O ASN S1236 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN S1241 " --> pdb=" O PRO S1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1236 through 1241' Processing helix chain 'S' and resid 1244 through 1250 Processing helix chain 'S' and resid 1266 through 1271 removed outlier: 3.593A pdb=" N PHE S1270 " --> pdb=" O CYS S1266 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS S1271 " --> pdb=" O ARG S1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1266 through 1271' Processing helix chain 'S' and resid 1271 through 1276 removed outlier: 3.554A pdb=" N ILE S1275 " --> pdb=" O HIS S1271 " (cutoff:3.500A) Processing helix chain 'S' and resid 1277 through 1280 removed outlier: 4.302A pdb=" N ARG S1280 " --> pdb=" O ARG S1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1277 through 1280' Processing helix chain 'S' and resid 1285 through 1290 removed outlier: 4.398A pdb=" N SER S1290 " --> pdb=" O VAL S1286 " (cutoff:3.500A) Processing helix chain 'S' and resid 1319 through 1324 Processing helix chain 'S' and resid 1334 through 1342 removed outlier: 3.900A pdb=" N LEU S1338 " --> pdb=" O HIS S1334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET S1342 " --> pdb=" O LEU S1338 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 39 through 44 removed outlier: 3.749A pdb=" N ALA T 43 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG T 44 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 73 removed outlier: 3.679A pdb=" N ALA T 72 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 133 through 138 Processing helix chain 'T' and resid 145 through 185 removed outlier: 3.648A pdb=" N ALA T 155 " --> pdb=" O GLU T 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS T 157 " --> pdb=" O ALA T 153 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR T 158 " --> pdb=" O GLY T 154 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 166 " --> pdb=" O ALA T 162 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU T 170 " --> pdb=" O GLY T 166 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY T 173 " --> pdb=" O ALA T 169 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL T 175 " --> pdb=" O GLU T 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS T 185 " --> pdb=" O VAL T 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 196 removed outlier: 4.643A pdb=" N THR T 194 " --> pdb=" O PHE T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 197 through 201 removed outlier: 3.747A pdb=" N TYR T 200 " --> pdb=" O ASP T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 224 removed outlier: 3.529A pdb=" N LYS T 210 " --> pdb=" O LYS T 206 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER T 215 " --> pdb=" O SER T 211 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET T 216 " --> pdb=" O ASP T 212 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU T 223 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 252 removed outlier: 3.828A pdb=" N LEU T 242 " --> pdb=" O LYS T 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP T 247 " --> pdb=" O THR T 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL T 252 " --> pdb=" O MET T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 261 removed outlier: 4.619A pdb=" N GLY T 260 " --> pdb=" O VAL T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 removed outlier: 3.774A pdb=" N GLY T 269 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN T 270 " --> pdb=" O ALA T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 270' Processing helix chain 'T' and resid 279 through 290 removed outlier: 3.935A pdb=" N ARG T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 310 through 319 removed outlier: 3.999A pdb=" N VAL T 314 " --> pdb=" O GLY T 310 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR T 315 " --> pdb=" O ALA T 311 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 334 removed outlier: 3.617A pdb=" N ARG T 332 " --> pdb=" O GLN T 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE T 333 " --> pdb=" O PHE T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 351 removed outlier: 3.612A pdb=" N LYS T 347 " --> pdb=" O VAL T 343 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA T 348 " --> pdb=" O GLU T 344 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA T 349 " --> pdb=" O GLY T 345 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU T 350 " --> pdb=" O ASP T 346 " (cutoff:3.500A) Processing helix chain 'T' and resid 380 through 385 removed outlier: 3.728A pdb=" N GLU T 385 " --> pdb=" O ARG T 381 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 454 removed outlier: 3.815A pdb=" N ALA T 449 " --> pdb=" O GLY T 445 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS T 451 " --> pdb=" O GLN T 447 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER T 452 " --> pdb=" O ASN T 448 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE T 453 " --> pdb=" O ALA T 449 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) Processing helix chain 'T' and resid 461 through 472 removed outlier: 3.745A pdb=" N ALA T 471 " --> pdb=" O ALA T 467 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE T 472 " --> pdb=" O LEU T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 497 through 502 removed outlier: 3.809A pdb=" N TYR T 501 " --> pdb=" O PHE T 497 " (cutoff:3.500A) Processing helix chain 'T' and resid 510 through 516 Processing helix chain 'T' and resid 519 through 524 removed outlier: 3.962A pdb=" N LEU T 524 " --> pdb=" O THR T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 528 through 533 removed outlier: 4.343A pdb=" N LEU T 532 " --> pdb=" O SER T 528 " (cutoff:3.500A) Processing helix chain 'T' and resid 561 through 565 removed outlier: 3.600A pdb=" N ASN T 564 " --> pdb=" O MET T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 571 through 587 removed outlier: 3.544A pdb=" N THR T 586 " --> pdb=" O PHE T 582 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN T 587 " --> pdb=" O ASP T 583 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 605 removed outlier: 4.208A pdb=" N VAL T 599 " --> pdb=" O LEU T 595 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE T 600 " --> pdb=" O THR T 596 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU T 602 " --> pdb=" O ASP T 598 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR T 603 " --> pdb=" O VAL T 599 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 604 " --> pdb=" O ILE T 600 " (cutoff:3.500A) Processing helix chain 'T' and resid 610 through 621 removed outlier: 3.848A pdb=" N TYR T 614 " --> pdb=" O PRO T 610 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA T 618 " --> pdb=" O TYR T 614 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET T 619 " --> pdb=" O VAL T 615 " (cutoff:3.500A) Processing helix chain 'T' and resid 624 through 630 removed outlier: 3.673A pdb=" N ASN T 630 " --> pdb=" O LYS T 626 " (cutoff:3.500A) Processing helix chain 'T' and resid 630 through 643 removed outlier: 3.705A pdb=" N ALA T 635 " --> pdb=" O MET T 631 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 636 " --> pdb=" O PRO T 632 " (cutoff:3.500A) Processing helix chain 'T' and resid 653 through 663 removed outlier: 3.727A pdb=" N VAL T 657 " --> pdb=" O SER T 653 " (cutoff:3.500A) Processing helix chain 'T' and resid 670 through 685 removed outlier: 4.190A pdb=" N HIS T 676 " --> pdb=" O GLU T 672 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR T 677 " --> pdb=" O ALA T 673 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS T 679 " --> pdb=" O GLY T 675 " (cutoff:3.500A) Processing helix chain 'T' and resid 685 through 695 removed outlier: 3.547A pdb=" N LEU T 692 " --> pdb=" O GLU T 688 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS T 693 " --> pdb=" O GLN T 689 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU T 694 " --> pdb=" O ALA T 690 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA T 695 " --> pdb=" O LEU T 691 " (cutoff:3.500A) Processing helix chain 'T' and resid 705 through 710 removed outlier: 4.475A pdb=" N SER T 710 " --> pdb=" O THR T 706 " (cutoff:3.500A) Processing helix chain 'T' and resid 726 through 733 removed outlier: 3.727A pdb=" N LYS T 733 " --> pdb=" O ASP T 729 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 751 No H-bonds generated for 'chain 'T' and resid 749 through 751' Processing helix chain 'T' and resid 752 through 756 removed outlier: 3.640A pdb=" N PHE T 756 " --> pdb=" O ASN T 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 752 through 756' Processing helix chain 'T' and resid 764 through 768 removed outlier: 3.905A pdb=" N VAL T 767 " --> pdb=" O GLU T 764 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN T 768 " --> pdb=" O ASP T 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 764 through 768' Processing helix chain 'T' and resid 769 through 775 removed outlier: 3.626A pdb=" N TYR T 774 " --> pdb=" O LEU T 770 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN T 775 " --> pdb=" O VAL T 771 " (cutoff:3.500A) Processing helix chain 'T' and resid 799 through 808 removed outlier: 3.846A pdb=" N GLU T 803 " --> pdb=" O ASN T 799 " (cutoff:3.500A) Processing helix chain 'T' and resid 809 through 815 removed outlier: 3.737A pdb=" N VAL T 813 " --> pdb=" O VAL T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 825 through 835 removed outlier: 3.509A pdb=" N VAL T 829 " --> pdb=" O ASP T 825 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU T 831 " --> pdb=" O GLN T 827 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR T 832 " --> pdb=" O ASN T 828 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU T 833 " --> pdb=" O VAL T 829 " (cutoff:3.500A) Processing helix chain 'T' and resid 836 through 841 removed outlier: 3.606A pdb=" N PHE T 840 " --> pdb=" O ASN T 836 " (cutoff:3.500A) Processing helix chain 'T' and resid 849 through 853 Processing helix chain 'T' and resid 857 through 865 removed outlier: 4.130A pdb=" N ASP T 861 " --> pdb=" O GLY T 857 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA T 865 " --> pdb=" O ASP T 861 " (cutoff:3.500A) Processing helix chain 'T' and resid 871 through 881 removed outlier: 3.664A pdb=" N ILE T 875 " --> pdb=" O THR T 871 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL T 877 " --> pdb=" O ASP T 873 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER T 881 " --> pdb=" O VAL T 877 " (cutoff:3.500A) Processing helix chain 'T' and resid 882 through 885 removed outlier: 3.533A pdb=" N CYS T 885 " --> pdb=" O PHE T 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 882 through 885' Processing helix chain 'T' and resid 950 through 958 removed outlier: 4.003A pdb=" N THR T 956 " --> pdb=" O LEU T 952 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU T 957 " --> pdb=" O VAL T 953 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS T 958 " --> pdb=" O ALA T 954 " (cutoff:3.500A) Processing helix chain 'T' and resid 958 through 966 Processing helix chain 'T' and resid 968 through 973 removed outlier: 3.850A pdb=" N GLN T 971 " --> pdb=" O LEU T 968 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN T 973 " --> pdb=" O ASN T 970 " (cutoff:3.500A) Processing helix chain 'T' and resid 992 through 1000 removed outlier: 4.243A pdb=" N ALA T 996 " --> pdb=" O LYS T 992 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR T 998 " --> pdb=" O PRO T 994 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA T1000 " --> pdb=" O ALA T 996 " (cutoff:3.500A) Processing helix chain 'T' and resid 1005 through 1016 removed outlier: 3.624A pdb=" N ILE T1009 " --> pdb=" O THR T1005 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER T1010 " --> pdb=" O PRO T1006 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET T1012 " --> pdb=" O ALA T1008 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL T1013 " --> pdb=" O ILE T1009 " (cutoff:3.500A) Processing helix chain 'T' and resid 1020 through 1030 removed outlier: 3.813A pdb=" N ILE T1025 " --> pdb=" O ALA T1021 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS T1026 " --> pdb=" O PRO T1022 " (cutoff:3.500A) Processing helix chain 'T' and resid 1117 through 1122 removed outlier: 3.522A pdb=" N ILE T1121 " --> pdb=" O ASP T1117 " (cutoff:3.500A) Processing helix chain 'T' and resid 1129 through 1141 Processing helix chain 'T' and resid 1187 through 1191 removed outlier: 3.518A pdb=" N TYR T1190 " --> pdb=" O ASP T1187 " (cutoff:3.500A) Processing helix chain 'T' and resid 1211 through 1221 removed outlier: 3.563A pdb=" N LEU T1219 " --> pdb=" O ALA T1215 " (cutoff:3.500A) Processing helix chain 'T' and resid 1244 through 1250 Processing helix chain 'T' and resid 1265 through 1271 removed outlier: 4.522A pdb=" N PHE T1269 " --> pdb=" O PRO T1265 " (cutoff:3.500A) Processing helix chain 'T' and resid 1271 through 1276 Processing helix chain 'T' and resid 1277 through 1279 No H-bonds generated for 'chain 'T' and resid 1277 through 1279' Processing helix chain 'T' and resid 1281 through 1288 Processing helix chain 'T' and resid 1319 through 1324 Processing helix chain 'T' and resid 1334 through 1344 removed outlier: 4.024A pdb=" N LEU T1338 " --> pdb=" O HIS T1334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP T1339 " --> pdb=" O ARG T1335 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET T1342 " --> pdb=" O LEU T1338 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 30 removed outlier: 4.023A pdb=" N ALA 3 26 " --> pdb=" O HIS 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 65 removed outlier: 3.712A pdb=" N VAL 3 43 " --> pdb=" O ALA 3 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 3 63 " --> pdb=" O GLU 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 77 removed outlier: 3.664A pdb=" N HIS 3 73 " --> pdb=" O GLN 3 69 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) Processing helix chain '4' and resid 69 through 73 removed outlier: 3.752A pdb=" N ALA 4 73 " --> pdb=" O ALA 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 133 through 139 Processing helix chain '4' and resid 148 through 185 removed outlier: 3.904A pdb=" N GLY 4 154 " --> pdb=" O THR 4 150 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA 4 155 " --> pdb=" O GLU 4 151 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR 4 158 " --> pdb=" O GLY 4 154 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE 4 165 " --> pdb=" O SER 4 161 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU 4 170 " --> pdb=" O GLY 4 166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY 4 173 " --> pdb=" O ALA 4 169 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS 4 185 " --> pdb=" O VAL 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 197 removed outlier: 3.508A pdb=" N LEU 4 192 " --> pdb=" O PRO 4 188 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR 4 194 " --> pdb=" O PHE 4 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 4 195 " --> pdb=" O ILE 4 191 " (cutoff:3.500A) Processing helix chain '4' and resid 198 through 204 removed outlier: 3.808A pdb=" N GLU 4 202 " --> pdb=" O PRO 4 198 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 4 203 " --> pdb=" O VAL 4 199 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY 4 204 " --> pdb=" O TYR 4 200 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 198 through 204' Processing helix chain '4' and resid 206 through 213 Processing helix chain '4' and resid 214 through 225 removed outlier: 3.582A pdb=" N LYS 4 218 " --> pdb=" O VAL 4 214 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS 4 220 " --> pdb=" O MET 4 216 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU 4 223 " --> pdb=" O ALA 4 219 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 231 Processing helix chain '4' and resid 236 through 252 removed outlier: 3.600A pdb=" N TYR 4 240 " --> pdb=" O ARG 4 236 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET 4 248 " --> pdb=" O MET 4 244 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA 4 251 " --> pdb=" O ASP 4 247 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL 4 252 " --> pdb=" O MET 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 266 through 270 removed outlier: 3.767A pdb=" N GLY 4 269 " --> pdb=" O THR 4 266 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN 4 270 " --> pdb=" O ALA 4 267 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 266 through 270' Processing helix chain '4' and resid 279 through 290 removed outlier: 3.738A pdb=" N ARG 4 284 " --> pdb=" O ASP 4 280 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 336 removed outlier: 3.539A pdb=" N GLN 4 328 " --> pdb=" O ARG 4 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 4 332 " --> pdb=" O GLN 4 328 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE 4 333 " --> pdb=" O PHE 4 329 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL 4 334 " --> pdb=" O MET 4 330 " (cutoff:3.500A) Processing helix chain '4' and resid 380 through 385 Processing helix chain '4' and resid 445 through 450 Processing helix chain '4' and resid 451 through 453 No H-bonds generated for 'chain '4' and resid 451 through 453' Processing helix chain '4' and resid 461 through 472 Processing helix chain '4' and resid 493 through 501 removed outlier: 3.729A pdb=" N PHE 4 497 " --> pdb=" O LEU 4 493 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS 4 498 " --> pdb=" O PHE 4 494 " (cutoff:3.500A) Processing helix chain '4' and resid 510 through 518 removed outlier: 3.683A pdb=" N LYS 4 515 " --> pdb=" O ASP 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 520 through 525 removed outlier: 3.820A pdb=" N LEU 4 523 " --> pdb=" O THR 4 520 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS 4 525 " --> pdb=" O ASP 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 561 through 565 Processing helix chain '4' and resid 571 through 585 removed outlier: 3.727A pdb=" N GLN 4 575 " --> pdb=" O PRO 4 571 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL 4 585 " --> pdb=" O GLN 4 581 " (cutoff:3.500A) Processing helix chain '4' and resid 596 through 606 removed outlier: 3.806A pdb=" N GLU 4 602 " --> pdb=" O ASP 4 598 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA 4 604 " --> pdb=" O ILE 4 600 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE 4 605 " --> pdb=" O GLN 4 601 " (cutoff:3.500A) Processing helix chain '4' and resid 615 through 620 Processing helix chain '4' and resid 624 through 629 Processing helix chain '4' and resid 637 through 645 removed outlier: 3.544A pdb=" N TRP 4 642 " --> pdb=" O ILE 4 638 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL 4 643 " --> pdb=" O GLN 4 639 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN 4 644 " --> pdb=" O THR 4 640 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER 4 645 " --> pdb=" O TYR 4 641 " (cutoff:3.500A) Processing helix chain '4' and resid 653 through 663 removed outlier: 3.813A pdb=" N VAL 4 657 " --> pdb=" O SER 4 653 " (cutoff:3.500A) Processing helix chain '4' and resid 674 through 682 removed outlier: 4.301A pdb=" N ARG 4 678 " --> pdb=" O HIS 4 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE 4 680 " --> pdb=" O HIS 4 676 " (cutoff:3.500A) Processing helix chain '4' and resid 683 through 688 Processing helix chain '4' and resid 688 through 694 Processing helix chain '4' and resid 704 through 709 removed outlier: 3.523A pdb=" N LEU 4 708 " --> pdb=" O ILE 4 705 " (cutoff:3.500A) Processing helix chain '4' and resid 726 through 734 removed outlier: 4.429A pdb=" N GLN 4 732 " --> pdb=" O THR 4 728 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER 4 734 " --> pdb=" O LEU 4 730 " (cutoff:3.500A) Processing helix chain '4' and resid 749 through 753 removed outlier: 3.687A pdb=" N ARG 4 753 " --> pdb=" O PRO 4 750 " (cutoff:3.500A) Processing helix chain '4' and resid 767 through 777 removed outlier: 3.543A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 798 removed outlier: 3.614A pdb=" N ASP 4 797 " --> pdb=" O ASP 4 794 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR 4 798 " --> pdb=" O GLU 4 795 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 794 through 798' Processing helix chain '4' and resid 800 through 802 No H-bonds generated for 'chain '4' and resid 800 through 802' Processing helix chain '4' and resid 803 through 808 removed outlier: 3.741A pdb=" N TYR 4 807 " --> pdb=" O GLU 4 803 " (cutoff:3.500A) Processing helix chain '4' and resid 810 through 815 Processing helix chain '4' and resid 829 through 833 Processing helix chain '4' and resid 858 through 863 removed outlier: 4.345A pdb=" N ILE 4 862 " --> pdb=" O THR 4 858 " (cutoff:3.500A) Processing helix chain '4' and resid 864 through 866 No H-bonds generated for 'chain '4' and resid 864 through 866' Processing helix chain '4' and resid 871 through 873 No H-bonds generated for 'chain '4' and resid 871 through 873' Processing helix chain '4' and resid 874 through 881 removed outlier: 3.624A pdb=" N LEU 4 878 " --> pdb=" O MET 4 874 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS 4 879 " --> pdb=" O ILE 4 875 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER 4 881 " --> pdb=" O VAL 4 877 " (cutoff:3.500A) Processing helix chain '4' and resid 882 through 885 removed outlier: 3.641A pdb=" N CYS 4 885 " --> pdb=" O PHE 4 882 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 882 through 885' Processing helix chain '4' and resid 931 through 938 removed outlier: 4.049A pdb=" N THR 4 937 " --> pdb=" O GLU 4 933 " (cutoff:3.500A) Processing helix chain '4' and resid 958 through 968 removed outlier: 3.703A pdb=" N VAL 4 965 " --> pdb=" O LEU 4 961 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR 4 966 " --> pdb=" O ALA 4 962 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU 4 968 " --> pdb=" O TYR 4 964 " (cutoff:3.500A) Processing helix chain '4' and resid 969 through 972 removed outlier: 3.919A pdb=" N ARG 4 972 " --> pdb=" O PRO 4 969 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 969 through 972' Processing helix chain '4' and resid 992 through 999 removed outlier: 3.598A pdb=" N ALA 4 999 " --> pdb=" O VAL 4 995 " (cutoff:3.500A) Processing helix chain '4' and resid 1005 through 1014 removed outlier: 4.070A pdb=" N SER 41010 " --> pdb=" O PRO 41006 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA 41011 " --> pdb=" O GLY 41007 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET 41012 " --> pdb=" O ALA 41008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL 41013 " --> pdb=" O ILE 41009 " (cutoff:3.500A) Processing helix chain '4' and resid 1021 through 1030 removed outlier: 4.199A pdb=" N GLN 41027 " --> pdb=" O SER 41023 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA 41028 " --> pdb=" O PHE 41024 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS 41029 " --> pdb=" O ILE 41025 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 41030 " --> pdb=" O CYS 41026 " (cutoff:3.500A) Processing helix chain '4' and resid 1117 through 1122 removed outlier: 3.813A pdb=" N ILE 41121 " --> pdb=" O ASP 41117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 41122 " --> pdb=" O LEU 41118 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 1117 through 1122' Processing helix chain '4' and resid 1132 through 1139 removed outlier: 3.542A pdb=" N LYS 41137 " --> pdb=" O HIS 41133 " (cutoff:3.500A) Processing helix chain '4' and resid 1187 through 1191 removed outlier: 3.647A pdb=" N TYR 41190 " --> pdb=" O ASP 41187 " (cutoff:3.500A) Processing helix chain '4' and resid 1214 through 1220 Processing helix chain '4' and resid 1236 through 1241 Processing helix chain '4' and resid 1244 through 1251 Processing helix chain '4' and resid 1266 through 1271 removed outlier: 3.943A pdb=" N PHE 41270 " --> pdb=" O CYS 41266 " (cutoff:3.500A) Processing helix chain '4' and resid 1271 through 1290 removed outlier: 3.670A pdb=" N TYR 41278 " --> pdb=" O ASP 41274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG 41280 " --> pdb=" O MET 41276 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY 41281 " --> pdb=" O ARG 41277 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU 41282 " --> pdb=" O TYR 41278 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 41284 " --> pdb=" O ARG 41280 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN 41287 " --> pdb=" O TYR 41283 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU 41288 " --> pdb=" O THR 41284 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR 41289 " --> pdb=" O LEU 41285 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER 41290 " --> pdb=" O VAL 41286 " (cutoff:3.500A) Processing helix chain '4' and resid 1319 through 1324 removed outlier: 3.501A pdb=" N LEU 41323 " --> pdb=" O PRO 41319 " (cutoff:3.500A) Processing helix chain '4' and resid 1335 through 1342 removed outlier: 3.951A pdb=" N ASP 41339 " --> pdb=" O ARG 41335 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 37 through 63 removed outlier: 3.636A pdb=" N LEU A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 16 removed outlier: 3.827A pdb=" N LEU 5 11 " --> pdb=" O ASN 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 46 removed outlier: 3.546A pdb=" N PHE 5 34 " --> pdb=" O ARG 5 30 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 5 35 " --> pdb=" O GLY 5 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY 5 37 " --> pdb=" O GLU 5 33 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS 5 44 " --> pdb=" O ASP 5 40 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA 5 46 " --> pdb=" O LEU 5 42 " (cutoff:3.500A) Processing helix chain '5' and resid 52 through 59 Processing helix chain '5' and resid 110 through 116 removed outlier: 3.693A pdb=" N LEU 5 114 " --> pdb=" O SER 5 110 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 132 removed outlier: 4.160A pdb=" N LYS 5 127 " --> pdb=" O PRO 5 123 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 141 removed outlier: 3.599A pdb=" N ALA 5 140 " --> pdb=" O GLY 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 152 removed outlier: 3.635A pdb=" N THR 5 152 " --> pdb=" O GLU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 251 through 263 removed outlier: 3.535A pdb=" N VAL 5 255 " --> pdb=" O GLY 5 251 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL 5 256 " --> pdb=" O PHE 5 252 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA 5 257 " --> pdb=" O ALA 5 253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP 5 261 " --> pdb=" O ALA 5 257 " (cutoff:3.500A) Processing helix chain '5' and resid 263 through 268 Processing helix chain '5' and resid 270 through 275 removed outlier: 3.625A pdb=" N LEU 5 274 " --> pdb=" O LYS 5 270 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 removed outlier: 3.887A pdb=" N LEU 5 283 " --> pdb=" O ILE 5 280 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.824A pdb=" N ALA 6 21 " --> pdb=" O ALA 6 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 6 22 " --> pdb=" O ASP 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 45 Processing helix chain '6' and resid 58 through 67 removed outlier: 3.611A pdb=" N SER 6 67 " --> pdb=" O MET 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 119 through 123 removed outlier: 3.683A pdb=" N SER 6 123 " --> pdb=" O SER 6 119 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 119 through 123' Processing helix chain '6' and resid 141 through 163 removed outlier: 4.019A pdb=" N ALA 6 147 " --> pdb=" O GLN 6 143 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU 6 149 " --> pdb=" O GLY 6 145 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS 6 160 " --> pdb=" O HIS 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 removed outlier: 3.647A pdb=" N LEU 6 204 " --> pdb=" O ALA 6 200 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET 6 209 " --> pdb=" O ASP 6 205 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR 6 210 " --> pdb=" O ASP 6 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS 6 212 " --> pdb=" O SER 6 208 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 6 213 " --> pdb=" O MET 6 209 " (cutoff:3.500A) Processing helix chain '6' and resid 219 through 228 removed outlier: 3.570A pdb=" N LEU 6 223 " --> pdb=" O PRO 6 219 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG 6 224 " --> pdb=" O ARG 6 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 6 226 " --> pdb=" O CYS 6 222 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR 6 227 " --> pdb=" O LEU 6 223 " (cutoff:3.500A) Processing helix chain '6' and resid 249 through 254 removed outlier: 3.804A pdb=" N LEU 6 254 " --> pdb=" O THR 6 250 " (cutoff:3.500A) Processing helix chain '6' and resid 258 through 262 Processing helix chain '6' and resid 263 through 275 removed outlier: 3.991A pdb=" N MET 6 269 " --> pdb=" O ARG 6 265 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 6 272 " --> pdb=" O VAL 6 268 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 6 273 " --> pdb=" O MET 6 269 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN 6 274 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) Processing helix chain '6' and resid 276 through 279 removed outlier: 3.540A pdb=" N ILE 6 279 " --> pdb=" O LEU 6 276 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 276 through 279' Processing helix chain '7' and resid 16 through 26 removed outlier: 4.106A pdb=" N ALA 7 21 " --> pdb=" O ALA 7 17 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 7 22 " --> pdb=" O ASP 7 18 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU 7 23 " --> pdb=" O GLU 7 19 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER 7 25 " --> pdb=" O ALA 7 21 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS 7 26 " --> pdb=" O ALA 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 58 through 68 removed outlier: 3.689A pdb=" N ILE 7 62 " --> pdb=" O ASP 7 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER 7 67 " --> pdb=" O MET 7 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 7 68 " --> pdb=" O GLN 7 64 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 123 Processing helix chain '7' and resid 142 through 146 Processing helix chain '7' and resid 148 through 165 removed outlier: 3.856A pdb=" N LEU 7 152 " --> pdb=" O ILE 7 148 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL 7 154 " --> pdb=" O GLN 7 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS 7 160 " --> pdb=" O HIS 7 156 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA 7 163 " --> pdb=" O SER 7 159 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY 7 164 " --> pdb=" O LYS 7 160 " (cutoff:3.500A) Processing helix chain '7' and resid 170 through 178 removed outlier: 4.095A pdb=" N LEU 7 176 " --> pdb=" O ALA 7 172 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 212 removed outlier: 3.597A pdb=" N CYS 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 227 removed outlier: 3.953A pdb=" N ARG 7 220 " --> pdb=" O ALA 7 216 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU 7 223 " --> pdb=" O PRO 7 219 " (cutoff:3.500A) Processing helix chain '7' and resid 235 through 240 Processing helix chain '7' and resid 248 through 252 removed outlier: 3.505A pdb=" N ILE 7 252 " --> pdb=" O VAL 7 249 " (cutoff:3.500A) Processing helix chain '7' and resid 253 through 257 removed outlier: 3.882A pdb=" N GLN 7 256 " --> pdb=" O ASP 7 253 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU 7 257 " --> pdb=" O LEU 7 254 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 253 through 257' Processing helix chain '7' and resid 258 through 263 Processing helix chain '7' and resid 263 through 268 removed outlier: 3.546A pdb=" N VAL 7 268 " --> pdb=" O THR 7 264 " (cutoff:3.500A) Processing helix chain '7' and resid 269 through 273 Processing helix chain 'b' and resid 5 through 18 removed outlier: 3.511A pdb=" N ARG b 10 " --> pdb=" O GLU b 6 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU b 11 " --> pdb=" O ASN b 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU b 16 " --> pdb=" O GLY b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 62 removed outlier: 3.951A pdb=" N GLN b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 109 through 116 removed outlier: 3.660A pdb=" N MET b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY b 116 " --> pdb=" O PHE b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 129 removed outlier: 3.814A pdb=" N VAL b 128 " --> pdb=" O GLN b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 147 removed outlier: 3.698A pdb=" N LEU b 146 " --> pdb=" O ILE b 143 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER b 147 " --> pdb=" O PRO b 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 143 through 147' Processing helix chain 'b' and resid 155 through 157 No H-bonds generated for 'chain 'b' and resid 155 through 157' Processing helix chain 'b' and resid 251 through 263 removed outlier: 3.554A pdb=" N VAL b 255 " --> pdb=" O GLY b 251 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL b 256 " --> pdb=" O PHE b 252 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA b 257 " --> pdb=" O ALA b 253 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS b 260 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP b 261 " --> pdb=" O ALA b 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 272 removed outlier: 3.691A pdb=" N ILE b 272 " --> pdb=" O ARG b 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 273 through 276 removed outlier: 3.522A pdb=" N HIS b 276 " --> pdb=" O GLN b 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 273 through 276' Processing helix chain 'b' and resid 279 through 284 removed outlier: 3.947A pdb=" N VAL b 284 " --> pdb=" O ASN b 281 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 26 removed outlier: 3.730A pdb=" N ALA c 22 " --> pdb=" O ASP c 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU c 23 " --> pdb=" O GLU c 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.702A pdb=" N ALA c 44 " --> pdb=" O ASN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 67 removed outlier: 3.577A pdb=" N SER c 67 " --> pdb=" O MET c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 119 through 123 Processing helix chain 'c' and resid 141 through 161 removed outlier: 3.967A pdb=" N LEU c 149 " --> pdb=" O GLY c 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS c 156 " --> pdb=" O LEU c 152 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS c 160 " --> pdb=" O HIS c 156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE c 161 " --> pdb=" O ILE c 157 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 215 removed outlier: 3.557A pdb=" N ARG c 202 " --> pdb=" O ARG c 198 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL c 203 " --> pdb=" O THR c 199 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU c 204 " --> pdb=" O ALA c 200 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET c 209 " --> pdb=" O ASP c 205 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS c 212 " --> pdb=" O SER c 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE c 213 " --> pdb=" O MET c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 230 Processing helix chain 'c' and resid 246 through 253 removed outlier: 3.983A pdb=" N THR c 250 " --> pdb=" O PRO c 246 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG c 251 " --> pdb=" O ASP c 247 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP c 253 " --> pdb=" O VAL c 249 " (cutoff:3.500A) Processing helix chain 'c' and resid 258 through 273 removed outlier: 3.777A pdb=" N ASP c 262 " --> pdb=" O SER c 258 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR c 264 " --> pdb=" O PRO c 260 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL c 268 " --> pdb=" O THR c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 274 through 278 removed outlier: 3.699A pdb=" N SER c 277 " --> pdb=" O GLN c 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 26 removed outlier: 3.616A pdb=" N LEU d 20 " --> pdb=" O PHE d 16 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA d 21 " --> pdb=" O ALA d 17 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA d 22 " --> pdb=" O ASP d 18 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU d 23 " --> pdb=" O GLU d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 45 removed outlier: 4.238A pdb=" N ALA d 44 " --> pdb=" O ASN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 69 removed outlier: 3.861A pdb=" N SER d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS d 68 " --> pdb=" O GLN d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 123 Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 147 through 163 removed outlier: 3.581A pdb=" N GLN d 151 " --> pdb=" O ALA d 147 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU d 152 " --> pdb=" O ILE d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 179 removed outlier: 3.854A pdb=" N TYR d 177 " --> pdb=" O GLU d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 201 through 203 No H-bonds generated for 'chain 'd' and resid 201 through 203' Processing helix chain 'd' and resid 204 through 228 removed outlier: 3.881A pdb=" N CYS d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) Proline residue: d 219 - end of helix removed outlier: 3.766A pdb=" N LEU d 223 " --> pdb=" O PRO d 219 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG d 224 " --> pdb=" O ARG d 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 239 through 244 removed outlier: 3.832A pdb=" N GLU d 242 " --> pdb=" O GLU d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 252 removed outlier: 3.578A pdb=" N ARG d 251 " --> pdb=" O GLU d 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE d 252 " --> pdb=" O VAL d 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 248 through 252' Processing helix chain 'd' and resid 258 through 282 removed outlier: 4.356A pdb=" N THR d 264 " --> pdb=" O PRO d 260 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU d 273 " --> pdb=" O MET d 269 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER d 275 " --> pdb=" O SER d 271 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER d 278 " --> pdb=" O GLN d 274 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE d 279 " --> pdb=" O SER d 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE d 280 " --> pdb=" O LEU d 276 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 30 removed outlier: 4.022A pdb=" N ALA 1 26 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 65 removed outlier: 3.713A pdb=" N VAL 1 43 " --> pdb=" O ALA 1 39 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 1 63 " --> pdb=" O GLU 1 59 " (cutoff:3.500A) Processing helix chain '1' and resid 69 through 77 removed outlier: 3.664A pdb=" N HIS 1 73 " --> pdb=" O GLN 1 69 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 1 76 " --> pdb=" O ASP 1 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 18 Processing helix chain 'X' and resid 19 through 24 Processing helix chain 'X' and resid 65 through 73 removed outlier: 3.643A pdb=" N THR X 69 " --> pdb=" O PHE X 66 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA X 70 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU X 71 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA X 72 " --> pdb=" O THR X 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA X 73 " --> pdb=" O ALA X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 137 removed outlier: 3.547A pdb=" N GLU X 137 " --> pdb=" O ALA X 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 133 through 137' Processing helix chain 'X' and resid 145 through 185 removed outlier: 3.805A pdb=" N THR X 150 " --> pdb=" O PRO X 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR X 152 " --> pdb=" O ASP X 148 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY X 154 " --> pdb=" O THR X 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS X 157 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR X 158 " --> pdb=" O GLY X 154 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY X 166 " --> pdb=" O ALA X 162 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY X 173 " --> pdb=" O ALA X 169 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 175 " --> pdb=" O GLU X 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL X 181 " --> pdb=" O THR X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 196 removed outlier: 4.782A pdb=" N THR X 194 " --> pdb=" O PHE X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 224 removed outlier: 3.596A pdb=" N LYS X 210 " --> pdb=" O LYS X 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER X 211 " --> pdb=" O LYS X 207 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP X 212 " --> pdb=" O ALA X 208 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET X 216 " --> pdb=" O ASP X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 231 Processing helix chain 'X' and resid 237 through 252 removed outlier: 3.544A pdb=" N THR X 243 " --> pdb=" O GLN X 239 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP X 247 " --> pdb=" O THR X 243 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET X 248 " --> pdb=" O MET X 244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU X 249 " --> pdb=" O LEU X 245 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL X 252 " --> pdb=" O MET X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 260 removed outlier: 4.615A pdb=" N GLY X 260 " --> pdb=" O VAL X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 279 through 290 removed outlier: 3.957A pdb=" N ARG X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN X 288 " --> pdb=" O ARG X 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 318 removed outlier: 4.038A pdb=" N THR X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 334 removed outlier: 3.516A pdb=" N PHE X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL X 334 " --> pdb=" O MET X 330 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 351 Processing helix chain 'X' and resid 379 through 384 removed outlier: 3.921A pdb=" N TYR X 383 " --> pdb=" O LEU X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 454 removed outlier: 3.762A pdb=" N ILE X 453 " --> pdb=" O ALA X 449 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS X 454 " --> pdb=" O LEU X 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 449 through 454' Processing helix chain 'X' and resid 463 through 472 removed outlier: 3.971A pdb=" N ALA X 467 " --> pdb=" O GLN X 463 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN X 469 " --> pdb=" O ALA X 465 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE X 472 " --> pdb=" O LEU X 468 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 501 removed outlier: 3.814A pdb=" N TYR X 500 " --> pdb=" O THR X 496 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR X 501 " --> pdb=" O PHE X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 528 through 534 removed outlier: 3.914A pdb=" N LEU X 532 " --> pdb=" O SER X 528 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU X 534 " --> pdb=" O ARG X 530 " (cutoff:3.500A) Processing helix chain 'X' and resid 571 through 587 removed outlier: 4.080A pdb=" N GLN X 581 " --> pdb=" O SER X 577 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA X 584 " --> pdb=" O ALA X 580 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL X 585 " --> pdb=" O GLN X 581 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR X 586 " --> pdb=" O PHE X 582 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 605 removed outlier: 3.692A pdb=" N ILE X 597 " --> pdb=" O ASP X 593 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL X 599 " --> pdb=" O LEU X 595 " (cutoff:3.500A) Processing helix chain 'X' and resid 611 through 621 removed outlier: 3.561A pdb=" N VAL X 615 " --> pdb=" O LEU X 611 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU X 617 " --> pdb=" O CYS X 613 " (cutoff:3.500A) Processing helix chain 'X' and resid 623 through 643 removed outlier: 3.716A pdb=" N PHE X 627 " --> pdb=" O GLN X 623 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL X 628 " --> pdb=" O GLU X 624 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN X 630 " --> pdb=" O LYS X 626 " (cutoff:3.500A) Proline residue: X 632 - end of helix removed outlier: 3.641A pdb=" N ALA X 635 " --> pdb=" O MET X 631 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU X 636 " --> pdb=" O PRO X 632 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN X 639 " --> pdb=" O ALA X 635 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 664 removed outlier: 3.799A pdb=" N VAL X 657 " --> pdb=" O SER X 653 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS X 661 " --> pdb=" O VAL X 657 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET X 664 " --> pdb=" O ILE X 660 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 696 removed outlier: 3.653A pdb=" N HIS X 676 " --> pdb=" O GLU X 672 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR X 677 " --> pdb=" O ALA X 673 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE X 680 " --> pdb=" O HIS X 676 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU X 681 " --> pdb=" O TYR X 677 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 686 " --> pdb=" O GLY X 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU X 692 " --> pdb=" O GLU X 688 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS X 693 " --> pdb=" O GLN X 689 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU X 694 " --> pdb=" O ALA X 690 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA X 695 " --> pdb=" O LEU X 691 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY X 696 " --> pdb=" O LEU X 692 " (cutoff:3.500A) Processing helix chain 'X' and resid 705 through 710 removed outlier: 4.580A pdb=" N SER X 710 " --> pdb=" O THR X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 730 removed outlier: 3.917A pdb=" N ASP X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) Processing helix chain 'X' and resid 749 through 751 No H-bonds generated for 'chain 'X' and resid 749 through 751' Processing helix chain 'X' and resid 752 through 756 removed outlier: 3.665A pdb=" N PHE X 756 " --> pdb=" O ASN X 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 752 through 756' Processing helix chain 'X' and resid 770 through 780 removed outlier: 3.806A pdb=" N TYR X 774 " --> pdb=" O LEU X 770 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR X 776 " --> pdb=" O ASN X 772 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG X 777 " --> pdb=" O ILE X 773 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL X 778 " --> pdb=" O TYR X 774 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU X 780 " --> pdb=" O THR X 776 " (cutoff:3.500A) Processing helix chain 'X' and resid 799 through 808 removed outlier: 3.861A pdb=" N GLU X 803 " --> pdb=" O ASN X 799 " (cutoff:3.500A) Processing helix chain 'X' and resid 809 through 815 removed outlier: 3.838A pdb=" N VAL X 813 " --> pdb=" O VAL X 809 " (cutoff:3.500A) Processing helix chain 'X' and resid 826 through 834 removed outlier: 3.608A pdb=" N ALA X 830 " --> pdb=" O TYR X 826 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU X 831 " --> pdb=" O GLN X 827 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR X 832 " --> pdb=" O ASN X 828 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU X 833 " --> pdb=" O VAL X 829 " (cutoff:3.500A) Processing helix chain 'X' and resid 858 through 866 removed outlier: 3.610A pdb=" N ALA X 865 " --> pdb=" O ASP X 861 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY X 866 " --> pdb=" O ILE X 862 " (cutoff:3.500A) Processing helix chain 'X' and resid 871 through 880 removed outlier: 3.697A pdb=" N ILE X 875 " --> pdb=" O THR X 871 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR X 880 " --> pdb=" O ARG X 876 " (cutoff:3.500A) Processing helix chain 'X' and resid 881 through 883 No H-bonds generated for 'chain 'X' and resid 881 through 883' Processing helix chain 'X' and resid 908 through 910 No H-bonds generated for 'chain 'X' and resid 908 through 910' Processing helix chain 'X' and resid 928 through 930 No H-bonds generated for 'chain 'X' and resid 928 through 930' Processing helix chain 'X' and resid 931 through 937 Processing helix chain 'X' and resid 950 through 958 removed outlier: 4.383A pdb=" N THR X 956 " --> pdb=" O LEU X 952 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU X 957 " --> pdb=" O VAL X 953 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS X 958 " --> pdb=" O ALA X 954 " (cutoff:3.500A) Processing helix chain 'X' and resid 958 through 968 removed outlier: 3.510A pdb=" N ALA X 962 " --> pdb=" O HIS X 958 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU X 968 " --> pdb=" O TYR X 964 " (cutoff:3.500A) Processing helix chain 'X' and resid 969 through 973 removed outlier: 3.635A pdb=" N ARG X 972 " --> pdb=" O PRO X 969 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN X 973 " --> pdb=" O ASN X 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 969 through 973' Processing helix chain 'X' and resid 993 through 1000 removed outlier: 3.525A pdb=" N TYR X 998 " --> pdb=" O PRO X 994 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA X 999 " --> pdb=" O VAL X 995 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA X1000 " --> pdb=" O ALA X 996 " (cutoff:3.500A) Processing helix chain 'X' and resid 1005 through 1014 removed outlier: 3.853A pdb=" N SER X1010 " --> pdb=" O PRO X1006 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER X1014 " --> pdb=" O SER X1010 " (cutoff:3.500A) Processing helix chain 'X' and resid 1023 through 1029 Processing helix chain 'X' and resid 1117 through 1122 removed outlier: 4.191A pdb=" N ILE X1121 " --> pdb=" O ASP X1117 " (cutoff:3.500A) Processing helix chain 'X' and resid 1132 through 1141 Processing helix chain 'X' and resid 1187 through 1191 removed outlier: 3.551A pdb=" N TYR X1190 " --> pdb=" O ASP X1187 " (cutoff:3.500A) Processing helix chain 'X' and resid 1211 through 1220 removed outlier: 4.017A pdb=" N ARG X1217 " --> pdb=" O GLU X1213 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU X1218 " --> pdb=" O SER X1214 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU X1219 " --> pdb=" O ALA X1215 " (cutoff:3.500A) Processing helix chain 'X' and resid 1236 through 1241 removed outlier: 4.342A pdb=" N GLN X1241 " --> pdb=" O PRO X1237 " (cutoff:3.500A) Processing helix chain 'X' and resid 1244 through 1250 Processing helix chain 'X' and resid 1266 through 1271 removed outlier: 3.582A pdb=" N HIS X1271 " --> pdb=" O ARG X1267 " (cutoff:3.500A) Processing helix chain 'X' and resid 1271 through 1276 removed outlier: 3.516A pdb=" N ILE X1275 " --> pdb=" O HIS X1271 " (cutoff:3.500A) Processing helix chain 'X' and resid 1277 through 1280 removed outlier: 4.182A pdb=" N ARG X1280 " --> pdb=" O ARG X1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1277 through 1280' Processing helix chain 'X' and resid 1281 through 1292 removed outlier: 3.978A pdb=" N SER X1290 " --> pdb=" O VAL X1286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA X1291 " --> pdb=" O ASN X1287 " (cutoff:3.500A) Processing helix chain 'X' and resid 1319 through 1324 removed outlier: 3.750A pdb=" N LEU X1323 " --> pdb=" O PRO X1319 " (cutoff:3.500A) Processing helix chain 'X' and resid 1334 through 1344 removed outlier: 4.050A pdb=" N LEU X1338 " --> pdb=" O HIS X1334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET X1342 " --> pdb=" O LEU X1338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER X1343 " --> pdb=" O ASP X1339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 13 through 15 removed outlier: 3.811A pdb=" N ASN S 59 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER T 96 " --> pdb=" O ASN S 59 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET T 97 " --> pdb=" O ARG T 112 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG T 112 " --> pdb=" O MET T 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 13 through 14 removed outlier: 10.063A pdb=" N LEU S 13 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL W 56 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE W 50 " --> pdb=" O ILE X 87 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY X 89 " --> pdb=" O PHE W 50 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA W 52 " --> pdb=" O GLY X 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE X 91 " --> pdb=" O ALA W 52 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU W 54 " --> pdb=" O ILE X 91 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N PHE X 93 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL W 56 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N ILE X 95 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N THR W 58 " --> pdb=" O ILE X 95 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N MET X 97 " --> pdb=" O THR W 58 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG X 112 " --> pdb=" O MET X 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 13 through 14 removed outlier: 10.063A pdb=" N LEU S 13 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL W 56 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU W 51 " --> pdb=" O ALA X 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'W' and resid 121 through 132 removed outlier: 3.514A pdb=" N ILE W 129 " --> pdb=" O PHE W1080 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL W 76 " --> pdb=" O MET W1061 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL W1063 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR W 78 " --> pdb=" O VAL W1063 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'W' and resid 121 through 132 removed outlier: 3.514A pdb=" N ILE W 129 " --> pdb=" O PHE W1080 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA W1077 " --> pdb=" O VAL W1073 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL W1073 " --> pdb=" O ALA W1077 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR W1079 " --> pdb=" O ARG W1071 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 90 through 95 removed outlier: 3.704A pdb=" N VAL W 116 " --> pdb=" O PHE W 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'W' and resid 365 through 369 removed outlier: 4.461A pdb=" N SER W 365 " --> pdb=" O ILE W 376 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA W 375 " --> pdb=" O ALA W 273 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL W 275 " --> pdb=" O ALA W 375 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU W 377 " --> pdb=" O VAL W 275 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU W 277 " --> pdb=" O GLU W 377 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU W1045 " --> pdb=" O ILE W1107 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE W1107 " --> pdb=" O GLU W1045 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU W1047 " --> pdb=" O ALA W1105 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE W1051 " --> pdb=" O PRO W1101 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR W1053 " --> pdb=" O ILE W1099 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE W1099 " --> pdb=" O TYR W1053 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER W1055 " --> pdb=" O SER W1097 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER W1097 " --> pdb=" O SER W1055 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 365 through 369 removed outlier: 4.461A pdb=" N SER W 365 " --> pdb=" O ILE W 376 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA W 375 " --> pdb=" O ALA W 273 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL W 275 " --> pdb=" O ALA W 375 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU W 377 " --> pdb=" O VAL W 275 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU W 277 " --> pdb=" O GLU W 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 297 through 300 removed outlier: 3.577A pdb=" N GLY W 299 " --> pdb=" O THR W 360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 1180 through 1182 Processing sheet with id=AB2, first strand: chain 'W' and resid 540 through 545 Processing sheet with id=AB3, first strand: chain 'W' and resid 721 through 722 removed outlier: 3.503A pdb=" N GLN W 890 " --> pdb=" O VAL W 919 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG W 893 " --> pdb=" O LYS W 741 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN W 745 " --> pdb=" O ILE W 742 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 922 through 924 removed outlier: 3.846A pdb=" N PHE W 922 " --> pdb=" O MET W 822 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 1331 through 1332 removed outlier: 3.630A pdb=" N ALA W1331 " --> pdb=" O ILE W1358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 76 through 77 removed outlier: 6.497A pdb=" N VAL S 76 " --> pdb=" O MET S1061 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL S1063 " --> pdb=" O VAL S 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 121 through 129 removed outlier: 3.711A pdb=" N GLU S1072 " --> pdb=" O THR S1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 90 through 97 removed outlier: 4.462A pdb=" N ARG S 112 " --> pdb=" O MET S 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 265 through 266 Processing sheet with id=AC1, first strand: chain 'S' and resid 1180 through 1182 removed outlier: 7.487A pdb=" N ALA S 375 " --> pdb=" O ALA S 273 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL S 275 " --> pdb=" O ALA S 375 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU S 377 " --> pdb=" O VAL S 275 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU S 277 " --> pdb=" O GLU S 377 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER S 365 " --> pdb=" O ILE S 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 1097 through 1107 removed outlier: 7.133A pdb=" N SER S1097 " --> pdb=" O SER S1055 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER S1055 " --> pdb=" O SER S1097 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE S1099 " --> pdb=" O TYR S1053 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR S1053 " --> pdb=" O ILE S1099 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE S1051 " --> pdb=" O PRO S1101 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU S1047 " --> pdb=" O ALA S1105 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE S1107 " --> pdb=" O GLU S1045 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU S1045 " --> pdb=" O ILE S1107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 1316 through 1317 removed outlier: 7.108A pdb=" N GLU S1045 " --> pdb=" O ILE S1107 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE S1107 " --> pdb=" O GLU S1045 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU S1047 " --> pdb=" O ALA S1105 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE S1051 " --> pdb=" O PRO S1101 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR S1053 " --> pdb=" O ILE S1099 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE S1099 " --> pdb=" O TYR S1053 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER S1055 " --> pdb=" O SER S1097 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER S1097 " --> pdb=" O SER S1055 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 432 through 435 removed outlier: 3.625A pdb=" N THR S 432 " --> pdb=" O PHE S 444 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 540 through 545 removed outlier: 3.534A pdb=" N SER S 553 " --> pdb=" O HIS S 545 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 721 through 722 removed outlier: 3.598A pdb=" N ALA S 722 " --> pdb=" O LEU S 918 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 757 through 759 Processing sheet with id=AC8, first strand: chain 'S' and resid 922 through 924 removed outlier: 3.519A pdb=" N PHE S 922 " --> pdb=" O MET S 822 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 1369 through 1370 removed outlier: 3.552A pdb=" N LEU S1370 " --> pdb=" O LYS S1373 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS S1373 " --> pdb=" O LEU S1370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'T' and resid 121 through 125 removed outlier: 6.258A pdb=" N VAL T 76 " --> pdb=" O MET T1061 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL T1063 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR T 78 " --> pdb=" O VAL T1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.529A pdb=" N THR T1079 " --> pdb=" O ARG T1071 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 366 through 369 removed outlier: 5.748A pdb=" N ALA T 375 " --> pdb=" O ALA T 273 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL T 275 " --> pdb=" O ALA T 375 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU T 377 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU T 277 " --> pdb=" O GLU T 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 296 through 300 Processing sheet with id=AD5, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.117A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.117A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N TYR T1327 " --> pdb=" O GLN T 397 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR T 399 " --> pdb=" O TYR T1327 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 432 through 435 removed outlier: 3.623A pdb=" N THR T 432 " --> pdb=" O PHE T 444 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 540 through 545 Processing sheet with id=AD9, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AE1, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AE2, first strand: chain 'T' and resid 757 through 759 removed outlier: 5.851A pdb=" N ASN T 758 " --> pdb=" O VAL T 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'T' and resid 922 through 924 removed outlier: 3.726A pdb=" N PHE T 922 " --> pdb=" O MET T 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 1109 through 1110 Processing sheet with id=AE5, first strand: chain 'T' and resid 1331 through 1332 removed outlier: 3.531A pdb=" N ALA T1331 " --> pdb=" O ILE T1358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 1368 through 1370 removed outlier: 3.569A pdb=" N LYS T1373 " --> pdb=" O LEU T1370 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '4' and resid 75 through 76 removed outlier: 6.463A pdb=" N VAL 4 76 " --> pdb=" O MET 41061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '4' and resid 78 through 79 Processing sheet with id=AE9, first strand: chain '4' and resid 91 through 96 removed outlier: 3.811A pdb=" N LYS 4 118 " --> pdb=" O ILE 4 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL 4 116 " --> pdb=" O PHE 4 93 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '4' and resid 126 through 132 removed outlier: 3.666A pdb=" N THR 41079 " --> pdb=" O ARG 41071 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS 5 24 " --> pdb=" O VAL 41068 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 368 through 369 removed outlier: 6.520A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 272 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY 4 274 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '4' and resid 1097 through 1107 removed outlier: 7.412A pdb=" N SER 41097 " --> pdb=" O SER 41055 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N SER 41055 " --> pdb=" O SER 41097 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE 41099 " --> pdb=" O TYR 41053 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR 41053 " --> pdb=" O ILE 41099 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE 41051 " --> pdb=" O PRO 41101 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS 41103 " --> pdb=" O GLU 41049 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU 41047 " --> pdb=" O ALA 41105 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE 41107 " --> pdb=" O GLU 41045 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLU 41045 " --> pdb=" O ILE 41107 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET 41038 " --> pdb=" O VAL 4 404 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '4' and resid 296 through 300 removed outlier: 3.538A pdb=" N GLY 4 299 " --> pdb=" O THR 4 360 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '4' and resid 307 through 309 removed outlier: 3.547A pdb=" N GLN X 36 " --> pdb=" O ARG 4 309 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA X 52 " --> pdb=" O SER X 34 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN X 36 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE X 50 " --> pdb=" O GLN X 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '4' and resid 432 through 435 removed outlier: 4.248A pdb=" N THR 4 432 " --> pdb=" O PHE 4 444 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '4' and resid 542 through 544 Processing sheet with id=AF8, first strand: chain '4' and resid 740 through 741 Processing sheet with id=AF9, first strand: chain '4' and resid 890 through 891 removed outlier: 4.374A pdb=" N GLN 4 890 " --> pdb=" O VAL 4 919 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '4' and resid 1331 through 1332 Processing sheet with id=AG2, first strand: chain '5' and resid 70 through 76 removed outlier: 6.472A pdb=" N LYS 5 176 " --> pdb=" O SER 5 168 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER 5 168 " --> pdb=" O LYS 5 176 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR 5 178 " --> pdb=" O VAL 5 166 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU 5 90 " --> pdb=" O VAL 5 162 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '5' and resid 185 through 186 removed outlier: 4.216A pdb=" N GLY 5 185 " --> pdb=" O VAL 5 195 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '5' and resid 198 through 200 Processing sheet with id=AG5, first strand: chain '5' and resid 204 through 206 removed outlier: 3.508A pdb=" N GLN 5 247 " --> pdb=" O VAL 5 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 5 224 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR 5 293 " --> pdb=" O VAL 5 224 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE 5 226 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU 5 321 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '5' and resid 204 through 206 removed outlier: 3.508A pdb=" N GLN 5 247 " --> pdb=" O VAL 5 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 5 224 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR 5 293 " --> pdb=" O VAL 5 224 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE 5 226 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY 5 286 " --> pdb=" O PHE 5 330 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '6' and resid 30 through 33 removed outlier: 3.716A pdb=" N THR 6 70 " --> pdb=" O LEU 6 33 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG 6 83 " --> pdb=" O GLU 6 75 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL 6 77 " --> pdb=" O SER 6 81 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER 6 81 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL 6 8 " --> pdb=" O GLN 6 40 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '6' and resid 92 through 96 removed outlier: 6.941A pdb=" N SER 6 299 " --> pdb=" O TYR 6 289 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '6' and resid 112 through 114 Processing sheet with id=AH1, first strand: chain '6' and resid 124 through 126 Processing sheet with id=AH2, first strand: chain '6' and resid 181 through 183 Processing sheet with id=AH3, first strand: chain '7' and resid 8 through 10 removed outlier: 4.002A pdb=" N GLU 7 76 " --> pdb=" O ARG 7 83 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '7' and resid 30 through 31 Processing sheet with id=AH5, first strand: chain '7' and resid 95 through 96 removed outlier: 3.597A pdb=" N ALA 7 290 " --> pdb=" O SER 7 299 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '7' and resid 138 through 141 removed outlier: 3.840A pdb=" N VAL 7 113 " --> pdb=" O PRO 7 284 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG 7 285 " --> pdb=" O SER 7 303 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '7' and resid 124 through 125 removed outlier: 3.566A pdb=" N ILE 7 134 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '7' and resid 180 through 183 Processing sheet with id=AH9, first strand: chain 'b' and resid 69 through 76 removed outlier: 3.513A pdb=" N GLY b 71 " --> pdb=" O SER b 179 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA b 180 " --> pdb=" O MET b 165 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET b 165 " --> pdb=" O ALA b 180 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 104 through 105 removed outlier: 4.611A pdb=" N MET b 104 " --> pdb=" O PHE b 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR b 160 " --> pdb=" O SER b 92 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 185 through 186 removed outlier: 4.402A pdb=" N GLY b 185 " --> pdb=" O VAL b 195 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'b' and resid 197 through 200 Processing sheet with id=AI4, first strand: chain 'b' and resid 204 through 206 removed outlier: 3.725A pdb=" N GLN b 247 " --> pdb=" O VAL b 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY b 292 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA b 228 " --> pdb=" O THR b 290 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR b 290 " --> pdb=" O ALA b 228 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU b 230 " --> pdb=" O VAL b 288 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL b 288 " --> pdb=" O LEU b 230 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR b 232 " --> pdb=" O GLY b 286 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLY b 286 " --> pdb=" O TYR b 232 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'c' and resid 30 through 33 removed outlier: 4.018A pdb=" N THR c 70 " --> pdb=" O LEU c 33 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU c 71 " --> pdb=" O MET c 87 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG c 83 " --> pdb=" O GLU c 75 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN c 40 " --> pdb=" O VAL c 8 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 92 through 93 removed outlier: 7.112A pdb=" N SER c 299 " --> pdb=" O TYR c 289 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP c 301 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS c 287 " --> pdb=" O TRP c 301 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'c' and resid 124 through 125 removed outlier: 3.532A pdb=" N ILE c 125 " --> pdb=" O ILE c 134 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'c' and resid 180 through 182 Processing sheet with id=AI9, first strand: chain 'd' and resid 30 through 33 removed outlier: 7.325A pdb=" N ARG d 83 " --> pdb=" O GLU d 75 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL d 8 " --> pdb=" O GLN d 40 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 92 through 96 removed outlier: 7.007A pdb=" N ALA d 297 " --> pdb=" O TYR d 291 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR d 291 " --> pdb=" O ALA d 297 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER d 299 " --> pdb=" O TYR d 289 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG d 285 " --> pdb=" O SER d 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL d 140 " --> pdb=" O ALA d 112 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 124 through 127 removed outlier: 3.785A pdb=" N ILE d 134 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 180 through 183 Processing sheet with id=AJ4, first strand: chain 'X' and resid 121 through 132 removed outlier: 6.209A pdb=" N VAL X 76 " --> pdb=" O MET X1061 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL X1063 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR X 78 " --> pdb=" O VAL X1063 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR X 306 " --> pdb=" O GLU X 79 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'X' and resid 121 through 132 removed outlier: 7.054A pdb=" N ALA X1077 " --> pdb=" O VAL X1073 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL X1073 " --> pdb=" O ALA X1077 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR X1079 " --> pdb=" O ARG X1071 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG X1071 " --> pdb=" O THR X1079 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'X' and resid 265 through 266 Processing sheet with id=AJ7, first strand: chain 'X' and resid 1178 through 1182 removed outlier: 7.414A pdb=" N ALA X 375 " --> pdb=" O ALA X 273 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL X 275 " --> pdb=" O ALA X 375 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU X 377 " --> pdb=" O VAL X 275 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU X 277 " --> pdb=" O GLU X 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS X 372 " --> pdb=" O ILE X 369 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'X' and resid 1097 through 1106 removed outlier: 7.254A pdb=" N SER X1097 " --> pdb=" O SER X1055 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER X1055 " --> pdb=" O SER X1097 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE X1099 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR X1053 " --> pdb=" O ILE X1099 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE X1051 " --> pdb=" O PRO X1101 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU X1047 " --> pdb=" O ALA X1105 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N TYR X1327 " --> pdb=" O GLN X 397 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR X 399 " --> pdb=" O TYR X1327 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'X' and resid 1316 through 1317 removed outlier: 3.536A pdb=" N ASP X1317 " --> pdb=" O ARG X 395 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU X1047 " --> pdb=" O ALA X1105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE X1051 " --> pdb=" O PRO X1101 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR X1053 " --> pdb=" O ILE X1099 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE X1099 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER X1055 " --> pdb=" O SER X1097 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER X1097 " --> pdb=" O SER X1055 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'X' and resid 432 through 434 Processing sheet with id=AK2, first strand: chain 'X' and resid 540 through 545 Processing sheet with id=AK3, first strand: chain 'X' and resid 721 through 722 removed outlier: 3.533A pdb=" N ARG X 893 " --> pdb=" O LYS X 741 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN X 745 " --> pdb=" O ILE X 742 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'X' and resid 757 through 759 Processing sheet with id=AK5, first strand: chain 'X' and resid 922 through 924 Processing sheet with id=AK6, first strand: chain 'X' and resid 1331 through 1332 removed outlier: 3.527A pdb=" N ALA X1331 " --> pdb=" O ILE X1358 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'X' and resid 1368 through 1369 2070 hydrogen bonds defined for protein. 5739 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: 31.02 Time building geometry restraints manager: 20.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18335 1.33 - 1.45: 14310 1.45 - 1.58: 36960 1.58 - 1.70: 0 1.70 - 1.82: 762 Bond restraints: 70367 Sorted by residual: bond pdb=" N THR W 263 " pdb=" CA THR W 263 " ideal model delta sigma weight residual 1.457 1.511 -0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" C MET 4 631 " pdb=" N PRO 4 632 " ideal model delta sigma weight residual 1.336 1.375 -0.039 9.80e-03 1.04e+04 1.60e+01 bond pdb=" C SER S 993 " pdb=" N PRO S 994 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N THR T 263 " pdb=" CA THR T 263 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.17e-02 7.31e+03 1.17e+01 bond pdb=" N ASP W 849 " pdb=" CA ASP W 849 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 ... (remaining 70362 not shown) Histogram of bond angle deviations from ideal: 94.17 - 104.43: 1533 104.43 - 114.70: 41986 114.70 - 124.96: 50877 124.96 - 135.23: 1225 135.23 - 145.49: 3 Bond angle restraints: 95624 Sorted by residual: angle pdb=" N GLY W 421 " pdb=" CA GLY W 421 " pdb=" C GLY W 421 " ideal model delta sigma weight residual 112.50 122.12 -9.62 1.16e+00 7.43e-01 6.88e+01 angle pdb=" C TYR 4 798 " pdb=" N ASN 4 799 " pdb=" CA ASN 4 799 " ideal model delta sigma weight residual 121.70 134.77 -13.07 1.80e+00 3.09e-01 5.27e+01 angle pdb=" N VAL T1113 " pdb=" CA VAL T1113 " pdb=" CB VAL T1113 " ideal model delta sigma weight residual 112.33 103.84 8.49 1.19e+00 7.06e-01 5.09e+01 angle pdb=" C VAL T1113 " pdb=" CA VAL T1113 " pdb=" CB VAL T1113 " ideal model delta sigma weight residual 110.62 118.25 -7.63 1.08e+00 8.57e-01 4.99e+01 angle pdb=" C ASP T 848 " pdb=" N ASP T 849 " pdb=" CA ASP T 849 " ideal model delta sigma weight residual 121.31 131.75 -10.44 1.49e+00 4.50e-01 4.91e+01 ... (remaining 95619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 40338 17.39 - 34.78: 1674 34.78 - 52.17: 333 52.17 - 69.56: 34 69.56 - 86.95: 36 Dihedral angle restraints: 42415 sinusoidal: 16807 harmonic: 25608 Sorted by residual: dihedral pdb=" CA PHE T 10 " pdb=" C PHE T 10 " pdb=" N PRO T 11 " pdb=" CA PRO T 11 " ideal model delta harmonic sigma weight residual 180.00 122.38 57.62 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA LEU 4 313 " pdb=" C LEU 4 313 " pdb=" N VAL 4 314 " pdb=" CA VAL 4 314 " ideal model delta harmonic sigma weight residual -180.00 -127.79 -52.21 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ASP 4 842 " pdb=" C ASP 4 842 " pdb=" N VAL 4 843 " pdb=" CA VAL 4 843 " ideal model delta harmonic sigma weight residual -180.00 -128.36 -51.64 0 5.00e+00 4.00e-02 1.07e+02 ... (remaining 42412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 9386 0.085 - 0.170: 1318 0.170 - 0.254: 86 0.254 - 0.339: 8 0.339 - 0.424: 1 Chirality restraints: 10799 Sorted by residual: chirality pdb=" CG LEU 4 788 " pdb=" CB LEU 4 788 " pdb=" CD1 LEU 4 788 " pdb=" CD2 LEU 4 788 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CB VAL S 422 " pdb=" CA VAL S 422 " pdb=" CG1 VAL S 422 " pdb=" CG2 VAL S 422 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE 4 895 " pdb=" CA ILE 4 895 " pdb=" CG1 ILE 4 895 " pdb=" CG2 ILE 4 895 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 10796 not shown) Planarity restraints: 12423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR W 263 " -0.033 2.00e-02 2.50e+03 6.59e-02 4.34e+01 pdb=" C THR W 263 " 0.114 2.00e-02 2.50e+03 pdb=" O THR W 263 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR W 264 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE T 10 " 0.078 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO T 11 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO T 11 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO T 11 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER W 262 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C SER W 262 " -0.057 2.00e-02 2.50e+03 pdb=" O SER W 262 " 0.021 2.00e-02 2.50e+03 pdb=" N THR W 263 " 0.020 2.00e-02 2.50e+03 ... (remaining 12420 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6700 2.74 - 3.28: 62929 3.28 - 3.82: 106913 3.82 - 4.36: 127782 4.36 - 4.90: 220558 Nonbonded interactions: 524882 Sorted by model distance: nonbonded pdb=" OH TYR W 481 " pdb=" O VAL W 979 " model vdw 2.203 2.440 nonbonded pdb=" O ARG T1071 " pdb=" OG1 THR T1079 " model vdw 2.225 2.440 nonbonded pdb=" OD2 ASP X 729 " pdb=" OH TYR X 798 " model vdw 2.235 2.440 nonbonded pdb=" O ARG 41071 " pdb=" OG1 THR 41079 " model vdw 2.244 2.440 nonbonded pdb=" NH2 ARG 2 70 " pdb=" O GLN 3 12 " model vdw 2.262 2.520 ... (remaining 524877 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' } ncs_group { reference = (chain '4' and (resid 47 through 300 or resid 361 through 547 or resid 551 throu \ gh 1252 or resid 1262 through 1376)) selection = (chain 'S' and (resid 47 through 253 or resid 263 through 409 or resid 427 throu \ gh 547 or resid 551 through 1141 or resid 1175 through 1293 or resid 1314 throug \ h 1344 or resid 1351 through 1376)) selection = (chain 'T' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 1141 or resid 1175 through 1252 or resid 1262 throug \ h 1293 or resid 1314 through 1344 or resid 1351 through 1376)) selection = (chain 'W' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 547 or resid 551 through 1141 or resid 1175 through \ 1252 or resid 1262 through 1293 or resid 1314 through 1344 or resid 1351 through \ 1376)) selection = (chain 'X' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 547 or resid 551 through 1141 or resid 1175 through \ 1293 or resid 1314 through 1344 or resid 1351 through 1376)) } ncs_group { reference = chain '5' selection = (chain 'b' and (resid 6 through 188 or resid 192 through 211 or resid 217 throug \ h 331)) } ncs_group { reference = (chain '6' and (resid 5 through 52 or resid 56 through 193 or resid 201 through \ 305)) selection = (chain '7' and (resid 5 through 163 or resid 174 through 305)) selection = (chain 'c' and (resid 5 through 52 or resid 56 through 193 or resid 201 through \ 305)) selection = (chain 'd' and (resid 5 through 52 or resid 56 through 163 or resid 174 through \ 193 or resid 201 through 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 14.340 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 139.380 Find NCS groups from input model: 4.280 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 70367 Z= 0.502 Angle : 1.102 23.542 95624 Z= 0.597 Chirality : 0.058 0.424 10799 Planarity : 0.007 0.121 12423 Dihedral : 10.722 86.952 25855 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 0.64 % Allowed : 2.85 % Favored : 96.51 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.82 % Twisted General : 0.27 % 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: -4.49 (0.07), residues: 8646 helix: -4.56 (0.04), residues: 2753 sheet: -1.81 (0.13), residues: 1248 loop : -2.26 (0.08), residues: 4645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP T 990 HIS 0.029 0.003 HIS T1321 PHE 0.053 0.004 PHE T 217 TYR 0.040 0.003 TYR T1095 ARG 0.026 0.001 ARG T 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2380 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 2332 time to evaluate : 5.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 164 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7630 (mm-40) REVERT: W 229 ASP cc_start: 0.8013 (t70) cc_final: 0.7813 (t0) REVERT: W 247 ASP cc_start: 0.6733 (t0) cc_final: 0.6517 (t0) REVERT: W 264 TYR cc_start: 0.8030 (m-80) cc_final: 0.7787 (m-80) REVERT: W 297 MET cc_start: 0.8282 (ptp) cc_final: 0.8078 (ptt) REVERT: W 491 MET cc_start: 0.8369 (mmt) cc_final: 0.8167 (mmm) REVERT: W 509 VAL cc_start: 0.7893 (t) cc_final: 0.7665 (p) REVERT: W 545 HIS cc_start: 0.8080 (t-90) cc_final: 0.7817 (t-170) REVERT: W 656 MET cc_start: 0.8642 (mmm) cc_final: 0.8381 (mmm) REVERT: W 684 LEU cc_start: 0.8863 (tt) cc_final: 0.8599 (tt) REVERT: W 769 ASN cc_start: 0.7215 (m-40) cc_final: 0.6987 (t0) REVERT: W 912 ASP cc_start: 0.7970 (t0) cc_final: 0.7567 (p0) REVERT: W 1079 THR cc_start: 0.8570 (p) cc_final: 0.6994 (p) REVERT: W 1322 MET cc_start: 0.7364 (tpt) cc_final: 0.6978 (tpp) REVERT: 2 15 LEU cc_start: 0.6983 (tp) cc_final: 0.6739 (tp) REVERT: 2 40 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7087 (mp0) REVERT: 2 41 TYR cc_start: 0.8471 (t80) cc_final: 0.8057 (t80) REVERT: S 86 MET cc_start: 0.4789 (ptt) cc_final: 0.3828 (mtt) REVERT: S 94 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7933 (mtpt) REVERT: S 206 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8616 (mmtt) REVERT: S 272 VAL cc_start: 0.9293 (t) cc_final: 0.9028 (m) REVERT: S 545 HIS cc_start: 0.8004 (t-90) cc_final: 0.7412 (t70) REVERT: S 700 VAL cc_start: 0.9192 (t) cc_final: 0.8983 (m) REVERT: S 811 MET cc_start: 0.8437 (mmt) cc_final: 0.7938 (mmt) REVERT: S 835 TYR cc_start: 0.8181 (t80) cc_final: 0.6860 (t80) REVERT: S 836 ASN cc_start: 0.7082 (t0) cc_final: 0.6823 (t0) REVERT: S 930 ARG cc_start: 0.7324 (ptm-80) cc_final: 0.5762 (tpp80) REVERT: S 932 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7382 (ttm110) REVERT: S 1337 MET cc_start: 0.8623 (mmm) cc_final: 0.8414 (mmm) REVERT: T 65 LYS cc_start: 0.7407 (ptpt) cc_final: 0.7106 (mtmt) REVERT: T 82 ASP cc_start: 0.8572 (p0) cc_final: 0.8132 (p0) REVERT: T 87 ILE cc_start: 0.8833 (mm) cc_final: 0.8624 (mt) REVERT: T 137 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7090 (tm-30) REVERT: T 671 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7683 (ttmt) REVERT: T 783 ASP cc_start: 0.7094 (m-30) cc_final: 0.6653 (m-30) REVERT: T 802 LEU cc_start: 0.8732 (mt) cc_final: 0.8529 (mp) REVERT: T 1116 GLN cc_start: 0.7957 (tt0) cc_final: 0.7614 (tt0) REVERT: T 1184 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9274 (m) REVERT: T 1359 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7583 (mp0) REVERT: T 1361 VAL cc_start: 0.9176 (t) cc_final: 0.8954 (t) REVERT: 4 214 VAL cc_start: 0.8843 (t) cc_final: 0.8444 (m) REVERT: 4 758 ASN cc_start: 0.5655 (t0) cc_final: 0.5355 (m110) REVERT: 4 1188 VAL cc_start: 0.7997 (t) cc_final: 0.7711 (p) REVERT: 4 1272 LYS cc_start: 0.7422 (tttt) cc_final: 0.7004 (mtmt) REVERT: 4 1322 MET cc_start: 0.6604 (tpt) cc_final: 0.6156 (mtt) REVERT: 4 1341 TYR cc_start: 0.7414 (t80) cc_final: 0.7018 (t80) REVERT: 5 13 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7774 (mtp85) REVERT: 5 101 SER cc_start: 0.7870 (m) cc_final: 0.7444 (p) REVERT: 5 173 PHE cc_start: 0.7004 (m-80) cc_final: 0.6711 (m-80) REVERT: 5 264 THR cc_start: 0.8599 (m) cc_final: 0.8274 (p) REVERT: 5 279 TYR cc_start: 0.6822 (m-80) cc_final: 0.5932 (m-80) REVERT: 5 300 PRO cc_start: 0.8329 (Cg_endo) cc_final: 0.8095 (Cg_exo) REVERT: 6 217 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7412 (pp) REVERT: 7 14 ARG cc_start: 0.5763 (mtp85) cc_final: 0.5206 (mpt180) REVERT: 7 96 LYS cc_start: 0.7569 (tttt) cc_final: 0.7266 (tttp) REVERT: 7 138 MET cc_start: 0.7380 (ttt) cc_final: 0.7083 (ttt) REVERT: 7 170 ASN cc_start: 0.6871 (m110) cc_final: 0.6469 (t0) REVERT: 7 186 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7045 (ttm110) REVERT: 7 256 GLN cc_start: 0.6652 (pt0) cc_final: 0.5789 (mp10) REVERT: b 150 MET cc_start: 0.7261 (mmm) cc_final: 0.7057 (mtt) REVERT: b 201 CYS cc_start: 0.7509 (m) cc_final: 0.7242 (t) REVERT: b 213 MET cc_start: 0.5007 (tpt) cc_final: 0.4587 (mmt) REVERT: c 58 ASP cc_start: 0.7640 (p0) cc_final: 0.7345 (p0) REVERT: c 144 LEU cc_start: 0.8078 (mt) cc_final: 0.7614 (tt) REVERT: c 191 ASP cc_start: 0.7405 (t0) cc_final: 0.6987 (t70) REVERT: c 210 TYR cc_start: 0.8342 (m-80) cc_final: 0.8100 (m-10) REVERT: c 262 ASP cc_start: 0.7269 (m-30) cc_final: 0.7062 (m-30) REVERT: c 305 ARG cc_start: 0.7492 (mtp-110) cc_final: 0.6660 (mtt90) REVERT: d 148 ILE cc_start: 0.8909 (tp) cc_final: 0.8649 (tp) REVERT: d 176 LEU cc_start: 0.8791 (tp) cc_final: 0.8389 (mt) REVERT: d 191 ASP cc_start: 0.6711 (m-30) cc_final: 0.6407 (m-30) REVERT: 1 18 ASP cc_start: 0.6783 (m-30) cc_final: 0.6536 (m-30) REVERT: 1 44 GLN cc_start: 0.7511 (mt0) cc_final: 0.7295 (mt0) REVERT: X 106 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7166 (ptt180) REVERT: X 234 MET cc_start: 0.8881 (mtt) cc_final: 0.8522 (mtt) REVERT: X 458 MET cc_start: 0.8757 (mmm) cc_final: 0.8505 (mmt) REVERT: X 469 ASN cc_start: 0.8790 (t0) cc_final: 0.8459 (t0) REVERT: X 678 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.7244 (tpt90) REVERT: X 725 ASP cc_start: 0.7775 (t0) cc_final: 0.7575 (t0) REVERT: X 789 ASP cc_start: 0.6775 (m-30) cc_final: 0.5112 (m-30) REVERT: X 856 ASN cc_start: 0.7370 (m-40) cc_final: 0.6394 (m-40) REVERT: X 879 CYS cc_start: 0.7752 (m) cc_final: 0.7416 (m) REVERT: X 1170 SER cc_start: 0.8576 (p) cc_final: 0.8294 (t) REVERT: X 1342 MET cc_start: 0.8992 (mmp) cc_final: 0.8711 (mmp) outliers start: 48 outliers final: 13 residues processed: 2363 average time/residue: 0.7108 time to fit residues: 2798.1189 Evaluate side-chains 1372 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1356 time to evaluate : 5.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 1184 VAL Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 947 LEU Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 217 LEU Chi-restraints excluded: chain X residue 106 ARG Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 732 optimal weight: 30.0000 chunk 657 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 443 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 679 optimal weight: 30.0000 chunk 262 optimal weight: 2.9990 chunk 413 optimal weight: 10.0000 chunk 505 optimal weight: 50.0000 chunk 787 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 HIS 0 73 HIS W 92 GLN W 102 HIS W 224 HIS W 428 GLN W 448 ASN W 498 HIS W 587 ASN W 590 HIS W 594 GLN W 663 HIS ** W 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 902 GLN W 982 ASN ** W1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1133 HIS W1192 GLN W1196 ASN W1321 HIS ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 17 HIS 2 47 HIS 2 55 HIS 2 75 GLN S 59 ASN S 77 ASN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 HIS S 384 ASN ** S 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 630 ASN S 644 ASN S 652 ASN S 674 HIS S 716 HIS S 746 ASN S 779 ASN S 856 ASN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN S 978 ASN S1084 HIS S1114 HIS ** S1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1173 GLN S1235 ASN S1268 GLN S1318 GLN S1344 ASN T 312 ASN T 397 GLN T 463 GLN T 466 GLN T 499 GLN ** T 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 558 HIS ** T 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 724 HIS T 853 HIS T 902 GLN ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1133 HIS T1236 ASN T1305 GLN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 17 HIS ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 44 GLN 4 270 GLN 4 336 HIS 4 498 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 545 HIS 4 567 GLN 4 601 GLN ** 4 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 724 HIS ** 4 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 816 ASN 4 828 ASN 4 978 ASN 41033 HIS 41196 ASN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS 5 24 HIS 5 62 GLN 5 67 GLN 5 319 ASN 6 24 GLN 6 40 GLN ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 142 GLN 6 150 GLN 6 232 HIS 6 235 HIS ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 64 GLN 7 92 ASN 7 97 ASN 7 281 ASN b 170 HIS ** b 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 40 GLN c 41 ASN ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN c 151 GLN c 287 HIS d 108 ASN d 130 ASN d 146 HIS d 156 HIS d 194 ASN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 17 HIS 1 47 HIS 1 55 HIS 1 75 GLN X 224 HIS X 288 ASN X 312 ASN X 325 ASN X 328 GLN X 393 ASN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN X 525 HIS X 575 GLN X 630 ASN X 716 HIS X 746 ASN X 779 ASN ** X 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 818 HIS X 978 ASN X1030 HIS X1084 HIS X1114 HIS X1171 HIS X1192 GLN X1235 ASN ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 70367 Z= 0.324 Angle : 0.735 13.271 95624 Z= 0.379 Chirality : 0.047 0.182 10799 Planarity : 0.006 0.103 12423 Dihedral : 6.668 89.260 9590 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 3.88 % Allowed : 11.17 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.41 % Twisted General : 0.12 % 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: -3.45 (0.08), residues: 8646 helix: -3.16 (0.07), residues: 2875 sheet: -1.35 (0.14), residues: 1287 loop : -1.91 (0.08), residues: 4484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 990 HIS 0.014 0.002 HIS W1114 PHE 0.031 0.002 PHE T 217 TYR 0.033 0.002 TYR W 614 ARG 0.010 0.001 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1739 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1448 time to evaluate : 5.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.0172 (mmm) cc_final: -0.0436 (mmm) REVERT: W 41 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8069 (tptt) REVERT: W 63 PHE cc_start: 0.7109 (p90) cc_final: 0.6903 (p90) REVERT: W 202 GLU cc_start: 0.3599 (tp30) cc_final: 0.2579 (tp30) REVERT: W 264 TYR cc_start: 0.7955 (m-80) cc_final: 0.7548 (m-80) REVERT: W 372 LYS cc_start: 0.8388 (mttt) cc_final: 0.7812 (mttm) REVERT: W 463 GLN cc_start: 0.6559 (tp40) cc_final: 0.6338 (tp40) REVERT: W 545 HIS cc_start: 0.8142 (t-90) cc_final: 0.7837 (t-170) REVERT: W 642 TRP cc_start: 0.8333 (t-100) cc_final: 0.7846 (t60) REVERT: W 769 ASN cc_start: 0.7347 (m-40) cc_final: 0.7104 (t0) REVERT: W 793 LEU cc_start: 0.8299 (tp) cc_final: 0.7945 (mp) REVERT: W 822 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7058 (ttt) REVERT: W 912 ASP cc_start: 0.7687 (t0) cc_final: 0.7316 (p0) REVERT: W 1032 MET cc_start: 0.8670 (mmm) cc_final: 0.7744 (mtp) REVERT: W 1278 TYR cc_start: 0.8780 (m-80) cc_final: 0.8424 (m-80) REVERT: W 1322 MET cc_start: 0.7355 (tpt) cc_final: 0.7146 (tpp) REVERT: S 86 MET cc_start: 0.4574 (ptt) cc_final: 0.3932 (mtt) REVERT: S 94 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7387 (mtmt) REVERT: S 117 MET cc_start: 0.8447 (tpt) cc_final: 0.8150 (tpp) REVERT: S 171 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7461 (mt-10) REVERT: S 206 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8574 (mmtt) REVERT: S 545 HIS cc_start: 0.7770 (t-90) cc_final: 0.7154 (t70) REVERT: S 555 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8177 (mtp85) REVERT: S 700 VAL cc_start: 0.9291 (t) cc_final: 0.8805 (m) REVERT: S 707 HIS cc_start: 0.8576 (m-70) cc_final: 0.8371 (m-70) REVERT: S 811 MET cc_start: 0.8353 (mmt) cc_final: 0.8006 (mmt) REVERT: S 822 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7315 (mtm) REVERT: S 835 TYR cc_start: 0.8409 (t80) cc_final: 0.6973 (t80) REVERT: S 930 ARG cc_start: 0.7439 (ptm-80) cc_final: 0.5945 (tpt-90) REVERT: S 971 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8012 (mm110) REVERT: S 1170 SER cc_start: 0.8849 (p) cc_final: 0.8355 (m) REVERT: T 65 LYS cc_start: 0.7723 (ptpt) cc_final: 0.6825 (mttt) REVERT: T 79 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7901 (tp30) REVERT: T 128 GLU cc_start: 0.7349 (tp30) cc_final: 0.6752 (tt0) REVERT: T 244 MET cc_start: 0.8362 (tpp) cc_final: 0.8073 (tpp) REVERT: T 330 MET cc_start: 0.8531 (ttp) cc_final: 0.8286 (ttp) REVERT: T 671 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7470 (tttt) REVERT: T 733 LYS cc_start: 0.6899 (ptpt) cc_final: 0.6340 (mmtp) REVERT: T 938 MET cc_start: 0.8259 (mmm) cc_final: 0.8035 (mtm) REVERT: T 1076 ASP cc_start: 0.7525 (t70) cc_final: 0.7186 (t0) REVERT: T 1339 ASP cc_start: 0.7700 (m-30) cc_final: 0.7492 (m-30) REVERT: 4 212 ASP cc_start: 0.7757 (t70) cc_final: 0.7259 (t0) REVERT: 4 214 VAL cc_start: 0.8935 (t) cc_final: 0.8671 (m) REVERT: 4 758 ASN cc_start: 0.5742 (t0) cc_final: 0.5366 (m110) REVERT: 4 1032 MET cc_start: 0.6614 (mtp) cc_final: 0.6128 (mtp) REVERT: 4 1091 THR cc_start: 0.6298 (p) cc_final: 0.6070 (p) REVERT: 4 1116 GLN cc_start: 0.7622 (pt0) cc_final: 0.7368 (pt0) REVERT: 4 1120 MET cc_start: 0.6719 (mtt) cc_final: 0.6511 (ttt) REVERT: 4 1280 ARG cc_start: 0.6129 (mtp180) cc_final: 0.5785 (mtp-110) REVERT: 4 1322 MET cc_start: 0.6619 (tpt) cc_final: 0.6322 (mtt) REVERT: 4 1341 TYR cc_start: 0.7598 (t80) cc_final: 0.7014 (t80) REVERT: A 28 MET cc_start: 0.3883 (ttp) cc_final: 0.3467 (ttp) REVERT: 5 67 GLN cc_start: 0.7700 (mm110) cc_final: 0.7411 (mm-40) REVERT: 5 101 SER cc_start: 0.7764 (m) cc_final: 0.7474 (p) REVERT: 5 173 PHE cc_start: 0.7251 (m-80) cc_final: 0.6674 (m-80) REVERT: 6 159 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7236 (p) REVERT: 6 206 ASP cc_start: 0.7601 (m-30) cc_final: 0.7332 (m-30) REVERT: 6 210 TYR cc_start: 0.8689 (m-80) cc_final: 0.8107 (m-80) REVERT: 6 266 MET cc_start: 0.8346 (tpp) cc_final: 0.8084 (tpp) REVERT: 7 14 ARG cc_start: 0.5655 (mtp85) cc_final: 0.5288 (mpt180) REVERT: 7 65 TYR cc_start: 0.8730 (t80) cc_final: 0.8262 (t80) REVERT: 7 83 ARG cc_start: 0.7168 (ttp80) cc_final: 0.5989 (mmt180) REVERT: 7 256 GLN cc_start: 0.6494 (pt0) cc_final: 0.5782 (mp10) REVERT: b 113 MET cc_start: 0.6986 (mmm) cc_final: 0.6533 (mmp) REVERT: b 139 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8727 (tt) REVERT: b 176 LYS cc_start: 0.8779 (tptp) cc_final: 0.8569 (tptm) REVERT: b 203 MET cc_start: 0.8664 (mmm) cc_final: 0.8162 (mtp) REVERT: c 35 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7054 (t0) REVERT: c 58 ASP cc_start: 0.7566 (p0) cc_final: 0.7155 (t0) REVERT: c 191 ASP cc_start: 0.7334 (t0) cc_final: 0.7014 (t70) REVERT: c 217 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8145 (pp) REVERT: c 305 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6625 (mtt90) REVERT: d 76 GLU cc_start: 0.7929 (pt0) cc_final: 0.7692 (pt0) REVERT: d 138 MET cc_start: 0.8051 (ttp) cc_final: 0.7727 (ttt) REVERT: d 176 LEU cc_start: 0.8909 (tp) cc_final: 0.8526 (mt) REVERT: d 237 LEU cc_start: 0.9103 (mt) cc_final: 0.8749 (tp) REVERT: d 267 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.8033 (mtp-110) REVERT: X 7 GLN cc_start: 0.7082 (mt0) cc_final: 0.6537 (mm-40) REVERT: X 161 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8383 (p) REVERT: X 234 MET cc_start: 0.8759 (mtt) cc_final: 0.8520 (mtt) REVERT: X 249 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8795 (mm) REVERT: X 328 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8163 (mp-120) REVERT: X 367 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8437 (m) REVERT: X 368 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8246 (tttp) REVERT: X 381 ARG cc_start: 0.7509 (ttp-110) cc_final: 0.7177 (ttp-110) REVERT: X 458 MET cc_start: 0.8791 (mmm) cc_final: 0.8590 (mmt) REVERT: X 593 ASP cc_start: 0.8037 (p0) cc_final: 0.7817 (p0) REVERT: X 678 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7313 (tpt90) REVERT: X 725 ASP cc_start: 0.7804 (t0) cc_final: 0.7594 (t0) REVERT: X 1170 SER cc_start: 0.8624 (p) cc_final: 0.8224 (t) REVERT: X 1247 ASP cc_start: 0.7902 (t0) cc_final: 0.7492 (t0) outliers start: 291 outliers final: 170 residues processed: 1620 average time/residue: 0.7121 time to fit residues: 1981.0811 Evaluate side-chains 1404 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1222 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 308 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 382 MET Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 708 LEU Chi-restraints excluded: chain W residue 746 ASN Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 859 LEU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 945 ASN Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1195 SER Chi-restraints excluded: chain W residue 1224 ILE Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1307 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 643 VAL Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 822 MET Chi-restraints excluded: chain S residue 872 VAL Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 971 GLN Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1059 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1218 LEU Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 281 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 561 MET Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 643 VAL Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 862 ILE Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 889 THR Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 69 GLN Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 191 ILE Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 328 GLN Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 655 HIS Chi-restraints excluded: chain 4 residue 684 LEU Chi-restraints excluded: chain 4 residue 788 LEU Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1125 ASP Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 197 LEU Chi-restraints excluded: chain 5 residue 265 ASP Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 40 GLN Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 159 SER Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 97 ASN Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 199 THR Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 161 SER Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 265 THR Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 328 GLN Chi-restraints excluded: chain X residue 336 HIS Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 368 LYS Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 613 CYS Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 880 THR Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 1104 VAL Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1333 SER Chi-restraints excluded: chain X residue 1340 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 437 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 655 optimal weight: 6.9990 chunk 536 optimal weight: 30.0000 chunk 217 optimal weight: 6.9990 chunk 788 optimal weight: 0.9990 chunk 852 optimal weight: 9.9990 chunk 702 optimal weight: 8.9990 chunk 782 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 632 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 47 HIS 0 73 HIS W 22 GLN W 124 HIS W 438 ASN W 448 ASN W 514 GLN W 674 HIS ** W 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 737 GLN ** W 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1017 GLN W1027 GLN W1114 HIS ** W1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 22 HIS 2 73 HIS S 77 ASN S 92 GLN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 ASN S 459 HIS S 469 ASN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN ** S 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1171 HIS T 224 HIS T 292 GLN T 470 GLN T 492 ASN ** T 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 978 ASN T1027 GLN T1030 HIS T1236 ASN T1318 GLN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 44 GLN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 674 HIS ** 4 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 697 HIS ** 4 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 816 ASN 4 828 ASN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 62 GLN 6 40 GLN ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 146 HIS b 236 ASN b 281 ASN ** c 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 ASN ** c 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 ASN d 287 HIS ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 459 HIS X 499 GLN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1344 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 70367 Z= 0.311 Angle : 0.679 13.475 95624 Z= 0.346 Chirality : 0.046 0.282 10799 Planarity : 0.005 0.099 12423 Dihedral : 6.218 87.421 9580 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 5.04 % Allowed : 12.94 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.41 % Twisted General : 0.10 % 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: -2.82 (0.08), residues: 8646 helix: -2.28 (0.08), residues: 2892 sheet: -1.08 (0.14), residues: 1271 loop : -1.77 (0.09), residues: 4483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 6 301 HIS 0.012 0.001 HIS T 537 PHE 0.035 0.002 PHE 4 650 TYR 0.027 0.002 TYR W 614 ARG 0.008 0.001 ARG 1 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1297 time to evaluate : 5.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 41 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8082 (tptp) REVERT: W 202 GLU cc_start: 0.3819 (tp30) cc_final: 0.3161 (tt0) REVERT: W 264 TYR cc_start: 0.8333 (m-80) cc_final: 0.7862 (m-80) REVERT: W 372 LYS cc_start: 0.8444 (mttt) cc_final: 0.8208 (mttm) REVERT: W 642 TRP cc_start: 0.8371 (t-100) cc_final: 0.7792 (t60) REVERT: W 687 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8403 (mp) REVERT: W 751 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8181 (mp10) REVERT: W 769 ASN cc_start: 0.7439 (m-40) cc_final: 0.7021 (t0) REVERT: W 822 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7045 (ttt) REVERT: W 912 ASP cc_start: 0.7872 (t0) cc_final: 0.7556 (p0) REVERT: W 1012 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8516 (mmm) REVERT: W 1032 MET cc_start: 0.8659 (mmm) cc_final: 0.8343 (mtt) REVERT: W 1108 THR cc_start: 0.9103 (m) cc_final: 0.8828 (p) REVERT: W 1278 TYR cc_start: 0.8797 (m-80) cc_final: 0.8209 (m-80) REVERT: W 1322 MET cc_start: 0.7483 (tpt) cc_final: 0.7160 (tpp) REVERT: 2 22 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6300 (t-90) REVERT: S 86 MET cc_start: 0.4981 (ptt) cc_final: 0.4001 (mtt) REVERT: S 171 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7451 (mt-10) REVERT: S 206 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8510 (mmtt) REVERT: S 254 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6685 (mm-30) REVERT: S 255 ASP cc_start: 0.7805 (m-30) cc_final: 0.7322 (m-30) REVERT: S 545 HIS cc_start: 0.7761 (t-90) cc_final: 0.7143 (t70) REVERT: S 611 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7689 (tt) REVERT: S 700 VAL cc_start: 0.9198 (t) cc_final: 0.8774 (m) REVERT: S 811 MET cc_start: 0.8283 (mmt) cc_final: 0.7933 (mmt) REVERT: S 822 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7363 (mtm) REVERT: S 835 TYR cc_start: 0.8336 (t80) cc_final: 0.6745 (t80) REVERT: S 930 ARG cc_start: 0.7545 (ptm-80) cc_final: 0.6066 (tpt-90) REVERT: S 1032 MET cc_start: 0.9042 (mmm) cc_final: 0.8816 (mtt) REVERT: S 1170 SER cc_start: 0.8898 (p) cc_final: 0.8536 (t) REVERT: T 65 LYS cc_start: 0.7555 (ptpt) cc_final: 0.7299 (pttt) REVERT: T 82 ASP cc_start: 0.8646 (p0) cc_final: 0.8346 (p0) REVERT: T 128 GLU cc_start: 0.7585 (tp30) cc_final: 0.6968 (tt0) REVERT: T 491 MET cc_start: 0.8858 (mmm) cc_final: 0.8389 (mtm) REVERT: T 522 ASP cc_start: 0.7972 (t0) cc_final: 0.7682 (t0) REVERT: T 671 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7482 (tttt) REVERT: T 731 MET cc_start: 0.7959 (mmm) cc_final: 0.7746 (mmm) REVERT: T 861 ASP cc_start: 0.7960 (m-30) cc_final: 0.7713 (m-30) REVERT: T 1076 ASP cc_start: 0.7503 (t70) cc_final: 0.7197 (t0) REVERT: T 1110 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8390 (p0) REVERT: T 1187 ASP cc_start: 0.7341 (t0) cc_final: 0.7080 (t0) REVERT: T 1247 ASP cc_start: 0.7829 (t70) cc_final: 0.7186 (t0) REVERT: T 1274 ASP cc_start: 0.7375 (m-30) cc_final: 0.7123 (m-30) REVERT: T 1358 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8877 (mp) REVERT: 4 167 MET cc_start: 0.7833 (tpp) cc_final: 0.7605 (tmm) REVERT: 4 212 ASP cc_start: 0.7754 (t70) cc_final: 0.7370 (t70) REVERT: 4 214 VAL cc_start: 0.9022 (t) cc_final: 0.8775 (m) REVERT: 4 629 MET cc_start: 0.1439 (ttt) cc_final: 0.1237 (ttp) REVERT: 4 758 ASN cc_start: 0.5817 (t0) cc_final: 0.5380 (m110) REVERT: 4 1012 MET cc_start: 0.4994 (tpp) cc_final: 0.4766 (tpp) REVERT: 4 1018 LYS cc_start: 0.6967 (tptt) cc_final: 0.5737 (tppt) REVERT: 4 1032 MET cc_start: 0.6796 (mtp) cc_final: 0.6453 (mtm) REVERT: 4 1138 MET cc_start: 0.5347 (mtm) cc_final: 0.4993 (mtm) REVERT: 4 1276 MET cc_start: 0.7136 (tpp) cc_final: 0.6419 (tpp) REVERT: 4 1322 MET cc_start: 0.6836 (tpt) cc_final: 0.6443 (mtt) REVERT: 4 1341 TYR cc_start: 0.7652 (t80) cc_final: 0.6969 (t80) REVERT: A 28 MET cc_start: 0.4095 (ttp) cc_final: 0.3521 (ttp) REVERT: 5 101 SER cc_start: 0.7949 (m) cc_final: 0.7647 (p) REVERT: 6 159 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7158 (p) REVERT: 6 266 MET cc_start: 0.8224 (tpp) cc_final: 0.7881 (tpp) REVERT: 6 269 MET cc_start: 0.8163 (ttt) cc_final: 0.7884 (ttt) REVERT: 7 83 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6168 (mmt180) REVERT: 7 256 GLN cc_start: 0.6395 (pt0) cc_final: 0.5691 (mp10) REVERT: b 78 GLN cc_start: 0.7514 (mt0) cc_final: 0.7101 (mm-40) REVERT: b 113 MET cc_start: 0.6713 (mmm) cc_final: 0.6467 (mmp) REVERT: b 139 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8636 (tt) REVERT: b 224 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8441 (m) REVERT: c 191 ASP cc_start: 0.7490 (t0) cc_final: 0.7218 (t70) REVERT: c 217 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8052 (pp) REVERT: c 305 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.6767 (mtt90) REVERT: d 4 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7589 (t70) REVERT: d 138 MET cc_start: 0.8082 (ttp) cc_final: 0.7837 (ttt) REVERT: d 176 LEU cc_start: 0.8869 (tp) cc_final: 0.8555 (mt) REVERT: d 267 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7997 (mtp-110) REVERT: 1 16 ASP cc_start: 0.7245 (m-30) cc_final: 0.6995 (m-30) REVERT: 1 36 MET cc_start: 0.5848 (ptp) cc_final: 0.5572 (pmm) REVERT: X 7 GLN cc_start: 0.6956 (mt0) cc_final: 0.6472 (mm-40) REVERT: X 83 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8938 (tt) REVERT: X 91 ILE cc_start: 0.8766 (mm) cc_final: 0.8258 (mt) REVERT: X 151 GLU cc_start: 0.7035 (tp30) cc_final: 0.6546 (tp30) REVERT: X 234 MET cc_start: 0.8727 (mtt) cc_final: 0.8473 (mtt) REVERT: X 313 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (tt) REVERT: X 368 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8167 (tttp) REVERT: X 678 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7324 (tpt90) REVERT: X 799 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8287 (p0) REVERT: X 852 LEU cc_start: 0.7977 (mt) cc_final: 0.7731 (mt) REVERT: X 1170 SER cc_start: 0.8648 (p) cc_final: 0.8260 (t) REVERT: X 1247 ASP cc_start: 0.8016 (t0) cc_final: 0.7645 (t0) outliers start: 378 outliers final: 233 residues processed: 1538 average time/residue: 0.6332 time to fit residues: 1681.6642 Evaluate side-chains 1435 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1185 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 386 THR Chi-restraints excluded: chain W residue 401 PHE Chi-restraints excluded: chain W residue 432 THR Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 746 ASN Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 765 ASP Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 859 LEU Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 881 SER Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 927 VAL Chi-restraints excluded: chain W residue 945 ASN Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 982 ASN Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1244 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 374 VAL Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 450 LEU Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 611 LEU Chi-restraints excluded: chain S residue 643 VAL Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 822 MET Chi-restraints excluded: chain S residue 827 GLN Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 872 VAL Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 979 VAL Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1015 MET Chi-restraints excluded: chain S residue 1059 THR Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1218 LEU Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1308 VAL Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 290 LEU Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 561 MET Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 783 ASP Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 889 THR Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1236 ASN Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 150 THR Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 276 LEU Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 684 LEU Chi-restraints excluded: chain 4 residue 828 ASN Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1083 THR Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1125 ASP Chi-restraints excluded: chain 4 residue 1176 THR Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 197 LEU Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 6 residue 159 SER Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 284 VAL Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 159 SER Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 36 CYS Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 250 THR Chi-restraints excluded: chain d residue 268 VAL Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 265 THR Chi-restraints excluded: chain X residue 313 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 336 HIS Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 368 LYS Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 842 ASP Chi-restraints excluded: chain X residue 850 ILE Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1204 VAL Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1340 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 779 optimal weight: 9.9990 chunk 593 optimal weight: 20.0000 chunk 409 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 376 optimal weight: 9.9990 chunk 529 optimal weight: 20.0000 chunk 791 optimal weight: 9.9990 chunk 838 optimal weight: 10.0000 chunk 413 optimal weight: 8.9990 chunk 750 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 73 HIS W 428 GLN ** W 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 724 HIS ** W 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS ** W1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 22 HIS ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 499 GLN S 707 HIS S 737 GLN S 847 GLN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 460 ASN T 463 GLN T 492 ASN T 697 HIS ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1236 ASN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN 4 270 GLN 4 466 GLN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 537 HIS ** 4 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 676 HIS 4 697 HIS ** 4 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 915 GLN ** 41116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41241 GLN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 62 GLN 6 40 GLN ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 94 GLN 7 108 ASN 7 130 ASN 7 146 HIS c 37 HIS c 41 ASN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 143 GLN ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 235 HIS ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN ** X 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 70367 Z= 0.281 Angle : 0.642 14.127 95624 Z= 0.327 Chirality : 0.045 0.210 10799 Planarity : 0.005 0.092 12423 Dihedral : 5.957 84.290 9579 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 5.38 % Allowed : 14.02 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.07 % 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: -2.45 (0.08), residues: 8646 helix: -1.77 (0.09), residues: 2930 sheet: -0.95 (0.14), residues: 1282 loop : -1.67 (0.09), residues: 4434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 41238 HIS 0.019 0.001 HIS 2 22 PHE 0.025 0.002 PHE T 497 TYR 0.025 0.002 TYR W 614 ARG 0.010 0.000 ARG 4 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 1249 time to evaluate : 5.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1842 (OUTLIER) cc_final: -0.2902 (mmm) REVERT: W 41 LYS cc_start: 0.8832 (tmmt) cc_final: 0.8168 (tptp) REVERT: W 92 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7838 (mm110) REVERT: W 202 GLU cc_start: 0.3669 (tp30) cc_final: 0.2998 (tt0) REVERT: W 264 TYR cc_start: 0.8322 (m-80) cc_final: 0.7791 (m-80) REVERT: W 372 LYS cc_start: 0.8528 (mttt) cc_final: 0.8280 (mttm) REVERT: W 463 GLN cc_start: 0.6717 (tp40) cc_final: 0.6485 (tp40) REVERT: W 642 TRP cc_start: 0.8359 (t-100) cc_final: 0.7928 (t60) REVERT: W 678 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6335 (mtt90) REVERT: W 683 GLU cc_start: 0.7274 (tp30) cc_final: 0.6967 (tp30) REVERT: W 687 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8323 (mp) REVERT: W 769 ASN cc_start: 0.7553 (m-40) cc_final: 0.7044 (t0) REVERT: W 770 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8711 (tt) REVERT: W 822 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7087 (ttt) REVERT: W 872 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7890 (m) REVERT: W 909 TYR cc_start: 0.6970 (m-80) cc_final: 0.6614 (m-80) REVERT: W 912 ASP cc_start: 0.7875 (t0) cc_final: 0.7609 (p0) REVERT: W 1012 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8651 (mmm) REVERT: W 1032 MET cc_start: 0.8656 (mmm) cc_final: 0.8012 (mtp) REVERT: W 1108 THR cc_start: 0.9158 (m) cc_final: 0.8866 (p) REVERT: W 1120 MET cc_start: 0.8655 (ptp) cc_final: 0.8364 (ptm) REVERT: W 1169 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (pp) REVERT: W 1322 MET cc_start: 0.7380 (tpt) cc_final: 0.7090 (tpp) REVERT: 2 61 TYR cc_start: 0.8601 (t80) cc_final: 0.8295 (t80) REVERT: S 86 MET cc_start: 0.5274 (ptt) cc_final: 0.4188 (mtt) REVERT: S 171 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7452 (mt-10) REVERT: S 206 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8586 (mmtt) REVERT: S 254 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6799 (mm-30) REVERT: S 255 ASP cc_start: 0.7835 (m-30) cc_final: 0.7338 (m-30) REVERT: S 545 HIS cc_start: 0.7754 (t-90) cc_final: 0.7069 (t70) REVERT: S 700 VAL cc_start: 0.9200 (t) cc_final: 0.8807 (m) REVERT: S 835 TYR cc_start: 0.8351 (t80) cc_final: 0.7001 (t80) REVERT: S 930 ARG cc_start: 0.7574 (ptm-80) cc_final: 0.6047 (tpt-90) REVERT: S 1032 MET cc_start: 0.8998 (mmm) cc_final: 0.8789 (mtt) REVERT: S 1170 SER cc_start: 0.8903 (p) cc_final: 0.8519 (m) REVERT: S 1190 TYR cc_start: 0.9053 (t80) cc_final: 0.8761 (t80) REVERT: T 82 ASP cc_start: 0.8606 (p0) cc_final: 0.8244 (p0) REVERT: T 87 ILE cc_start: 0.8905 (mm) cc_final: 0.8623 (mt) REVERT: T 491 MET cc_start: 0.8847 (mmm) cc_final: 0.8434 (mtm) REVERT: T 576 GLU cc_start: 0.7494 (pt0) cc_final: 0.7273 (pt0) REVERT: T 648 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8660 (pp) REVERT: T 671 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7509 (tttt) REVERT: T 731 MET cc_start: 0.7867 (mmm) cc_final: 0.7618 (mmm) REVERT: T 733 LYS cc_start: 0.7118 (ptpt) cc_final: 0.6510 (mmtp) REVERT: T 854 LEU cc_start: 0.6741 (mt) cc_final: 0.6336 (mt) REVERT: T 1076 ASP cc_start: 0.7511 (t70) cc_final: 0.7217 (t0) REVERT: T 1187 ASP cc_start: 0.7417 (t0) cc_final: 0.7125 (t0) REVERT: T 1247 ASP cc_start: 0.7935 (t70) cc_final: 0.7442 (t0) REVERT: T 1299 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8958 (p) REVERT: T 1358 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8906 (mp) REVERT: 3 28 MET cc_start: 0.8173 (ttt) cc_final: 0.7924 (ttp) REVERT: 4 212 ASP cc_start: 0.7758 (t70) cc_final: 0.7427 (t0) REVERT: 4 407 HIS cc_start: 0.5110 (OUTLIER) cc_final: 0.4824 (p-80) REVERT: 4 648 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6388 (pt) REVERT: 4 758 ASN cc_start: 0.5813 (t0) cc_final: 0.5375 (m-40) REVERT: 4 1032 MET cc_start: 0.6848 (mtp) cc_final: 0.6568 (mmm) REVERT: 4 1138 MET cc_start: 0.5329 (mtm) cc_final: 0.4918 (mtm) REVERT: 4 1190 TYR cc_start: 0.8133 (t80) cc_final: 0.7777 (t80) REVERT: 4 1192 GLN cc_start: 0.8676 (mp10) cc_final: 0.8321 (mt0) REVERT: 4 1341 TYR cc_start: 0.7799 (t80) cc_final: 0.7183 (t80) REVERT: A 28 MET cc_start: 0.4260 (ttp) cc_final: 0.3516 (ttp) REVERT: 5 101 SER cc_start: 0.7975 (m) cc_final: 0.7692 (p) REVERT: 6 11 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7800 (mm) REVERT: 6 159 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7280 (p) REVERT: 7 42 ILE cc_start: 0.5658 (mp) cc_final: 0.4704 (tt) REVERT: 7 65 TYR cc_start: 0.8584 (t80) cc_final: 0.8209 (t80) REVERT: 7 83 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6066 (mmt180) REVERT: 7 148 ILE cc_start: 0.9192 (tp) cc_final: 0.8751 (tt) REVERT: 7 225 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (tt) REVERT: 7 256 GLN cc_start: 0.6475 (pt0) cc_final: 0.5746 (mp10) REVERT: b 78 GLN cc_start: 0.7621 (mt0) cc_final: 0.7301 (mm-40) REVERT: b 224 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8484 (m) REVERT: c 191 ASP cc_start: 0.7605 (t0) cc_final: 0.7332 (t70) REVERT: c 217 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (pp) REVERT: c 305 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.6694 (mtt90) REVERT: d 4 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7682 (t70) REVERT: d 76 GLU cc_start: 0.7914 (pt0) cc_final: 0.7669 (pt0) REVERT: d 86 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7418 (tmm-80) REVERT: d 122 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.6054 (t0) REVERT: d 176 LEU cc_start: 0.8858 (tp) cc_final: 0.8511 (mt) REVERT: X 7 GLN cc_start: 0.6927 (mt0) cc_final: 0.6618 (mm-40) REVERT: X 83 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (tt) REVERT: X 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6877 (t0) REVERT: X 91 ILE cc_start: 0.8786 (mm) cc_final: 0.8307 (mt) REVERT: X 151 GLU cc_start: 0.7095 (tp30) cc_final: 0.6570 (tp30) REVERT: X 161 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8444 (p) REVERT: X 234 MET cc_start: 0.8714 (mtt) cc_final: 0.8460 (mtt) REVERT: X 367 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8447 (m) REVERT: X 368 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8071 (tttp) REVERT: X 377 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7800 (tt0) REVERT: X 678 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7328 (tpt90) REVERT: X 799 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8354 (p0) REVERT: X 852 LEU cc_start: 0.8025 (mt) cc_final: 0.7812 (mt) REVERT: X 1170 SER cc_start: 0.8656 (p) cc_final: 0.8219 (t) REVERT: X 1247 ASP cc_start: 0.8088 (t0) cc_final: 0.7700 (t0) outliers start: 404 outliers final: 277 residues processed: 1516 average time/residue: 0.6262 time to fit residues: 1641.2118 Evaluate side-chains 1466 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1162 time to evaluate : 5.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 651 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 669 ILE Chi-restraints excluded: chain W residue 678 ARG Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 698 GLU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 706 THR Chi-restraints excluded: chain W residue 746 ASN Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 773 ILE Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 859 LEU Chi-restraints excluded: chain W residue 872 VAL Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 927 VAL Chi-restraints excluded: chain W residue 945 ASN Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 982 ASN Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1244 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 374 VAL Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 643 VAL Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 827 GLN Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 908 GLU Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 979 VAL Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1015 MET Chi-restraints excluded: chain S residue 1039 THR Chi-restraints excluded: chain S residue 1059 THR Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1218 LEU Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 281 SER Chi-restraints excluded: chain T residue 290 LEU Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 561 MET Chi-restraints excluded: chain T residue 589 THR Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 636 LEU Chi-restraints excluded: chain T residue 643 VAL Chi-restraints excluded: chain T residue 648 LEU Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 783 ASP Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 889 THR Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 961 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1169 LEU Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1236 ASN Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1299 THR Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 191 ILE Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 266 THR Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 512 VAL Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 684 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1120 MET Chi-restraints excluded: chain 4 residue 1125 ASP Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 10 ASN Chi-restraints excluded: chain 6 residue 11 LEU Chi-restraints excluded: chain 6 residue 40 GLN Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 6 residue 159 SER Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 295 THR Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 223 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 284 VAL Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 268 VAL Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 161 SER Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 265 THR Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 336 HIS Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 368 LYS Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 613 CYS Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 748 ASP Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 842 ASP Chi-restraints excluded: chain X residue 850 ILE Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1083 THR Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1340 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 697 optimal weight: 40.0000 chunk 475 optimal weight: 0.0970 chunk 12 optimal weight: 8.9990 chunk 623 optimal weight: 6.9990 chunk 345 optimal weight: 0.9990 chunk 715 optimal weight: 0.0570 chunk 579 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 427 optimal weight: 6.9990 chunk 752 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 73 HIS W 428 GLN W 438 ASN ** W 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1103 HIS W1114 HIS W1116 GLN W1133 HIS W1241 GLN ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN S 77 ASN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 707 HIS S 796 ASN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN ** T 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1241 GLN T1268 GLN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 HIS 3 29 ASN 4 466 GLN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 41027 GLN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 62 GLN 6 24 GLN 6 40 GLN ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 108 ASN c 41 ASN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 397 GLN ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 529 HIS X 575 GLN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1318 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 70367 Z= 0.179 Angle : 0.585 12.521 95624 Z= 0.296 Chirality : 0.043 0.352 10799 Planarity : 0.004 0.087 12423 Dihedral : 5.638 82.703 9579 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 4.42 % Allowed : 15.59 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.06 % 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: -2.08 (0.08), residues: 8646 helix: -1.33 (0.09), residues: 2920 sheet: -0.76 (0.14), residues: 1247 loop : -1.54 (0.09), residues: 4479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 41238 HIS 0.011 0.001 HIS W1114 PHE 0.026 0.001 PHE 1 51 TYR 0.024 0.001 TYR 1 57 ARG 0.010 0.000 ARG 1 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1236 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1836 (OUTLIER) cc_final: -0.2858 (mmm) REVERT: W 41 LYS cc_start: 0.8816 (tmmt) cc_final: 0.8174 (tptp) REVERT: W 92 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7787 (mm110) REVERT: W 202 GLU cc_start: 0.3873 (tp30) cc_final: 0.3244 (tt0) REVERT: W 264 TYR cc_start: 0.8295 (m-80) cc_final: 0.7652 (m-80) REVERT: W 463 GLN cc_start: 0.6726 (tp40) cc_final: 0.6478 (tp40) REVERT: W 545 HIS cc_start: 0.7924 (t70) cc_final: 0.7187 (t-170) REVERT: W 642 TRP cc_start: 0.8336 (t-100) cc_final: 0.7957 (t60) REVERT: W 678 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6474 (mtt90) REVERT: W 683 GLU cc_start: 0.7297 (tp30) cc_final: 0.6935 (tp30) REVERT: W 687 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8376 (mp) REVERT: W 746 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: W 769 ASN cc_start: 0.7518 (m-40) cc_final: 0.7058 (t0) REVERT: W 770 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (tt) REVERT: W 788 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7448 (mp) REVERT: W 797 ASP cc_start: 0.6993 (t0) cc_final: 0.6759 (t0) REVERT: W 822 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7101 (ttt) REVERT: W 912 ASP cc_start: 0.7933 (t0) cc_final: 0.7663 (p0) REVERT: W 1032 MET cc_start: 0.8650 (mmm) cc_final: 0.8014 (mtp) REVERT: W 1108 THR cc_start: 0.9156 (m) cc_final: 0.8883 (p) REVERT: W 1120 MET cc_start: 0.8655 (ptp) cc_final: 0.8438 (ptm) REVERT: W 1169 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8189 (pp) REVERT: W 1310 ASN cc_start: 0.7411 (t0) cc_final: 0.7201 (p0) REVERT: 2 15 LEU cc_start: 0.7727 (tp) cc_final: 0.7420 (tp) REVERT: 2 61 TYR cc_start: 0.8554 (t80) cc_final: 0.8300 (t80) REVERT: S 86 MET cc_start: 0.5353 (ptt) cc_final: 0.4184 (mtt) REVERT: S 206 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8561 (mmtt) REVERT: S 254 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6866 (mm-30) REVERT: S 255 ASP cc_start: 0.7763 (m-30) cc_final: 0.7257 (m-30) REVERT: S 287 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8790 (mmm) REVERT: S 545 HIS cc_start: 0.7733 (t-90) cc_final: 0.6992 (t70) REVERT: S 561 MET cc_start: 0.8451 (mtp) cc_final: 0.8073 (mtt) REVERT: S 700 VAL cc_start: 0.9219 (t) cc_final: 0.8780 (m) REVERT: S 770 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7995 (tt) REVERT: S 835 TYR cc_start: 0.8421 (t80) cc_final: 0.6946 (t80) REVERT: S 930 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.5952 (tpt-90) REVERT: S 1032 MET cc_start: 0.8895 (mmm) cc_final: 0.8652 (mtt) REVERT: S 1076 ASP cc_start: 0.7715 (m-30) cc_final: 0.7490 (m-30) REVERT: S 1170 SER cc_start: 0.8779 (p) cc_final: 0.8297 (m) REVERT: S 1190 TYR cc_start: 0.8996 (t80) cc_final: 0.8622 (t80) REVERT: S 1292 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.6913 (ptt90) REVERT: S 1353 MET cc_start: 0.7792 (mmm) cc_final: 0.7432 (mmt) REVERT: T 82 ASP cc_start: 0.8559 (p0) cc_final: 0.8243 (p0) REVERT: T 87 ILE cc_start: 0.8882 (mm) cc_final: 0.8629 (mt) REVERT: T 117 MET cc_start: 0.8265 (ttp) cc_final: 0.7887 (ttp) REVERT: T 335 ASP cc_start: 0.7886 (t0) cc_final: 0.7478 (t0) REVERT: T 336 HIS cc_start: 0.6778 (m90) cc_final: 0.6162 (m170) REVERT: T 367 VAL cc_start: 0.8817 (t) cc_final: 0.8462 (m) REVERT: T 491 MET cc_start: 0.8821 (mmm) cc_final: 0.8415 (mtm) REVERT: T 671 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7466 (tttt) REVERT: T 731 MET cc_start: 0.7839 (mmm) cc_final: 0.7552 (mmm) REVERT: T 733 LYS cc_start: 0.7001 (ptpt) cc_final: 0.6321 (mmtp) REVERT: T 854 LEU cc_start: 0.6782 (mt) cc_final: 0.6353 (mt) REVERT: T 1076 ASP cc_start: 0.7407 (t70) cc_final: 0.7123 (t0) REVERT: T 1110 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8419 (p0) REVERT: T 1178 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: T 1187 ASP cc_start: 0.7510 (t0) cc_final: 0.7292 (t0) REVERT: T 1247 ASP cc_start: 0.7872 (t70) cc_final: 0.7403 (t0) REVERT: 3 28 MET cc_start: 0.8220 (ttt) cc_final: 0.7843 (ttp) REVERT: 4 212 ASP cc_start: 0.7742 (t70) cc_final: 0.7508 (t0) REVERT: 4 252 VAL cc_start: 0.8343 (t) cc_final: 0.7887 (m) REVERT: 4 407 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4836 (p-80) REVERT: 4 561 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.5579 (mpp) REVERT: 4 648 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.5455 (tp) REVERT: 4 758 ASN cc_start: 0.5817 (t0) cc_final: 0.5386 (m-40) REVERT: 4 802 LEU cc_start: 0.5749 (mm) cc_final: 0.5506 (mt) REVERT: 4 1032 MET cc_start: 0.6863 (mtp) cc_final: 0.6656 (mmm) REVERT: 4 1038 MET cc_start: 0.8593 (ptp) cc_final: 0.8330 (ptt) REVERT: 4 1138 MET cc_start: 0.5445 (mtm) cc_final: 0.5188 (mtm) REVERT: 4 1190 TYR cc_start: 0.7953 (t80) cc_final: 0.7568 (t80) REVERT: 4 1192 GLN cc_start: 0.8640 (mp10) cc_final: 0.8406 (mt0) REVERT: 4 1341 TYR cc_start: 0.7734 (t80) cc_final: 0.7057 (t80) REVERT: A 28 MET cc_start: 0.4147 (ttp) cc_final: 0.3407 (ttp) REVERT: 5 101 SER cc_start: 0.8019 (m) cc_final: 0.7699 (p) REVERT: 6 159 SER cc_start: 0.7682 (m) cc_final: 0.7319 (p) REVERT: 6 266 MET cc_start: 0.8241 (tpp) cc_final: 0.7962 (tpp) REVERT: 7 65 TYR cc_start: 0.8591 (t80) cc_final: 0.8331 (t80) REVERT: 7 94 GLN cc_start: 0.7150 (mm110) cc_final: 0.6811 (mm-40) REVERT: 7 148 ILE cc_start: 0.9158 (tp) cc_final: 0.8806 (tt) REVERT: 7 256 GLN cc_start: 0.6403 (pt0) cc_final: 0.5695 (mp10) REVERT: b 78 GLN cc_start: 0.7626 (mt0) cc_final: 0.7258 (mm-40) REVERT: b 224 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8467 (m) REVERT: c 191 ASP cc_start: 0.7629 (t0) cc_final: 0.7364 (t70) REVERT: c 217 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8293 (pp) REVERT: c 305 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.6628 (mtt90) REVERT: d 4 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7630 (t70) REVERT: d 76 GLU cc_start: 0.7831 (pt0) cc_final: 0.7583 (pt0) REVERT: d 86 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7252 (tmm-80) REVERT: d 122 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.5958 (t0) REVERT: d 176 LEU cc_start: 0.8855 (tp) cc_final: 0.8531 (mt) REVERT: X 7 GLN cc_start: 0.6879 (mt0) cc_final: 0.6610 (mm-40) REVERT: X 151 GLU cc_start: 0.7078 (tp30) cc_final: 0.6644 (tp30) REVERT: X 234 MET cc_start: 0.8704 (mtt) cc_final: 0.8464 (mtt) REVERT: X 377 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7827 (tt0) REVERT: X 678 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7299 (tpt90) REVERT: X 799 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8268 (p0) REVERT: X 826 TYR cc_start: 0.8303 (m-80) cc_final: 0.8085 (m-80) REVERT: X 884 THR cc_start: 0.8369 (p) cc_final: 0.8065 (t) REVERT: X 973 ASN cc_start: 0.8438 (t0) cc_final: 0.8226 (t0) REVERT: X 1170 SER cc_start: 0.8696 (p) cc_final: 0.8282 (t) REVERT: X 1247 ASP cc_start: 0.8055 (t0) cc_final: 0.7661 (t0) outliers start: 332 outliers final: 234 residues processed: 1459 average time/residue: 0.6263 time to fit residues: 1581.0090 Evaluate side-chains 1406 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1151 time to evaluate : 5.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 678 ARG Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 699 THR Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 746 ASN Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 765 ASP Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 788 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 859 LEU Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 927 VAL Chi-restraints excluded: chain W residue 945 ASN Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 982 ASN Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1182 THR Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 277 GLU Chi-restraints excluded: chain S residue 287 MET Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 708 LEU Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 827 GLN Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 968 LEU Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1218 LEU Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 228 LEU Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 281 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 355 ASP Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 402 PHE Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 494 PHE Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 636 LEU Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 853 HIS Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1169 LEU Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 191 ILE Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 512 VAL Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 684 LEU Chi-restraints excluded: chain 4 residue 697 HIS Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 223 LEU Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 250 THR Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 336 HIS Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 842 ASP Chi-restraints excluded: chain X residue 850 ILE Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1069 VAL Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1204 VAL Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1340 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 281 optimal weight: 8.9990 chunk 754 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 492 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 838 optimal weight: 20.0000 chunk 696 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 440 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 HIS 0 73 HIS ** W 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 384 ASN S 689 GLN S 707 HIS S 796 ASN S 847 GLN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1268 GLN T 354 HIS ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1236 ASN T1305 GLN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 818 HIS 4 828 ASN ** 41241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN 5 62 GLN ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 ASN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 70367 Z= 0.263 Angle : 0.616 13.379 95624 Z= 0.311 Chirality : 0.045 0.262 10799 Planarity : 0.005 0.082 12423 Dihedral : 5.599 79.014 9579 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 5.58 % Allowed : 15.15 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.09), residues: 8646 helix: -1.08 (0.09), residues: 2934 sheet: -0.66 (0.14), residues: 1258 loop : -1.53 (0.09), residues: 4454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 41238 HIS 0.011 0.001 HIS W1114 PHE 0.031 0.002 PHE X1122 TYR 0.024 0.002 TYR T 501 ARG 0.016 0.001 ARG 7 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1202 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1752 (OUTLIER) cc_final: -0.2781 (mmm) REVERT: W 33 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7848 (mtmt) REVERT: W 41 LYS cc_start: 0.8923 (tmmt) cc_final: 0.8691 (tttt) REVERT: W 92 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7801 (mm110) REVERT: W 137 GLU cc_start: 0.7536 (pp20) cc_final: 0.7296 (pp20) REVERT: W 202 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.3005 (tt0) REVERT: W 264 TYR cc_start: 0.8276 (m-80) cc_final: 0.7825 (m-80) REVERT: W 463 GLN cc_start: 0.6839 (tp40) cc_final: 0.6620 (tp40) REVERT: W 614 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7141 (t80) REVERT: W 642 TRP cc_start: 0.8357 (t-100) cc_final: 0.7890 (t60) REVERT: W 678 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6574 (mtt90) REVERT: W 683 GLU cc_start: 0.7527 (tp30) cc_final: 0.7135 (tp30) REVERT: W 687 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8304 (mp) REVERT: W 769 ASN cc_start: 0.7620 (m-40) cc_final: 0.7099 (t0) REVERT: W 770 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8677 (tt) REVERT: W 797 ASP cc_start: 0.7027 (t0) cc_final: 0.6784 (t0) REVERT: W 1032 MET cc_start: 0.8695 (mmm) cc_final: 0.8072 (mtp) REVERT: W 1108 THR cc_start: 0.9220 (m) cc_final: 0.8916 (p) REVERT: W 1169 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8456 (pp) REVERT: W 1278 TYR cc_start: 0.8865 (m-80) cc_final: 0.8193 (m-80) REVERT: W 1292 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7244 (mtp-110) REVERT: 2 61 TYR cc_start: 0.8583 (t80) cc_final: 0.8377 (t80) REVERT: S 86 MET cc_start: 0.5364 (ptt) cc_final: 0.4226 (mtt) REVERT: S 206 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8544 (mmtt) REVERT: S 545 HIS cc_start: 0.7731 (t-90) cc_final: 0.6989 (t70) REVERT: S 700 VAL cc_start: 0.9245 (t) cc_final: 0.8790 (m) REVERT: S 770 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8007 (tt) REVERT: S 835 TYR cc_start: 0.8479 (t80) cc_final: 0.6931 (t80) REVERT: S 930 ARG cc_start: 0.7467 (ptm-80) cc_final: 0.5940 (tpt-90) REVERT: S 1170 SER cc_start: 0.8920 (p) cc_final: 0.8508 (m) REVERT: S 1190 TYR cc_start: 0.9031 (t80) cc_final: 0.8660 (t80) REVERT: S 1292 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.6880 (ptt180) REVERT: S 1353 MET cc_start: 0.7954 (mmm) cc_final: 0.7644 (mmt) REVERT: T 87 ILE cc_start: 0.8891 (mm) cc_final: 0.8614 (mt) REVERT: T 335 ASP cc_start: 0.8003 (t0) cc_final: 0.7515 (t0) REVERT: T 336 HIS cc_start: 0.6955 (m90) cc_final: 0.6316 (m170) REVERT: T 367 VAL cc_start: 0.8796 (t) cc_final: 0.8430 (m) REVERT: T 491 MET cc_start: 0.8807 (mmm) cc_final: 0.8513 (mtm) REVERT: T 671 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7448 (tttt) REVERT: T 731 MET cc_start: 0.7910 (mmm) cc_final: 0.7555 (mmm) REVERT: T 733 LYS cc_start: 0.7167 (ptpt) cc_final: 0.6464 (mmtp) REVERT: T 854 LEU cc_start: 0.6846 (mt) cc_final: 0.6388 (mt) REVERT: T 1076 ASP cc_start: 0.7448 (t70) cc_final: 0.7176 (t0) REVERT: T 1110 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8346 (p0) REVERT: T 1178 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: T 1247 ASP cc_start: 0.7913 (t70) cc_final: 0.7374 (t0) REVERT: T 1299 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8938 (p) REVERT: T 1358 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8908 (mp) REVERT: 3 28 MET cc_start: 0.8338 (ttt) cc_final: 0.8024 (ttp) REVERT: 4 212 ASP cc_start: 0.7859 (t70) cc_final: 0.7625 (t0) REVERT: 4 252 VAL cc_start: 0.8410 (t) cc_final: 0.8055 (m) REVERT: 4 287 MET cc_start: 0.8408 (mmm) cc_final: 0.8190 (mmp) REVERT: 4 361 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7351 (mmm-85) REVERT: 4 407 HIS cc_start: 0.5285 (OUTLIER) cc_final: 0.4930 (p-80) REVERT: 4 619 MET cc_start: 0.3039 (ptm) cc_final: 0.2763 (mmm) REVERT: 4 648 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5668 (tp) REVERT: 4 758 ASN cc_start: 0.5855 (t0) cc_final: 0.5377 (m-40) REVERT: 4 819 MET cc_start: 0.2454 (tpp) cc_final: 0.2031 (tpp) REVERT: 4 1038 MET cc_start: 0.8663 (ptp) cc_final: 0.8421 (ptt) REVERT: 4 1138 MET cc_start: 0.5693 (mtm) cc_final: 0.5422 (mtm) REVERT: 4 1190 TYR cc_start: 0.7991 (t80) cc_final: 0.7551 (t80) REVERT: 4 1219 LEU cc_start: 0.7553 (mt) cc_final: 0.7322 (mt) REVERT: 4 1341 TYR cc_start: 0.7827 (t80) cc_final: 0.7207 (t80) REVERT: A 28 MET cc_start: 0.4116 (ttp) cc_final: 0.3442 (ttp) REVERT: 5 101 SER cc_start: 0.8070 (m) cc_final: 0.7732 (p) REVERT: 5 303 GLN cc_start: 0.8212 (mm110) cc_final: 0.7519 (mt0) REVERT: 6 117 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7935 (mt) REVERT: 6 133 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6659 (p0) REVERT: 6 159 SER cc_start: 0.7759 (m) cc_final: 0.7430 (p) REVERT: 7 65 TYR cc_start: 0.8636 (t80) cc_final: 0.8341 (t80) REVERT: 7 83 ARG cc_start: 0.7293 (mtp-110) cc_final: 0.5882 (mmt180) REVERT: 7 94 GLN cc_start: 0.7206 (mm110) cc_final: 0.6861 (mm-40) REVERT: 7 256 GLN cc_start: 0.6439 (pt0) cc_final: 0.5729 (mp10) REVERT: b 78 GLN cc_start: 0.7635 (mt0) cc_final: 0.7321 (mm-40) REVERT: b 150 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6218 (mmt) REVERT: b 224 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8518 (m) REVERT: b 231 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9081 (m) REVERT: c 191 ASP cc_start: 0.7752 (t0) cc_final: 0.7528 (t70) REVERT: c 217 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (pp) REVERT: c 305 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.6462 (mtt90) REVERT: d 4 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (t70) REVERT: d 76 GLU cc_start: 0.7850 (pt0) cc_final: 0.7611 (pt0) REVERT: d 86 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7487 (tmm-80) REVERT: d 122 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.6060 (t0) REVERT: d 176 LEU cc_start: 0.8816 (tp) cc_final: 0.8498 (mt) REVERT: d 248 GLU cc_start: 0.6444 (tt0) cc_final: 0.6174 (tm-30) REVERT: 1 3 ASN cc_start: 0.7819 (p0) cc_final: 0.6422 (m-40) REVERT: 1 77 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6978 (pp) REVERT: X 91 ILE cc_start: 0.8812 (mm) cc_final: 0.8343 (mt) REVERT: X 151 GLU cc_start: 0.7057 (tp30) cc_final: 0.6529 (tp30) REVERT: X 234 MET cc_start: 0.8723 (mtt) cc_final: 0.8426 (mtt) REVERT: X 367 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8444 (m) REVERT: X 377 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7922 (tt0) REVERT: X 678 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7286 (tpt90) REVERT: X 799 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8335 (p0) REVERT: X 826 TYR cc_start: 0.8337 (m-80) cc_final: 0.8094 (m-80) REVERT: X 852 LEU cc_start: 0.7932 (mt) cc_final: 0.7717 (mt) REVERT: X 884 THR cc_start: 0.8451 (p) cc_final: 0.8123 (t) REVERT: X 1170 SER cc_start: 0.8715 (p) cc_final: 0.8269 (t) REVERT: X 1247 ASP cc_start: 0.8087 (t0) cc_final: 0.7688 (t0) outliers start: 419 outliers final: 308 residues processed: 1479 average time/residue: 0.6330 time to fit residues: 1620.5843 Evaluate side-chains 1486 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1150 time to evaluate : 5.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 75 CYS Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 202 GLU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 386 THR Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 553 SER Chi-restraints excluded: chain W residue 575 GLN Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 614 TYR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 651 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 669 ILE Chi-restraints excluded: chain W residue 678 ARG Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 706 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 765 ASP Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 859 LEU Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 927 VAL Chi-restraints excluded: chain W residue 938 MET Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 982 ASN Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1182 THR Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 32 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 277 GLU Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 453 ILE Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 652 ASN Chi-restraints excluded: chain S residue 692 LEU Chi-restraints excluded: chain S residue 698 GLU Chi-restraints excluded: chain S residue 699 THR Chi-restraints excluded: chain S residue 708 LEU Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 827 GLN Chi-restraints excluded: chain S residue 850 ILE Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 897 LYS Chi-restraints excluded: chain S residue 908 GLU Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 968 LEU Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1039 THR Chi-restraints excluded: chain S residue 1059 THR Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1182 THR Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 228 LEU Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 281 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 343 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 355 ASP Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 402 PHE Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 453 ILE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 497 PHE Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 589 THR Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 742 ILE Chi-restraints excluded: chain T residue 783 ASP Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 853 HIS Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1109 THR Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1236 ASN Chi-restraints excluded: chain T residue 1238 TRP Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1299 THR Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 152 TYR Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 191 ILE Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 512 VAL Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 631 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 947 LEU Chi-restraints excluded: chain 4 residue 976 VAL Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 56 LEU Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 306 ASN Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 10 ASN Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 273 LEU Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 18 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 231 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 250 THR Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 336 HIS Chi-restraints excluded: chain X residue 342 SER Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 591 VAL Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 688 GLU Chi-restraints excluded: chain X residue 699 THR Chi-restraints excluded: chain X residue 731 MET Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 767 VAL Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 822 MET Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 842 ASP Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1005 THR Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1083 THR Chi-restraints excluded: chain X residue 1097 SER Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1316 LEU Chi-restraints excluded: chain X residue 1340 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 808 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 477 optimal weight: 40.0000 chunk 612 optimal weight: 30.0000 chunk 474 optimal weight: 7.9990 chunk 706 optimal weight: 0.9980 chunk 468 optimal weight: 7.9990 chunk 835 optimal weight: 4.9990 chunk 522 optimal weight: 0.0770 chunk 509 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 HIS W 438 ASN ** W 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 594 GLN ** W 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS W1131 GLN ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN S 77 ASN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 707 HIS ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 590 HIS ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN 3 44 GLN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41241 GLN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN 5 62 GLN ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 180 ASN c 41 ASN c 110 GLN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 150 GLN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 22 HIS ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 70367 Z= 0.245 Angle : 0.603 13.116 95624 Z= 0.304 Chirality : 0.044 0.229 10799 Planarity : 0.004 0.078 12423 Dihedral : 5.518 76.118 9579 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 5.30 % Allowed : 15.79 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.09), residues: 8646 helix: -0.90 (0.09), residues: 2927 sheet: -0.54 (0.14), residues: 1261 loop : -1.48 (0.09), residues: 4458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 6 301 HIS 0.011 0.001 HIS W1114 PHE 0.025 0.002 PHE T 497 TYR 0.031 0.001 TYR T 614 ARG 0.009 0.000 ARG b 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 1210 time to evaluate : 5.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1727 (OUTLIER) cc_final: -0.2713 (mmm) REVERT: W 92 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7722 (mm110) REVERT: W 202 GLU cc_start: 0.3750 (OUTLIER) cc_final: 0.3051 (tm-30) REVERT: W 264 TYR cc_start: 0.8426 (m-80) cc_final: 0.7853 (m-80) REVERT: W 614 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7181 (t80) REVERT: W 642 TRP cc_start: 0.8329 (t-100) cc_final: 0.7871 (t60) REVERT: W 687 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8353 (mp) REVERT: W 769 ASN cc_start: 0.7635 (m-40) cc_final: 0.7183 (t0) REVERT: W 770 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8674 (tt) REVERT: W 797 ASP cc_start: 0.7028 (t0) cc_final: 0.6709 (t0) REVERT: W 810 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8551 (tt) REVERT: W 1032 MET cc_start: 0.8712 (mmm) cc_final: 0.8090 (mtp) REVERT: W 1108 THR cc_start: 0.9216 (m) cc_final: 0.8925 (p) REVERT: W 1120 MET cc_start: 0.8573 (ptm) cc_final: 0.8334 (ptm) REVERT: W 1169 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8403 (pp) REVERT: W 1278 TYR cc_start: 0.8818 (m-80) cc_final: 0.8239 (m-80) REVERT: W 1292 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6875 (mtp-110) REVERT: W 1310 ASN cc_start: 0.7767 (p0) cc_final: 0.7224 (p0) REVERT: S 86 MET cc_start: 0.5633 (ptt) cc_final: 0.4211 (mtt) REVERT: S 206 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8525 (mmtt) REVERT: S 700 VAL cc_start: 0.9219 (t) cc_final: 0.8759 (m) REVERT: S 725 ASP cc_start: 0.7695 (t0) cc_final: 0.7323 (t0) REVERT: S 770 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7987 (tt) REVERT: S 835 TYR cc_start: 0.8494 (t80) cc_final: 0.6881 (t80) REVERT: S 930 ARG cc_start: 0.7475 (ptm-80) cc_final: 0.5939 (tpt-90) REVERT: S 1170 SER cc_start: 0.8912 (p) cc_final: 0.8522 (m) REVERT: S 1190 TYR cc_start: 0.9016 (t80) cc_final: 0.8442 (t80) REVERT: S 1292 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.6900 (ptt180) REVERT: S 1353 MET cc_start: 0.7911 (mmm) cc_final: 0.7589 (mmt) REVERT: T 87 ILE cc_start: 0.8925 (mm) cc_final: 0.8695 (mt) REVERT: T 335 ASP cc_start: 0.8009 (t0) cc_final: 0.7494 (t0) REVERT: T 336 HIS cc_start: 0.7046 (m90) cc_final: 0.6300 (m170) REVERT: T 367 VAL cc_start: 0.8834 (t) cc_final: 0.8490 (m) REVERT: T 402 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6916 (t80) REVERT: T 491 MET cc_start: 0.8780 (mmm) cc_final: 0.8531 (mtm) REVERT: T 671 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7377 (tttt) REVERT: T 731 MET cc_start: 0.7894 (mmm) cc_final: 0.7516 (mmm) REVERT: T 733 LYS cc_start: 0.7209 (ptpt) cc_final: 0.6455 (mmtp) REVERT: T 854 LEU cc_start: 0.6725 (mt) cc_final: 0.6270 (mt) REVERT: T 1076 ASP cc_start: 0.7439 (t70) cc_final: 0.7175 (t0) REVERT: T 1110 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8324 (p0) REVERT: T 1178 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: T 1247 ASP cc_start: 0.8016 (t70) cc_final: 0.7496 (t0) REVERT: T 1255 ARG cc_start: 0.6959 (ptm160) cc_final: 0.6571 (ptm-80) REVERT: T 1299 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8933 (p) REVERT: T 1342 MET cc_start: 0.8358 (mmm) cc_final: 0.8130 (mmt) REVERT: T 1358 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8878 (mp) REVERT: 3 28 MET cc_start: 0.8341 (ttt) cc_final: 0.8055 (ttp) REVERT: 4 212 ASP cc_start: 0.7842 (t70) cc_final: 0.7607 (t0) REVERT: 4 252 VAL cc_start: 0.8414 (t) cc_final: 0.8070 (m) REVERT: 4 361 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7403 (mmm-85) REVERT: 4 407 HIS cc_start: 0.5238 (OUTLIER) cc_final: 0.4651 (p-80) REVERT: 4 619 MET cc_start: 0.3078 (ptm) cc_final: 0.2703 (mmm) REVERT: 4 627 PHE cc_start: 0.5728 (t80) cc_final: 0.5376 (t80) REVERT: 4 648 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5652 (tp) REVERT: 4 758 ASN cc_start: 0.5911 (t0) cc_final: 0.5436 (m-40) REVERT: 4 819 MET cc_start: 0.2666 (tpp) cc_final: 0.2031 (tpp) REVERT: 4 822 MET cc_start: 0.4801 (tpp) cc_final: 0.4572 (mmm) REVERT: 4 847 GLN cc_start: 0.3983 (mt0) cc_final: 0.2878 (pm20) REVERT: 4 1038 MET cc_start: 0.8654 (ptp) cc_final: 0.8420 (ptt) REVERT: 4 1138 MET cc_start: 0.5654 (mtm) cc_final: 0.5295 (ttm) REVERT: 4 1190 TYR cc_start: 0.7919 (t80) cc_final: 0.7465 (t80) REVERT: 4 1219 LEU cc_start: 0.7648 (mt) cc_final: 0.7426 (mt) REVERT: 4 1341 TYR cc_start: 0.7848 (t80) cc_final: 0.7291 (t80) REVERT: A 28 MET cc_start: 0.4217 (ttp) cc_final: 0.3610 (ttp) REVERT: 5 101 SER cc_start: 0.8094 (m) cc_final: 0.7759 (p) REVERT: 5 303 GLN cc_start: 0.8161 (mm110) cc_final: 0.7527 (mt0) REVERT: 6 117 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7940 (mt) REVERT: 6 133 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6634 (p0) REVERT: 6 159 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7434 (p) REVERT: 6 266 MET cc_start: 0.8274 (tpp) cc_final: 0.8014 (tpp) REVERT: 7 65 TYR cc_start: 0.8663 (t80) cc_final: 0.8333 (t80) REVERT: 7 94 GLN cc_start: 0.7195 (mm110) cc_final: 0.6780 (mm-40) REVERT: 7 256 GLN cc_start: 0.6421 (pt0) cc_final: 0.5719 (mp10) REVERT: b 78 GLN cc_start: 0.7632 (mt0) cc_final: 0.7318 (mm-40) REVERT: b 150 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6251 (mmt) REVERT: b 224 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8526 (m) REVERT: c 217 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8337 (pp) REVERT: c 305 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.6460 (mtt90) REVERT: d 4 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7756 (t70) REVERT: d 76 GLU cc_start: 0.7824 (pt0) cc_final: 0.7595 (pt0) REVERT: d 86 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7532 (tmm-80) REVERT: d 122 ASP cc_start: 0.6285 (OUTLIER) cc_final: 0.6056 (t0) REVERT: d 176 LEU cc_start: 0.8877 (tp) cc_final: 0.8552 (mt) REVERT: d 248 GLU cc_start: 0.6306 (tt0) cc_final: 0.6092 (tm-30) REVERT: 1 3 ASN cc_start: 0.7750 (p0) cc_final: 0.6516 (m-40) REVERT: 1 77 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6775 (pp) REVERT: X 7 GLN cc_start: 0.7264 (mt0) cc_final: 0.6332 (mm-40) REVERT: X 88 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6767 (t0) REVERT: X 91 ILE cc_start: 0.8848 (mm) cc_final: 0.8391 (mt) REVERT: X 151 GLU cc_start: 0.7063 (tp30) cc_final: 0.6636 (tp30) REVERT: X 234 MET cc_start: 0.8683 (mtt) cc_final: 0.8363 (mtt) REVERT: X 367 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8426 (m) REVERT: X 377 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: X 678 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7344 (tpt90) REVERT: X 799 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8335 (p0) REVERT: X 804 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.7966 (mtmt) REVERT: X 826 TYR cc_start: 0.8294 (m-80) cc_final: 0.8043 (m-80) REVERT: X 884 THR cc_start: 0.8462 (p) cc_final: 0.8178 (t) REVERT: X 1170 SER cc_start: 0.8714 (p) cc_final: 0.8220 (t) REVERT: X 1247 ASP cc_start: 0.8094 (t0) cc_final: 0.7708 (t0) REVERT: X 1359 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8083 (mt-10) outliers start: 398 outliers final: 303 residues processed: 1474 average time/residue: 0.6364 time to fit residues: 1634.8926 Evaluate side-chains 1491 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1156 time to evaluate : 5.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 59 GLU Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 75 CYS Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 202 GLU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 386 THR Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 502 MET Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 553 SER Chi-restraints excluded: chain W residue 575 GLN Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 614 TYR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 765 ASP Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 789 ASP Chi-restraints excluded: chain W residue 810 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 927 VAL Chi-restraints excluded: chain W residue 938 MET Chi-restraints excluded: chain W residue 945 ASN Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1043 THR Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1130 ARG Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1182 THR Chi-restraints excluded: chain W residue 1184 VAL Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 136 ILE Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 277 GLU Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 427 ILE Chi-restraints excluded: chain S residue 453 ILE Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 652 ASN Chi-restraints excluded: chain S residue 692 LEU Chi-restraints excluded: chain S residue 698 GLU Chi-restraints excluded: chain S residue 699 THR Chi-restraints excluded: chain S residue 708 LEU Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 827 GLN Chi-restraints excluded: chain S residue 850 ILE Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 897 LYS Chi-restraints excluded: chain S residue 908 GLU Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 968 LEU Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1039 THR Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1182 THR Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 281 SER Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 343 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 352 ASP Chi-restraints excluded: chain T residue 355 ASP Chi-restraints excluded: chain T residue 382 MET Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 402 PHE Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 453 ILE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 520 THR Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 589 THR Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 593 ASP Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 742 ILE Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 853 HIS Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1182 THR Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1238 TRP Chi-restraints excluded: chain T residue 1299 THR Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 512 VAL Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 684 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 976 VAL Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 56 LEU Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 159 SER Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 273 LEU Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 20 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 243 LEU Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 110 GLN Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 250 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 79 ASP Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 342 SER Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 377 GLU Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 529 HIS Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 688 GLU Chi-restraints excluded: chain X residue 731 MET Chi-restraints excluded: chain X residue 748 ASP Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 767 VAL Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 804 LYS Chi-restraints excluded: chain X residue 822 MET Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 842 ASP Chi-restraints excluded: chain X residue 854 LEU Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1005 THR Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1316 LEU Chi-restraints excluded: chain X residue 1340 GLU Chi-restraints excluded: chain X residue 1359 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 516 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 499 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 531 optimal weight: 2.9990 chunk 569 optimal weight: 0.8980 chunk 413 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 656 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 HIS W 22 GLN W 799 ASN ** W 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 22 HIS 2 75 GLN S 92 GLN ** S 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 707 HIS ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 564 ASN ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1236 ASN ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 110 GLN 6 274 GLN c 41 ASN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 354 HIS ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN X 745 GLN ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 70367 Z= 0.180 Angle : 0.581 11.990 95624 Z= 0.292 Chirality : 0.043 0.326 10799 Planarity : 0.004 0.074 12423 Dihedral : 5.341 75.680 9579 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 4.70 % Allowed : 16.72 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 8646 helix: -0.68 (0.09), residues: 2945 sheet: -0.45 (0.15), residues: 1267 loop : -1.41 (0.09), residues: 4434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 6 301 HIS 0.014 0.001 HIS W 674 PHE 0.027 0.001 PHE T 497 TYR 0.032 0.001 TYR T 614 ARG 0.010 0.000 ARG S 678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 1218 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1709 (OUTLIER) cc_final: -0.2687 (mmm) REVERT: W 92 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7699 (mm110) REVERT: W 202 GLU cc_start: 0.3666 (OUTLIER) cc_final: 0.3006 (tm-30) REVERT: W 264 TYR cc_start: 0.8376 (m-80) cc_final: 0.7817 (m-80) REVERT: W 614 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7124 (t80) REVERT: W 642 TRP cc_start: 0.8330 (t-100) cc_final: 0.7866 (t60) REVERT: W 687 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8361 (mp) REVERT: W 769 ASN cc_start: 0.7620 (m-40) cc_final: 0.7231 (t0) REVERT: W 770 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8668 (tt) REVERT: W 797 ASP cc_start: 0.7036 (t0) cc_final: 0.6691 (t0) REVERT: W 1032 MET cc_start: 0.8716 (mmm) cc_final: 0.8072 (mtp) REVERT: W 1108 THR cc_start: 0.9201 (m) cc_final: 0.8891 (p) REVERT: W 1120 MET cc_start: 0.8466 (ptm) cc_final: 0.8234 (ptm) REVERT: W 1169 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8294 (pp) REVERT: W 1276 MET cc_start: 0.9135 (mmp) cc_final: 0.8768 (mmm) REVERT: W 1292 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6599 (mtp-110) REVERT: W 1310 ASN cc_start: 0.7787 (p0) cc_final: 0.7279 (p0) REVERT: S 86 MET cc_start: 0.5712 (ptt) cc_final: 0.4230 (mtt) REVERT: S 206 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8510 (mmtt) REVERT: S 545 HIS cc_start: 0.7836 (t-90) cc_final: 0.7548 (t70) REVERT: S 725 ASP cc_start: 0.7680 (t0) cc_final: 0.7340 (t0) REVERT: S 770 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7981 (tt) REVERT: S 835 TYR cc_start: 0.8476 (t80) cc_final: 0.6860 (t80) REVERT: S 930 ARG cc_start: 0.7448 (ptm-80) cc_final: 0.5883 (tpt-90) REVERT: S 1170 SER cc_start: 0.8812 (p) cc_final: 0.8414 (m) REVERT: S 1190 TYR cc_start: 0.8970 (t80) cc_final: 0.8388 (t80) REVERT: S 1292 ARG cc_start: 0.7396 (ttp-110) cc_final: 0.6918 (ptt180) REVERT: S 1353 MET cc_start: 0.7832 (mmm) cc_final: 0.7482 (mmt) REVERT: T 117 MET cc_start: 0.8280 (ttp) cc_final: 0.7891 (ttp) REVERT: T 335 ASP cc_start: 0.7965 (t0) cc_final: 0.7465 (t0) REVERT: T 336 HIS cc_start: 0.7074 (m90) cc_final: 0.6263 (m170) REVERT: T 367 VAL cc_start: 0.8836 (t) cc_final: 0.8519 (m) REVERT: T 491 MET cc_start: 0.8740 (mmm) cc_final: 0.8522 (mtm) REVERT: T 671 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7321 (tttt) REVERT: T 731 MET cc_start: 0.7876 (mmm) cc_final: 0.7511 (mmm) REVERT: T 733 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6400 (mmtp) REVERT: T 854 LEU cc_start: 0.6737 (mt) cc_final: 0.6270 (mt) REVERT: T 1110 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8363 (p0) REVERT: T 1178 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: T 1247 ASP cc_start: 0.7976 (t70) cc_final: 0.7557 (t0) REVERT: T 1255 ARG cc_start: 0.6928 (ptm160) cc_final: 0.6530 (ptm-80) REVERT: T 1358 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8855 (mp) REVERT: 3 28 MET cc_start: 0.8324 (ttt) cc_final: 0.8082 (ttp) REVERT: 3 48 TYR cc_start: 0.8136 (t80) cc_final: 0.7833 (t80) REVERT: 4 167 MET cc_start: 0.7529 (tmm) cc_final: 0.7327 (tmm) REVERT: 4 212 ASP cc_start: 0.7817 (t70) cc_final: 0.7594 (t0) REVERT: 4 252 VAL cc_start: 0.8372 (t) cc_final: 0.7904 (m) REVERT: 4 287 MET cc_start: 0.8400 (mmm) cc_final: 0.8173 (mmp) REVERT: 4 361 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7426 (mmm-85) REVERT: 4 407 HIS cc_start: 0.5280 (OUTLIER) cc_final: 0.4856 (p-80) REVERT: 4 619 MET cc_start: 0.3159 (ptm) cc_final: 0.2901 (mmm) REVERT: 4 627 PHE cc_start: 0.5801 (t80) cc_final: 0.5364 (t80) REVERT: 4 648 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5709 (tp) REVERT: 4 758 ASN cc_start: 0.5884 (t0) cc_final: 0.5431 (m-40) REVERT: 4 802 LEU cc_start: 0.5412 (mm) cc_final: 0.5146 (mt) REVERT: 4 819 MET cc_start: 0.2867 (tpp) cc_final: 0.2113 (tpp) REVERT: 4 1138 MET cc_start: 0.5668 (mtm) cc_final: 0.5252 (ttm) REVERT: 4 1190 TYR cc_start: 0.7720 (t80) cc_final: 0.7326 (t80) REVERT: 4 1219 LEU cc_start: 0.7750 (mt) cc_final: 0.7541 (mt) REVERT: 4 1341 TYR cc_start: 0.7804 (t80) cc_final: 0.7260 (t80) REVERT: A 28 MET cc_start: 0.4034 (ttp) cc_final: 0.3443 (ttp) REVERT: 5 101 SER cc_start: 0.8103 (m) cc_final: 0.7738 (p) REVERT: 5 303 GLN cc_start: 0.8168 (mm110) cc_final: 0.7530 (mt0) REVERT: 6 19 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: 6 117 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7918 (mt) REVERT: 6 133 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6631 (p0) REVERT: 6 159 SER cc_start: 0.7768 (m) cc_final: 0.7426 (p) REVERT: 6 266 MET cc_start: 0.8291 (tpp) cc_final: 0.8057 (tpp) REVERT: 6 269 MET cc_start: 0.7855 (ttm) cc_final: 0.7452 (ttt) REVERT: 7 65 TYR cc_start: 0.8658 (t80) cc_final: 0.8356 (t80) REVERT: 7 94 GLN cc_start: 0.7057 (mm110) cc_final: 0.6676 (mm-40) REVERT: 7 119 SER cc_start: 0.6708 (m) cc_final: 0.6502 (p) REVERT: 7 256 GLN cc_start: 0.6355 (pt0) cc_final: 0.5695 (mp10) REVERT: b 78 GLN cc_start: 0.7629 (mt0) cc_final: 0.7311 (mm-40) REVERT: b 150 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6338 (mmt) REVERT: b 224 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8527 (m) REVERT: c 305 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.6426 (mtt90) REVERT: d 4 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7730 (t70) REVERT: d 86 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (tmm-80) REVERT: d 176 LEU cc_start: 0.8841 (tp) cc_final: 0.8530 (mt) REVERT: d 248 GLU cc_start: 0.6385 (tt0) cc_final: 0.6157 (tm-30) REVERT: 1 3 ASN cc_start: 0.7910 (p0) cc_final: 0.6754 (m-40) REVERT: X 7 GLN cc_start: 0.7305 (mt0) cc_final: 0.6346 (mm-40) REVERT: X 91 ILE cc_start: 0.8837 (mm) cc_final: 0.8357 (mt) REVERT: X 117 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7914 (tpt) REVERT: X 151 GLU cc_start: 0.7028 (tp30) cc_final: 0.6597 (tp30) REVERT: X 161 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8468 (p) REVERT: X 234 MET cc_start: 0.8689 (mtt) cc_final: 0.8393 (mtt) REVERT: X 367 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8369 (m) REVERT: X 377 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: X 491 MET cc_start: 0.7820 (mmm) cc_final: 0.7604 (mmt) REVERT: X 500 TYR cc_start: 0.8475 (t80) cc_final: 0.8248 (t80) REVERT: X 678 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7338 (tpt90) REVERT: X 799 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8277 (p0) REVERT: X 804 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: X 826 TYR cc_start: 0.8283 (m-80) cc_final: 0.8073 (m-80) REVERT: X 884 THR cc_start: 0.8465 (p) cc_final: 0.8190 (t) REVERT: X 1223 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8643 (t) REVERT: X 1247 ASP cc_start: 0.8078 (t0) cc_final: 0.7664 (t0) REVERT: X 1359 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8073 (mt-10) outliers start: 353 outliers final: 276 residues processed: 1446 average time/residue: 0.6191 time to fit residues: 1553.3301 Evaluate side-chains 1461 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1157 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 75 CYS Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 202 GLU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 502 MET Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 575 GLN Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 614 TYR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1043 THR Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1093 LEU Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1182 THR Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1264 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 32 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 253 CYS Chi-restraints excluded: chain S residue 277 GLU Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 427 ILE Chi-restraints excluded: chain S residue 453 ILE Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 652 ASN Chi-restraints excluded: chain S residue 692 LEU Chi-restraints excluded: chain S residue 698 GLU Chi-restraints excluded: chain S residue 699 THR Chi-restraints excluded: chain S residue 708 LEU Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 790 VAL Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 850 ILE Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 968 LEU Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1015 MET Chi-restraints excluded: chain S residue 1068 VAL Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1182 THR Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 352 ASP Chi-restraints excluded: chain T residue 355 ASP Chi-restraints excluded: chain T residue 382 MET Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 453 ILE Chi-restraints excluded: chain T residue 494 PHE Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 520 THR Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 593 ASP Chi-restraints excluded: chain T residue 636 LEU Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 742 ILE Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 853 HIS Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1169 LEU Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1238 TRP Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 79 ASP Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 976 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1098 VAL Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain 5 residue 56 LEU Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 152 THR Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 10 ASN Chi-restraints excluded: chain 6 residue 19 GLU Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 273 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 110 GLN Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 211 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 69 CYS Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 187 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 247 ASP Chi-restraints excluded: chain d residue 250 THR Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 79 ASP Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 161 SER Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 342 SER Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 377 GLU Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 529 HIS Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 688 GLU Chi-restraints excluded: chain X residue 731 MET Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 767 VAL Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 804 LYS Chi-restraints excluded: chain X residue 822 MET Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 854 LEU Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1005 THR Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1069 VAL Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1316 LEU Chi-restraints excluded: chain X residue 1340 GLU Chi-restraints excluded: chain X residue 1359 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 760 optimal weight: 9.9990 chunk 800 optimal weight: 10.0000 chunk 730 optimal weight: 5.9990 chunk 778 optimal weight: 10.0000 chunk 468 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 611 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 703 optimal weight: 20.0000 chunk 736 optimal weight: 9.9990 chunk 775 optimal weight: 0.0070 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 HIS ** W 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 991 HIS W1114 HIS ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 GLN 2 75 GLN S 92 GLN S 109 ASN S 529 HIS S 590 HIS S 674 HIS S 707 HIS ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1173 GLN ** T 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 564 ASN T 707 HIS ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 567 GLN 4 623 GLN ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 40 GLN c 41 ASN ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 469 ASN X 499 GLN ** X 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 70367 Z= 0.356 Angle : 0.670 14.405 95624 Z= 0.337 Chirality : 0.047 0.348 10799 Planarity : 0.005 0.080 12423 Dihedral : 5.629 74.360 9578 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 5.10 % Allowed : 16.71 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 8646 helix: -0.72 (0.09), residues: 2910 sheet: -0.48 (0.14), residues: 1277 loop : -1.49 (0.09), residues: 4459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 6 301 HIS 0.015 0.001 HIS T 537 PHE 0.027 0.002 PHE S 882 TYR 0.052 0.002 TYR T 614 ARG 0.009 0.001 ARG 6 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1185 time to evaluate : 5.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1672 (OUTLIER) cc_final: -0.2648 (mmm) REVERT: W 202 GLU cc_start: 0.3867 (OUTLIER) cc_final: 0.3141 (tm-30) REVERT: W 264 TYR cc_start: 0.8469 (m-80) cc_final: 0.7976 (m-80) REVERT: W 463 GLN cc_start: 0.6866 (tp40) cc_final: 0.6661 (tp40) REVERT: W 491 MET cc_start: 0.8238 (tpp) cc_final: 0.8008 (tpp) REVERT: W 537 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7809 (p90) REVERT: W 614 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7245 (t80) REVERT: W 642 TRP cc_start: 0.8433 (t-100) cc_final: 0.8052 (t-100) REVERT: W 683 GLU cc_start: 0.7238 (tp30) cc_final: 0.6831 (tp30) REVERT: W 687 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8351 (mp) REVERT: W 769 ASN cc_start: 0.7900 (m-40) cc_final: 0.7346 (t0) REVERT: W 770 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8702 (tt) REVERT: W 797 ASP cc_start: 0.7259 (t0) cc_final: 0.6943 (t0) REVERT: W 1032 MET cc_start: 0.8707 (mmm) cc_final: 0.8119 (mtp) REVERT: W 1108 THR cc_start: 0.9336 (m) cc_final: 0.9100 (m) REVERT: W 1120 MET cc_start: 0.8624 (ptm) cc_final: 0.8393 (ptm) REVERT: W 1128 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: W 1169 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8566 (pp) REVERT: W 1276 MET cc_start: 0.9191 (mmp) cc_final: 0.8823 (mmm) REVERT: W 1278 TYR cc_start: 0.8753 (m-80) cc_final: 0.8183 (m-80) REVERT: W 1292 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6641 (mtp-110) REVERT: W 1310 ASN cc_start: 0.8108 (p0) cc_final: 0.7628 (p0) REVERT: S 86 MET cc_start: 0.5814 (ptt) cc_final: 0.4303 (mtt) REVERT: S 206 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8533 (mmtt) REVERT: S 244 MET cc_start: 0.8274 (tpp) cc_final: 0.7933 (mmt) REVERT: S 725 ASP cc_start: 0.7707 (t0) cc_final: 0.7289 (t70) REVERT: S 770 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8029 (tt) REVERT: S 811 MET cc_start: 0.8187 (mmt) cc_final: 0.7932 (mmt) REVERT: S 930 ARG cc_start: 0.7486 (ptm-80) cc_final: 0.5866 (tpt-90) REVERT: S 1170 SER cc_start: 0.9010 (p) cc_final: 0.8709 (m) REVERT: S 1292 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7007 (ptt180) REVERT: S 1353 MET cc_start: 0.8049 (mmm) cc_final: 0.7730 (mmt) REVERT: T 335 ASP cc_start: 0.7984 (t0) cc_final: 0.7505 (t0) REVERT: T 336 HIS cc_start: 0.7177 (m90) cc_final: 0.6378 (m170) REVERT: T 367 VAL cc_start: 0.8869 (t) cc_final: 0.8510 (m) REVERT: T 474 ASP cc_start: 0.7062 (m-30) cc_final: 0.6538 (p0) REVERT: T 491 MET cc_start: 0.8766 (mmm) cc_final: 0.8534 (mtm) REVERT: T 671 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7445 (tttt) REVERT: T 731 MET cc_start: 0.7947 (mmm) cc_final: 0.7576 (mmm) REVERT: T 733 LYS cc_start: 0.7229 (ptpt) cc_final: 0.6486 (mmtp) REVERT: T 1110 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.7945 (p0) REVERT: T 1178 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: T 1247 ASP cc_start: 0.8201 (t70) cc_final: 0.7762 (t0) REVERT: T 1255 ARG cc_start: 0.7022 (ptm160) cc_final: 0.6639 (ptm-80) REVERT: T 1322 MET cc_start: 0.9061 (tpp) cc_final: 0.8860 (ttt) REVERT: T 1358 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8910 (mp) REVERT: 3 28 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: 3 44 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7896 (mm-40) REVERT: 4 124 HIS cc_start: 0.7084 (m-70) cc_final: 0.6613 (m170) REVERT: 4 167 MET cc_start: 0.7523 (tmm) cc_final: 0.7233 (tmm) REVERT: 4 212 ASP cc_start: 0.7810 (t70) cc_final: 0.7607 (t0) REVERT: 4 252 VAL cc_start: 0.8412 (t) cc_final: 0.8080 (m) REVERT: 4 361 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7359 (mmm-85) REVERT: 4 407 HIS cc_start: 0.5538 (OUTLIER) cc_final: 0.4893 (p-80) REVERT: 4 619 MET cc_start: 0.3309 (ptm) cc_final: 0.2890 (mmm) REVERT: 4 648 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5752 (tp) REVERT: 4 758 ASN cc_start: 0.5898 (t0) cc_final: 0.5543 (m-40) REVERT: 4 819 MET cc_start: 0.2927 (tpp) cc_final: 0.2357 (tpt) REVERT: 4 822 MET cc_start: 0.4939 (tpp) cc_final: 0.4683 (mmm) REVERT: 4 1138 MET cc_start: 0.5770 (mtm) cc_final: 0.5353 (ttm) REVERT: 4 1219 LEU cc_start: 0.7903 (mt) cc_final: 0.7635 (mt) REVERT: 4 1341 TYR cc_start: 0.7912 (t80) cc_final: 0.7480 (t80) REVERT: A 28 MET cc_start: 0.4078 (ttp) cc_final: 0.3295 (ttp) REVERT: 5 173 PHE cc_start: 0.7347 (m-80) cc_final: 0.6961 (m-80) REVERT: 5 206 ASP cc_start: 0.8499 (t0) cc_final: 0.8156 (t0) REVERT: 5 303 GLN cc_start: 0.8124 (mm110) cc_final: 0.7601 (mt0) REVERT: 6 19 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: 6 117 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7978 (mt) REVERT: 6 133 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6591 (p0) REVERT: 6 159 SER cc_start: 0.7783 (m) cc_final: 0.7471 (p) REVERT: 6 210 TYR cc_start: 0.8546 (m-80) cc_final: 0.8044 (m-80) REVERT: 6 266 MET cc_start: 0.8309 (tpp) cc_final: 0.8072 (tpp) REVERT: 6 269 MET cc_start: 0.7812 (ttm) cc_final: 0.7434 (ttt) REVERT: 7 65 TYR cc_start: 0.8749 (t80) cc_final: 0.8401 (t80) REVERT: 7 94 GLN cc_start: 0.7123 (mm110) cc_final: 0.6728 (mm-40) REVERT: 7 256 GLN cc_start: 0.6474 (pt0) cc_final: 0.5799 (mp10) REVERT: 7 269 MET cc_start: 0.8080 (tmm) cc_final: 0.7839 (ttt) REVERT: b 78 GLN cc_start: 0.7648 (mt0) cc_final: 0.7349 (mm-40) REVERT: b 150 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6225 (mmt) REVERT: b 224 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8577 (m) REVERT: c 217 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8363 (pp) REVERT: c 305 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.6362 (mtt90) REVERT: d 4 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7950 (t70) REVERT: d 86 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7712 (tmm-80) REVERT: d 176 LEU cc_start: 0.8797 (tp) cc_final: 0.8527 (mt) REVERT: 1 3 ASN cc_start: 0.7644 (p0) cc_final: 0.6806 (m-40) REVERT: 1 77 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6686 (pp) REVERT: X 7 GLN cc_start: 0.7238 (mt0) cc_final: 0.6235 (mm-40) REVERT: X 88 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6845 (t0) REVERT: X 91 ILE cc_start: 0.8865 (mm) cc_final: 0.8343 (mt) REVERT: X 117 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7981 (tpt) REVERT: X 151 GLU cc_start: 0.7075 (tp30) cc_final: 0.6665 (tp30) REVERT: X 161 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8488 (p) REVERT: X 377 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: X 678 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7321 (tpt90) REVERT: X 799 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8296 (p0) REVERT: X 804 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7924 (mtmt) REVERT: X 826 TYR cc_start: 0.8375 (m-80) cc_final: 0.8136 (m-80) REVERT: X 852 LEU cc_start: 0.7849 (mt) cc_final: 0.7621 (mt) REVERT: X 884 THR cc_start: 0.8528 (p) cc_final: 0.8265 (t) REVERT: X 1170 SER cc_start: 0.8654 (p) cc_final: 0.8138 (t) REVERT: X 1223 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8779 (t) REVERT: X 1247 ASP cc_start: 0.8148 (t0) cc_final: 0.7783 (t0) REVERT: X 1359 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8114 (mt-10) outliers start: 383 outliers final: 299 residues processed: 1436 average time/residue: 0.6821 time to fit residues: 1705.5998 Evaluate side-chains 1483 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1151 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 75 CYS Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 202 GLU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 386 THR Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 419 VAL Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 502 MET Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 553 SER Chi-restraints excluded: chain W residue 575 GLN Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 614 TYR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 938 MET Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1043 THR Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1128 GLN Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1182 THR Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 32 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 253 CYS Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 427 ILE Chi-restraints excluded: chain S residue 453 ILE Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 652 ASN Chi-restraints excluded: chain S residue 692 LEU Chi-restraints excluded: chain S residue 698 GLU Chi-restraints excluded: chain S residue 699 THR Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 798 TYR Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 850 ILE Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 897 LYS Chi-restraints excluded: chain S residue 908 GLU Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 968 LEU Chi-restraints excluded: chain S residue 971 GLN Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1015 MET Chi-restraints excluded: chain S residue 1039 THR Chi-restraints excluded: chain S residue 1059 THR Chi-restraints excluded: chain S residue 1068 VAL Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1182 THR Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1308 VAL Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 290 LEU Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 343 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 355 ASP Chi-restraints excluded: chain T residue 382 MET Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 453 ILE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 497 PHE Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 520 THR Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 593 ASP Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 742 ILE Chi-restraints excluded: chain T residue 783 ASP Chi-restraints excluded: chain T residue 788 LEU Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 853 HIS Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1109 THR Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1238 TRP Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1314 VAL Chi-restraints excluded: chain T residue 1323 LEU Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 28 MET Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 561 MET Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 947 LEU Chi-restraints excluded: chain 4 residue 976 VAL Chi-restraints excluded: chain 4 residue 995 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1078 VAL Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1176 THR Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 152 THR Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 10 ASN Chi-restraints excluded: chain 6 residue 19 GLU Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 222 CYS Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 20 LEU Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 212 CYS Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 261 ASP Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 167 GLN Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 110 GLN Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 192 VAL Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 79 ASP Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 161 SER Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 342 SER Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 377 GLU Chi-restraints excluded: chain X residue 382 MET Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 453 ILE Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 529 HIS Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 688 GLU Chi-restraints excluded: chain X residue 699 THR Chi-restraints excluded: chain X residue 708 LEU Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 765 ASP Chi-restraints excluded: chain X residue 767 VAL Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 804 LYS Chi-restraints excluded: chain X residue 822 MET Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 953 VAL Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1005 THR Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1069 VAL Chi-restraints excluded: chain X residue 1083 THR Chi-restraints excluded: chain X residue 1097 SER Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1316 LEU Chi-restraints excluded: chain X residue 1340 GLU Chi-restraints excluded: chain X residue 1359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 511 optimal weight: 20.0000 chunk 823 optimal weight: 8.9990 chunk 502 optimal weight: 30.0000 chunk 390 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 863 optimal weight: 2.9990 chunk 794 optimal weight: 10.0000 chunk 687 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 531 optimal weight: 6.9990 chunk 421 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 HIS ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 799 ASN ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN S 707 HIS ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN ** 4 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 HIS ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 ASN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN X 652 ASN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1268 GLN X1271 HIS ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1352 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 70367 Z= 0.340 Angle : 0.668 14.541 95624 Z= 0.337 Chirality : 0.047 0.312 10799 Planarity : 0.005 0.081 12423 Dihedral : 5.722 73.811 9578 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 5.00 % Allowed : 17.02 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.09), residues: 8646 helix: -0.79 (0.09), residues: 2923 sheet: -0.51 (0.14), residues: 1295 loop : -1.53 (0.09), residues: 4428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 41238 HIS 0.013 0.001 HIS T 537 PHE 0.034 0.002 PHE c 132 TYR 0.042 0.002 TYR T 614 ARG 0.012 0.001 ARG S 972 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1161 time to evaluate : 6.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 MET cc_start: -0.1669 (OUTLIER) cc_final: -0.2586 (mmm) REVERT: W 32 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8470 (p90) REVERT: W 202 GLU cc_start: 0.3889 (OUTLIER) cc_final: 0.3199 (tm-30) REVERT: W 247 ASP cc_start: 0.6912 (t0) cc_final: 0.6634 (t0) REVERT: W 264 TYR cc_start: 0.8547 (m-80) cc_final: 0.8000 (m-80) REVERT: W 537 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7634 (p90) REVERT: W 614 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7276 (t80) REVERT: W 642 TRP cc_start: 0.8445 (t-100) cc_final: 0.8060 (t-100) REVERT: W 683 GLU cc_start: 0.7309 (tp30) cc_final: 0.6897 (tp30) REVERT: W 687 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8352 (mp) REVERT: W 770 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8756 (tt) REVERT: W 797 ASP cc_start: 0.7360 (t0) cc_final: 0.7058 (t0) REVERT: W 982 ASN cc_start: 0.7901 (t0) cc_final: 0.7646 (t0) REVERT: W 1032 MET cc_start: 0.8749 (mmm) cc_final: 0.8183 (mtp) REVERT: W 1120 MET cc_start: 0.8654 (ptm) cc_final: 0.8406 (ptm) REVERT: W 1128 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: W 1169 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (pp) REVERT: W 1276 MET cc_start: 0.9218 (mmp) cc_final: 0.8882 (mmm) REVERT: W 1278 TYR cc_start: 0.8757 (m-80) cc_final: 0.8096 (m-80) REVERT: W 1292 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6501 (mtp-110) REVERT: W 1310 ASN cc_start: 0.8226 (p0) cc_final: 0.7815 (p0) REVERT: S 86 MET cc_start: 0.5650 (ptt) cc_final: 0.4259 (mtt) REVERT: S 206 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8521 (mmtt) REVERT: S 688 GLU cc_start: 0.7768 (pt0) cc_final: 0.7529 (pt0) REVERT: S 725 ASP cc_start: 0.7707 (t0) cc_final: 0.7247 (t70) REVERT: S 770 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8019 (tt) REVERT: S 811 MET cc_start: 0.8159 (mmt) cc_final: 0.7894 (mmt) REVERT: S 826 TYR cc_start: 0.8413 (m-80) cc_final: 0.8152 (m-80) REVERT: S 930 ARG cc_start: 0.7495 (ptm-80) cc_final: 0.5900 (tpt-90) REVERT: S 1170 SER cc_start: 0.9008 (p) cc_final: 0.8721 (m) REVERT: S 1190 TYR cc_start: 0.9060 (t80) cc_final: 0.8702 (t80) REVERT: S 1292 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7068 (ptt180) REVERT: S 1353 MET cc_start: 0.8024 (mmm) cc_final: 0.7673 (mmt) REVERT: T 117 MET cc_start: 0.8308 (ttp) cc_final: 0.7991 (ttp) REVERT: T 335 ASP cc_start: 0.7944 (t0) cc_final: 0.7489 (t0) REVERT: T 336 HIS cc_start: 0.7159 (m90) cc_final: 0.6456 (m170) REVERT: T 367 VAL cc_start: 0.8871 (t) cc_final: 0.8513 (m) REVERT: T 402 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6932 (t80) REVERT: T 474 ASP cc_start: 0.7164 (m-30) cc_final: 0.6532 (p0) REVERT: T 491 MET cc_start: 0.8772 (mmm) cc_final: 0.8544 (mtm) REVERT: T 671 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7551 (tptt) REVERT: T 731 MET cc_start: 0.7940 (mmm) cc_final: 0.7550 (mmm) REVERT: T 733 LYS cc_start: 0.7236 (ptpt) cc_final: 0.6464 (mmtp) REVERT: T 873 ASP cc_start: 0.7740 (p0) cc_final: 0.7506 (t0) REVERT: T 1110 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (t0) REVERT: T 1178 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: T 1247 ASP cc_start: 0.8196 (t70) cc_final: 0.7759 (t0) REVERT: T 1255 ARG cc_start: 0.7058 (ptm160) cc_final: 0.6665 (ptm-80) REVERT: T 1358 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8874 (mp) REVERT: 3 5 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7215 (tttt) REVERT: 3 28 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7989 (ttp) REVERT: 3 44 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7938 (mm-40) REVERT: 3 48 TYR cc_start: 0.8195 (t80) cc_final: 0.7967 (t80) REVERT: 4 124 HIS cc_start: 0.7104 (m-70) cc_final: 0.6653 (m-70) REVERT: 4 167 MET cc_start: 0.7561 (tmm) cc_final: 0.7204 (tmm) REVERT: 4 212 ASP cc_start: 0.7711 (t70) cc_final: 0.7493 (t0) REVERT: 4 252 VAL cc_start: 0.8405 (t) cc_final: 0.8074 (m) REVERT: 4 361 ARG cc_start: 0.7843 (tpp80) cc_final: 0.7468 (mmm-85) REVERT: 4 407 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.4987 (p-80) REVERT: 4 619 MET cc_start: 0.3414 (ptm) cc_final: 0.2949 (mmm) REVERT: 4 648 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5875 (tp) REVERT: 4 707 HIS cc_start: 0.5110 (m90) cc_final: 0.3519 (m-70) REVERT: 4 819 MET cc_start: 0.2864 (tpp) cc_final: 0.1878 (tpp) REVERT: 4 822 MET cc_start: 0.5094 (tpp) cc_final: 0.4848 (mmm) REVERT: 4 1076 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6328 (m-30) REVERT: 4 1138 MET cc_start: 0.5730 (mtm) cc_final: 0.5372 (ttm) REVERT: 4 1219 LEU cc_start: 0.8011 (mt) cc_final: 0.7730 (mt) REVERT: 4 1341 TYR cc_start: 0.8004 (t80) cc_final: 0.7590 (t80) REVERT: A 28 MET cc_start: 0.4074 (ttp) cc_final: 0.3264 (ttp) REVERT: 5 206 ASP cc_start: 0.8507 (t0) cc_final: 0.8159 (t0) REVERT: 5 303 GLN cc_start: 0.8161 (mm110) cc_final: 0.7661 (mt0) REVERT: 6 19 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: 6 117 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7947 (mt) REVERT: 6 133 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6565 (p0) REVERT: 6 159 SER cc_start: 0.7761 (m) cc_final: 0.7464 (p) REVERT: 6 210 TYR cc_start: 0.8528 (m-80) cc_final: 0.8111 (m-80) REVERT: 6 269 MET cc_start: 0.7825 (ttm) cc_final: 0.7551 (ttt) REVERT: 7 65 TYR cc_start: 0.8751 (t80) cc_final: 0.8347 (t80) REVERT: 7 94 GLN cc_start: 0.7121 (mm110) cc_final: 0.6735 (mm-40) REVERT: 7 256 GLN cc_start: 0.6555 (pt0) cc_final: 0.5874 (mp10) REVERT: 7 269 MET cc_start: 0.8052 (tmm) cc_final: 0.7837 (ttt) REVERT: b 78 GLN cc_start: 0.7628 (mt0) cc_final: 0.7346 (mm-40) REVERT: b 150 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6382 (mmt) REVERT: b 224 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (m) REVERT: c 217 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8372 (pp) REVERT: c 305 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.6345 (mtt90) REVERT: d 4 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8002 (t70) REVERT: d 86 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7770 (tmm-80) REVERT: d 176 LEU cc_start: 0.8810 (tp) cc_final: 0.8516 (mt) REVERT: 1 3 ASN cc_start: 0.7470 (p0) cc_final: 0.6817 (m-40) REVERT: 1 22 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.7154 (t-170) REVERT: 1 77 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6681 (pp) REVERT: X 88 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6837 (t0) REVERT: X 91 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8462 (tt) REVERT: X 117 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7974 (tpt) REVERT: X 151 GLU cc_start: 0.7020 (tp30) cc_final: 0.6606 (tp30) REVERT: X 161 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8499 (p) REVERT: X 367 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (m) REVERT: X 377 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: X 678 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7282 (tpt90) REVERT: X 799 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8288 (p0) REVERT: X 804 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7921 (mtmt) REVERT: X 826 TYR cc_start: 0.8398 (m-80) cc_final: 0.8147 (m-80) REVERT: X 884 THR cc_start: 0.8550 (p) cc_final: 0.8282 (t) REVERT: X 1170 SER cc_start: 0.8738 (p) cc_final: 0.8169 (t) REVERT: X 1223 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8708 (t) REVERT: X 1247 ASP cc_start: 0.8157 (t0) cc_final: 0.7794 (t0) REVERT: X 1353 MET cc_start: 0.8403 (mmt) cc_final: 0.7964 (mmt) REVERT: X 1359 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8104 (mt-10) outliers start: 375 outliers final: 300 residues processed: 1412 average time/residue: 0.6369 time to fit residues: 1556.2153 Evaluate side-chains 1476 residues out of total 7504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1136 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 76 THR Chi-restraints excluded: chain 0 residue 79 ASP Chi-restraints excluded: chain W residue 32 PHE Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 75 CYS Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 202 GLU Chi-restraints excluded: chain W residue 257 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 330 MET Chi-restraints excluded: chain W residue 347 LYS Chi-restraints excluded: chain W residue 377 GLU Chi-restraints excluded: chain W residue 386 THR Chi-restraints excluded: chain W residue 402 PHE Chi-restraints excluded: chain W residue 419 VAL Chi-restraints excluded: chain W residue 462 THR Chi-restraints excluded: chain W residue 502 MET Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 537 HIS Chi-restraints excluded: chain W residue 553 SER Chi-restraints excluded: chain W residue 575 GLN Chi-restraints excluded: chain W residue 596 THR Chi-restraints excluded: chain W residue 614 TYR Chi-restraints excluded: chain W residue 628 VAL Chi-restraints excluded: chain W residue 662 THR Chi-restraints excluded: chain W residue 669 ILE Chi-restraints excluded: chain W residue 687 LEU Chi-restraints excluded: chain W residue 705 ILE Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain W residue 770 LEU Chi-restraints excluded: chain W residue 820 CYS Chi-restraints excluded: chain W residue 822 MET Chi-restraints excluded: chain W residue 853 HIS Chi-restraints excluded: chain W residue 875 ILE Chi-restraints excluded: chain W residue 888 VAL Chi-restraints excluded: chain W residue 899 ASP Chi-restraints excluded: chain W residue 903 SER Chi-restraints excluded: chain W residue 917 VAL Chi-restraints excluded: chain W residue 938 MET Chi-restraints excluded: chain W residue 960 LEU Chi-restraints excluded: chain W residue 965 VAL Chi-restraints excluded: chain W residue 981 SER Chi-restraints excluded: chain W residue 1012 MET Chi-restraints excluded: chain W residue 1043 THR Chi-restraints excluded: chain W residue 1075 SER Chi-restraints excluded: chain W residue 1088 SER Chi-restraints excluded: chain W residue 1091 THR Chi-restraints excluded: chain W residue 1110 ASP Chi-restraints excluded: chain W residue 1113 VAL Chi-restraints excluded: chain W residue 1128 GLN Chi-restraints excluded: chain W residue 1169 LEU Chi-restraints excluded: chain W residue 1234 THR Chi-restraints excluded: chain W residue 1240 SER Chi-restraints excluded: chain W residue 1292 ARG Chi-restraints excluded: chain W residue 1308 VAL Chi-restraints excluded: chain W residue 1309 VAL Chi-restraints excluded: chain W residue 1347 THR Chi-restraints excluded: chain W residue 1348 HIS Chi-restraints excluded: chain W residue 1353 MET Chi-restraints excluded: chain W residue 1364 MET Chi-restraints excluded: chain W residue 1375 VAL Chi-restraints excluded: chain 2 residue 32 ASP Chi-restraints excluded: chain 2 residue 79 ASP Chi-restraints excluded: chain S residue 4 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 213 MET Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain S residue 253 CYS Chi-restraints excluded: chain S residue 281 SER Chi-restraints excluded: chain S residue 378 SER Chi-restraints excluded: chain S residue 382 MET Chi-restraints excluded: chain S residue 404 VAL Chi-restraints excluded: chain S residue 419 VAL Chi-restraints excluded: chain S residue 427 ILE Chi-restraints excluded: chain S residue 453 ILE Chi-restraints excluded: chain S residue 497 PHE Chi-restraints excluded: chain S residue 596 THR Chi-restraints excluded: chain S residue 651 VAL Chi-restraints excluded: chain S residue 652 ASN Chi-restraints excluded: chain S residue 692 LEU Chi-restraints excluded: chain S residue 698 GLU Chi-restraints excluded: chain S residue 699 THR Chi-restraints excluded: chain S residue 742 ILE Chi-restraints excluded: chain S residue 767 VAL Chi-restraints excluded: chain S residue 770 LEU Chi-restraints excluded: chain S residue 798 TYR Chi-restraints excluded: chain S residue 799 ASN Chi-restraints excluded: chain S residue 850 ILE Chi-restraints excluded: chain S residue 868 ILE Chi-restraints excluded: chain S residue 897 LYS Chi-restraints excluded: chain S residue 908 GLU Chi-restraints excluded: chain S residue 922 PHE Chi-restraints excluded: chain S residue 952 LEU Chi-restraints excluded: chain S residue 971 GLN Chi-restraints excluded: chain S residue 1005 THR Chi-restraints excluded: chain S residue 1015 MET Chi-restraints excluded: chain S residue 1039 THR Chi-restraints excluded: chain S residue 1068 VAL Chi-restraints excluded: chain S residue 1079 THR Chi-restraints excluded: chain S residue 1083 THR Chi-restraints excluded: chain S residue 1169 LEU Chi-restraints excluded: chain S residue 1182 THR Chi-restraints excluded: chain S residue 1184 VAL Chi-restraints excluded: chain S residue 1248 VAL Chi-restraints excluded: chain S residue 1303 ASP Chi-restraints excluded: chain S residue 1308 VAL Chi-restraints excluded: chain S residue 1316 LEU Chi-restraints excluded: chain S residue 1336 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 111 GLN Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 211 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 247 ASP Chi-restraints excluded: chain T residue 265 THR Chi-restraints excluded: chain T residue 290 LEU Chi-restraints excluded: chain T residue 295 SER Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 308 VAL Chi-restraints excluded: chain T residue 343 VAL Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain T residue 382 MET Chi-restraints excluded: chain T residue 401 PHE Chi-restraints excluded: chain T residue 402 PHE Chi-restraints excluded: chain T residue 404 VAL Chi-restraints excluded: chain T residue 450 LEU Chi-restraints excluded: chain T residue 453 ILE Chi-restraints excluded: chain T residue 488 THR Chi-restraints excluded: chain T residue 490 ASN Chi-restraints excluded: chain T residue 497 PHE Chi-restraints excluded: chain T residue 498 HIS Chi-restraints excluded: chain T residue 520 THR Chi-restraints excluded: chain T residue 575 GLN Chi-restraints excluded: chain T residue 589 THR Chi-restraints excluded: chain T residue 591 VAL Chi-restraints excluded: chain T residue 593 ASP Chi-restraints excluded: chain T residue 662 THR Chi-restraints excluded: chain T residue 683 GLU Chi-restraints excluded: chain T residue 783 ASP Chi-restraints excluded: chain T residue 790 VAL Chi-restraints excluded: chain T residue 849 ASP Chi-restraints excluded: chain T residue 884 THR Chi-restraints excluded: chain T residue 922 PHE Chi-restraints excluded: chain T residue 947 LEU Chi-restraints excluded: chain T residue 952 LEU Chi-restraints excluded: chain T residue 966 THR Chi-restraints excluded: chain T residue 976 VAL Chi-restraints excluded: chain T residue 1005 THR Chi-restraints excluded: chain T residue 1073 VAL Chi-restraints excluded: chain T residue 1098 VAL Chi-restraints excluded: chain T residue 1109 THR Chi-restraints excluded: chain T residue 1110 ASP Chi-restraints excluded: chain T residue 1113 VAL Chi-restraints excluded: chain T residue 1178 GLU Chi-restraints excluded: chain T residue 1208 ASP Chi-restraints excluded: chain T residue 1238 TRP Chi-restraints excluded: chain T residue 1244 SER Chi-restraints excluded: chain T residue 1248 VAL Chi-restraints excluded: chain T residue 1303 ASP Chi-restraints excluded: chain T residue 1307 VAL Chi-restraints excluded: chain T residue 1314 VAL Chi-restraints excluded: chain T residue 1318 GLN Chi-restraints excluded: chain T residue 1348 HIS Chi-restraints excluded: chain T residue 1358 ILE Chi-restraints excluded: chain T residue 1368 LEU Chi-restraints excluded: chain T residue 1375 VAL Chi-restraints excluded: chain 3 residue 3 ASN Chi-restraints excluded: chain 3 residue 5 LYS Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 28 MET Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain 4 residue 80 PHE Chi-restraints excluded: chain 4 residue 114 TYR Chi-restraints excluded: chain 4 residue 135 ASP Chi-restraints excluded: chain 4 residue 138 LEU Chi-restraints excluded: chain 4 residue 147 LEU Chi-restraints excluded: chain 4 residue 158 THR Chi-restraints excluded: chain 4 residue 161 SER Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 229 ASP Chi-restraints excluded: chain 4 residue 307 VAL Chi-restraints excluded: chain 4 residue 407 HIS Chi-restraints excluded: chain 4 residue 648 LEU Chi-restraints excluded: chain 4 residue 916 THR Chi-restraints excluded: chain 4 residue 947 LEU Chi-restraints excluded: chain 4 residue 976 VAL Chi-restraints excluded: chain 4 residue 1076 ASP Chi-restraints excluded: chain 4 residue 1078 VAL Chi-restraints excluded: chain 4 residue 1093 LEU Chi-restraints excluded: chain 4 residue 1176 THR Chi-restraints excluded: chain 4 residue 1372 ASN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 111 LEU Chi-restraints excluded: chain 5 residue 117 MET Chi-restraints excluded: chain 5 residue 125 THR Chi-restraints excluded: chain 5 residue 152 THR Chi-restraints excluded: chain 5 residue 168 SER Chi-restraints excluded: chain 5 residue 184 VAL Chi-restraints excluded: chain 5 residue 224 VAL Chi-restraints excluded: chain 5 residue 230 LEU Chi-restraints excluded: chain 5 residue 233 LEU Chi-restraints excluded: chain 5 residue 244 THR Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 293 THR Chi-restraints excluded: chain 6 residue 8 VAL Chi-restraints excluded: chain 6 residue 10 ASN Chi-restraints excluded: chain 6 residue 19 GLU Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 215 SER Chi-restraints excluded: chain 6 residue 218 VAL Chi-restraints excluded: chain 6 residue 222 CYS Chi-restraints excluded: chain 6 residue 273 LEU Chi-restraints excluded: chain 6 residue 300 CYS Chi-restraints excluded: chain 7 residue 23 LEU Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 181 VAL Chi-restraints excluded: chain 7 residue 212 CYS Chi-restraints excluded: chain 7 residue 230 VAL Chi-restraints excluded: chain 7 residue 239 GLU Chi-restraints excluded: chain 7 residue 286 LEU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 88 THR Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 150 MET Chi-restraints excluded: chain b residue 152 THR Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 224 VAL Chi-restraints excluded: chain b residue 244 THR Chi-restraints excluded: chain b residue 280 ILE Chi-restraints excluded: chain b residue 312 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 63 MET Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 110 GLN Chi-restraints excluded: chain c residue 126 VAL Chi-restraints excluded: chain c residue 133 ASP Chi-restraints excluded: chain c residue 217 LEU Chi-restraints excluded: chain d residue 4 ASP Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 173 GLU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain d residue 238 THR Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 286 LEU Chi-restraints excluded: chain d residue 295 THR Chi-restraints excluded: chain 1 residue 22 HIS Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 65 MET Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 79 ASP Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 145 THR Chi-restraints excluded: chain X residue 161 SER Chi-restraints excluded: chain X residue 228 LEU Chi-restraints excluded: chain X residue 233 LEU Chi-restraints excluded: chain X residue 249 LEU Chi-restraints excluded: chain X residue 290 LEU Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 342 SER Chi-restraints excluded: chain X residue 367 VAL Chi-restraints excluded: chain X residue 377 GLU Chi-restraints excluded: chain X residue 404 VAL Chi-restraints excluded: chain X residue 419 VAL Chi-restraints excluded: chain X residue 427 ILE Chi-restraints excluded: chain X residue 453 ILE Chi-restraints excluded: chain X residue 497 PHE Chi-restraints excluded: chain X residue 519 THR Chi-restraints excluded: chain X residue 520 THR Chi-restraints excluded: chain X residue 529 HIS Chi-restraints excluded: chain X residue 534 LEU Chi-restraints excluded: chain X residue 560 THR Chi-restraints excluded: chain X residue 577 SER Chi-restraints excluded: chain X residue 589 THR Chi-restraints excluded: chain X residue 591 VAL Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 648 LEU Chi-restraints excluded: chain X residue 651 VAL Chi-restraints excluded: chain X residue 681 LEU Chi-restraints excluded: chain X residue 688 GLU Chi-restraints excluded: chain X residue 699 THR Chi-restraints excluded: chain X residue 708 LEU Chi-restraints excluded: chain X residue 731 MET Chi-restraints excluded: chain X residue 748 ASP Chi-restraints excluded: chain X residue 752 ASN Chi-restraints excluded: chain X residue 755 THR Chi-restraints excluded: chain X residue 767 VAL Chi-restraints excluded: chain X residue 788 LEU Chi-restraints excluded: chain X residue 789 ASP Chi-restraints excluded: chain X residue 799 ASN Chi-restraints excluded: chain X residue 804 LYS Chi-restraints excluded: chain X residue 822 MET Chi-restraints excluded: chain X residue 827 GLN Chi-restraints excluded: chain X residue 850 ILE Chi-restraints excluded: chain X residue 859 LEU Chi-restraints excluded: chain X residue 922 PHE Chi-restraints excluded: chain X residue 953 VAL Chi-restraints excluded: chain X residue 965 VAL Chi-restraints excluded: chain X residue 976 VAL Chi-restraints excluded: chain X residue 979 VAL Chi-restraints excluded: chain X residue 981 SER Chi-restraints excluded: chain X residue 1005 THR Chi-restraints excluded: chain X residue 1068 VAL Chi-restraints excluded: chain X residue 1069 VAL Chi-restraints excluded: chain X residue 1083 THR Chi-restraints excluded: chain X residue 1169 LEU Chi-restraints excluded: chain X residue 1182 THR Chi-restraints excluded: chain X residue 1223 SER Chi-restraints excluded: chain X residue 1248 VAL Chi-restraints excluded: chain X residue 1268 GLN Chi-restraints excluded: chain X residue 1303 ASP Chi-restraints excluded: chain X residue 1308 VAL Chi-restraints excluded: chain X residue 1316 LEU Chi-restraints excluded: chain X residue 1340 GLU Chi-restraints excluded: chain X residue 1359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 546 optimal weight: 9.9990 chunk 732 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 634 optimal weight: 30.0000 chunk 101 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 688 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 707 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 73 HIS ** W 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1114 HIS W1324 GLN ** W1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN S 92 GLN ** S 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 ASN 4 601 GLN ** 4 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 769 ASN 4 816 ASN ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 ASN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 499 GLN ** X 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.124011 restraints weight = 91051.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.122125 restraints weight = 168004.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.122998 restraints weight = 159891.407| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 70367 Z= 0.200 Angle : 0.604 12.919 95624 Z= 0.305 Chirality : 0.044 0.286 10799 Planarity : 0.004 0.074 12423 Dihedral : 5.472 74.602 9578 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 4.10 % Allowed : 18.12 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.09 % Twisted Proline : 0.21 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.09), residues: 8646 helix: -0.56 (0.10), residues: 2948 sheet: -0.45 (0.14), residues: 1286 loop : -1.44 (0.09), residues: 4412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 6 301 HIS 0.012 0.001 HIS W1114 PHE 0.029 0.001 PHE T 497 TYR 0.029 0.001 TYR T 614 ARG 0.010 0.000 ARG X 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22831.40 seconds wall clock time: 395 minutes 33.63 seconds (23733.63 seconds total)