Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 02:28:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppb_20432/10_2023/6ppb_20432.pdb" } resolution = 4.3 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= 0.002 sd= 0.006 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 403 5.16 5 C 39868 2.51 5 N 10896 2.21 5 O 11504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "k ARG 17": "NH1" <-> "NH2" Residue "l ARG 22": "NH1" <-> "NH2" Residue "l ARG 80": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "n ARG 2610": "NH1" <-> "NH2" Residue "o ARG 2610": "NH1" <-> "NH2" 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 TYR 413": "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 "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 "W ARG 106": "NH1" <-> "NH2" Residue "W ARG 702": "NH1" <-> "NH2" Residue "W ARG 753": "NH1" <-> "NH2" Residue "W TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 106": "NH1" <-> "NH2" Residue "X ARG 112": "NH1" <-> "NH2" Residue "X ARG 309": "NH1" <-> "NH2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X ARG 572": "NH1" <-> "NH2" Residue "X ARG 702": "NH1" <-> "NH2" Residue "X ARG 753": "NH1" <-> "NH2" Residue "b ARG 238": "NH1" <-> "NH2" Residue "c TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "d ARG 231": "NH1" <-> "NH2" Residue "d ARG 305": "NH1" <-> "NH2" Residue "5 ARG 66": "NH1" <-> "NH2" Residue "5 ARG 188": "NH1" <-> "NH2" Residue "5 ARG 238": "NH1" <-> "NH2" Residue "7 ARG 267": "NH1" <-> "NH2" Residue "7 ARG 285": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 62671 Number of models: 1 Model: "" Number of chains: 19 Chain: "k" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2680 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 313} Chain breaks: 4 Chain: "l" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 686 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "m" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain breaks: 1 Chain: "n" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 323 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "o" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 323 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} 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: {'PCIS': 1, 'PTRANS': 72, '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: "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: "X" Number of atoms: 10108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1288, 10108 Classifications: {'peptide': 1288} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1214} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "5" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2074 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 250} Chain breaks: 2 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: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2315 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 277} Chain breaks: 2 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: "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: "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: "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} Time building chain proxies: 23.45, per 1000 atoms: 0.37 Number of scatterers: 62671 At special positions: 0 Unit cell: (214.24, 235.87, 209.09, 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 403 16.00 O 11504 8.00 N 10896 7.00 C 39868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS k 365 " - pdb=" SG CYS k 389 " distance=2.03 Simple disulfide: pdb=" SG CYS S 443 " - pdb=" SG CYS T1231 " distance=2.03 Simple disulfide: pdb=" SG CYS S1231 " - pdb=" SG CYS X 443 " 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 Simple disulfide: pdb=" SG CYS 6 212 " - pdb=" SG CYS 7 222 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 222 " - pdb=" SG CYS 7 212 " 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: 17.88 Conformation dependent library (CDL) restraints added in 6.9 seconds 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15086 Finding SS restraints... Secondary structure from input PDB file: 338 helices and 83 sheets defined 40.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'k' and resid 1 through 11 removed outlier: 4.538A pdb=" N ALA k 5 " --> pdb=" O MET k 1 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG k 9 " --> pdb=" O ALA k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 32 removed outlier: 3.776A pdb=" N HIS k 30 " --> pdb=" O THR k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 91 removed outlier: 4.202A pdb=" N GLY k 90 " --> pdb=" O SER k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 118 through 120 No H-bonds generated for 'chain 'k' and resid 118 through 120' Processing helix chain 'k' and resid 278 through 284 removed outlier: 4.166A pdb=" N PHE k 284 " --> pdb=" O PRO k 280 " (cutoff:3.500A) Processing helix chain 'k' and resid 284 through 309 removed outlier: 3.772A pdb=" N ASN k 291 " --> pdb=" O ASP k 287 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR k 292 " --> pdb=" O LEU k 288 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP k 299 " --> pdb=" O CYS k 295 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR k 300 " --> pdb=" O ASP k 296 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG k 306 " --> pdb=" O GLU k 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN k 308 " --> pdb=" O ALA k 304 " (cutoff:3.500A) Processing helix chain 'k' and resid 323 through 344 removed outlier: 3.513A pdb=" N ALA k 327 " --> pdb=" O ASP k 323 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS k 331 " --> pdb=" O ALA k 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE k 334 " --> pdb=" O VAL k 330 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG k 342 " --> pdb=" O CYS k 338 " (cutoff:3.500A) Processing helix chain 'k' and resid 349 through 356 removed outlier: 3.577A pdb=" N ARG k 353 " --> pdb=" O SER k 349 " (cutoff:3.500A) Processing helix chain 'k' and resid 371 through 375 removed outlier: 3.718A pdb=" N GLU k 374 " --> pdb=" O GLY k 371 " (cutoff:3.500A) Processing helix chain 'k' and resid 394 through 401 removed outlier: 4.165A pdb=" N GLU k 398 " --> pdb=" O GLY k 394 " (cutoff:3.500A) Processing helix chain 'k' and resid 402 through 410 removed outlier: 3.685A pdb=" N GLN k 406 " --> pdb=" O GLN k 402 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS k 407 " --> pdb=" O PRO k 403 " (cutoff:3.500A) Processing helix chain 'k' and resid 442 through 453 removed outlier: 3.665A pdb=" N ARG k 452 " --> pdb=" O PHE k 448 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 96 removed outlier: 3.535A pdb=" N MET l 39 " --> pdb=" O HIS l 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL l 45 " --> pdb=" O GLU l 41 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY l 48 " --> pdb=" O ARG l 44 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU l 53 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN l 56 " --> pdb=" O GLN l 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG l 59 " --> pdb=" O ARG l 55 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA l 63 " --> pdb=" O ARG l 59 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU l 66 " --> pdb=" O LYS l 62 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER l 67 " --> pdb=" O ALA l 63 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU l 68 " --> pdb=" O HIS l 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER l 79 " --> pdb=" O GLN l 75 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL l 83 " --> pdb=" O SER l 79 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 102 Processing helix chain 'm' and resid 35 through 53 removed outlier: 3.517A pdb=" N GLU m 41 " --> pdb=" O PRO m 37 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER m 51 " --> pdb=" O LEU m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 104 removed outlier: 3.854A pdb=" N GLU m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU m 70 " --> pdb=" O LEU m 66 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL m 74 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS m 92 " --> pdb=" O ILE m 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN m 93 " --> pdb=" O ASP m 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET m 94 " --> pdb=" O ALA m 90 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY m 96 " --> pdb=" O LYS m 92 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR m 99 " --> pdb=" O ILE m 95 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP m 100 " --> pdb=" O GLY m 96 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER m 101 " --> pdb=" O ASN m 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP m 102 " --> pdb=" O MET m 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE m 104 " --> pdb=" O TRP m 100 " (cutoff:3.500A) Processing helix chain 'n' and resid 2598 through 2634 removed outlier: 3.617A pdb=" N ILE n2606 " --> pdb=" O LYS n2602 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER n2607 " --> pdb=" O ILE n2603 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE n2609 " --> pdb=" O LEU n2605 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS n2615 " --> pdb=" O ARG n2611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA n2618 " --> pdb=" O GLN n2614 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU n2619 " --> pdb=" O LYS n2615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER n2620 " --> pdb=" O VAL n2616 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU n2625 " --> pdb=" O ALA n2621 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP n2628 " --> pdb=" O ALA n2624 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS n2632 " --> pdb=" O ASP n2628 " (cutoff:3.500A) Processing helix chain 'o' and resid 2598 through 2634 removed outlier: 3.618A pdb=" N ILE o2606 " --> pdb=" O LYS o2602 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER o2607 " --> pdb=" O ILE o2603 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE o2609 " --> pdb=" O LEU o2605 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS o2615 " --> pdb=" O ARG o2611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA o2618 " --> pdb=" O GLN o2614 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU o2619 " --> pdb=" O LYS o2615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER o2620 " --> pdb=" O VAL o2616 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU o2625 " --> pdb=" O ALA o2621 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP o2628 " --> pdb=" O ALA o2624 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS o2632 " --> pdb=" O ASP o2628 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 43 removed outlier: 3.540A pdb=" N ASP S 42 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 75 removed outlier: 5.882A pdb=" N ALA S 70 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU S 71 " --> pdb=" O GLU S 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 137 Processing helix chain 'S' and resid 152 through 183 removed outlier: 3.956A pdb=" N THR S 158 " --> pdb=" O GLY S 154 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER S 161 " --> pdb=" O LYS S 157 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN S 164 " --> pdb=" O THR S 160 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE S 165 " --> pdb=" O SER S 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL S 175 " --> pdb=" O GLU S 171 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL S 181 " --> pdb=" O THR S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 197 removed outlier: 4.680A pdb=" N THR S 194 " --> pdb=" O PHE S 190 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 195 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP S 197 " --> pdb=" O LYS S 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 224 removed outlier: 4.022A pdb=" N SER S 211 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP S 212 " --> pdb=" O ALA S 208 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET S 216 " --> pdb=" O ASP S 212 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE S 217 " --> pdb=" O MET S 213 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA S 219 " --> pdb=" O SER S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 Processing helix chain 'S' and resid 237 through 250 removed outlier: 3.555A pdb=" N SER S 246 " --> pdb=" O LEU S 242 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP S 247 " --> pdb=" O THR S 243 " (cutoff:3.500A) Processing helix chain 'S' and resid 279 through 287 removed outlier: 4.671A pdb=" N ARG S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.691A pdb=" N GLU S 385 " --> pdb=" O ARG S 381 " (cutoff:3.500A) Processing helix chain 'S' and resid 447 through 452 removed outlier: 3.517A pdb=" N LEU S 450 " --> pdb=" O GLN S 447 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS S 451 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER S 452 " --> pdb=" O ALA S 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 447 through 452' Processing helix chain 'S' and resid 466 through 472 Processing helix chain 'S' and resid 492 through 499 Processing helix chain 'S' and resid 512 through 516 removed outlier: 3.647A pdb=" N ALA S 516 " --> pdb=" O ALA S 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 586 removed outlier: 3.661A pdb=" N GLU S 576 " --> pdb=" O ARG S 572 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN S 581 " --> pdb=" O SER S 577 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA S 584 " --> pdb=" O ALA S 580 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR S 586 " --> pdb=" O PHE S 582 " (cutoff:3.500A) Processing helix chain 'S' and resid 593 through 605 removed outlier: 3.539A pdb=" N ILE S 597 " --> pdb=" O ASP S 593 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL S 599 " --> pdb=" O LEU S 595 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU S 602 " --> pdb=" O ASP S 598 " (cutoff:3.500A) Processing helix chain 'S' and resid 611 through 621 removed outlier: 3.699A pdb=" N VAL S 615 " --> pdb=" O LEU S 611 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU S 617 " --> pdb=" O CYS S 613 " (cutoff:3.500A) Processing helix chain 'S' and resid 623 through 629 removed outlier: 3.794A pdb=" N VAL S 628 " --> pdb=" O GLU S 624 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET S 629 " --> pdb=" O GLU S 625 " (cutoff:3.500A) Processing helix chain 'S' and resid 633 through 638 removed outlier: 3.566A pdb=" N VAL S 637 " --> pdb=" O LEU S 633 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE S 638 " --> pdb=" O ILE S 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 633 through 638' Processing helix chain 'S' and resid 638 through 643 Processing helix chain 'S' and resid 653 through 664 removed outlier: 3.770A pdb=" N PHE S 659 " --> pdb=" O HIS S 655 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET S 664 " --> pdb=" O ILE S 660 " (cutoff:3.500A) Processing helix chain 'S' and resid 670 through 695 removed outlier: 3.549A pdb=" N GLY S 675 " --> pdb=" O LYS S 671 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS S 676 " --> pdb=" O GLU S 672 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR S 677 " --> pdb=" O ALA S 673 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE S 680 " --> pdb=" O HIS S 676 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU S 681 " --> pdb=" O TYR S 677 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU S 683 " --> pdb=" O LYS S 679 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE S 685 " --> pdb=" O LEU S 681 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA S 686 " --> pdb=" O GLY S 682 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA S 690 " --> pdb=" O ALA S 686 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU S 692 " --> pdb=" O GLU S 688 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS S 693 " --> pdb=" O GLN S 689 " (cutoff:3.500A) Processing helix chain 'S' and resid 705 through 710 removed outlier: 4.779A pdb=" N SER S 710 " --> pdb=" O THR S 706 " (cutoff:3.500A) Processing helix chain 'S' and resid 726 through 732 removed outlier: 3.527A pdb=" N MET S 731 " --> pdb=" O PHE S 727 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN S 732 " --> pdb=" O THR S 728 " (cutoff:3.500A) Processing helix chain 'S' and resid 749 through 755 removed outlier: 4.769A pdb=" N ALA S 754 " --> pdb=" O GLN S 751 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR S 755 " --> pdb=" O ASN S 752 " (cutoff:3.500A) Processing helix chain 'S' and resid 770 through 780 removed outlier: 3.613A pdb=" N TYR S 774 " --> pdb=" O LEU S 770 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 776 " --> pdb=" O ASN S 772 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG S 777 " --> pdb=" O ILE S 773 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL S 778 " --> pdb=" O TYR S 774 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN S 779 " --> pdb=" O GLN S 775 " (cutoff:3.500A) Processing helix chain 'S' and resid 781 through 785 removed outlier: 3.952A pdb=" N ARG S 785 " --> pdb=" O HIS S 782 " (cutoff:3.500A) Processing helix chain 'S' and resid 799 through 808 removed outlier: 3.739A pdb=" N PHE S 806 " --> pdb=" O LEU S 802 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR S 807 " --> pdb=" O GLU S 803 " (cutoff:3.500A) Processing helix chain 'S' and resid 810 through 815 Processing helix chain 'S' and resid 825 through 835 removed outlier: 3.727A pdb=" N ALA S 830 " --> pdb=" O TYR S 826 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU S 831 " --> pdb=" O GLN S 827 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR S 832 " --> pdb=" O ASN S 828 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU S 833 " --> pdb=" O VAL S 829 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR S 835 " --> pdb=" O LEU S 831 " (cutoff:3.500A) Processing helix chain 'S' and resid 858 through 866 removed outlier: 3.634A pdb=" N GLN S 864 " --> pdb=" O LYS S 860 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY S 866 " --> pdb=" O ILE S 862 " (cutoff:3.500A) Processing helix chain 'S' and resid 871 through 880 removed outlier: 3.608A pdb=" N ILE S 875 " --> pdb=" O THR S 871 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG S 876 " --> pdb=" O VAL S 872 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL S 877 " --> pdb=" O ASP S 873 " (cutoff:3.500A) removed outlier: 3.656A 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 908 through 910 No H-bonds generated for 'chain 'S' and resid 908 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 removed outlier: 3.568A pdb=" N GLU S 936 " --> pdb=" O ARG S 932 " (cutoff:3.500A) Processing helix chain 'S' and resid 950 through 958 removed outlier: 4.618A pdb=" N THR S 956 " --> pdb=" O LEU S 952 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU S 957 " --> pdb=" O VAL S 953 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS S 958 " --> pdb=" O ALA S 954 " (cutoff:3.500A) Processing helix chain 'S' and resid 958 through 968 removed outlier: 3.647A pdb=" N ALA S 962 " --> pdb=" O HIS S 958 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU S 968 " --> pdb=" O TYR S 964 " (cutoff:3.500A) Processing helix chain 'S' and resid 993 through 1000 removed outlier: 3.614A pdb=" N ALA S 997 " --> pdb=" O SER S 993 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR S 998 " --> pdb=" O PRO S 994 " (cutoff:3.500A) Processing helix chain 'S' and resid 1005 through 1016 removed outlier: 4.093A pdb=" N SER S1010 " --> pdb=" O PRO S1006 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET S1012 " --> pdb=" O ALA S1008 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS S1016 " --> pdb=" O MET S1012 " (cutoff:3.500A) Processing helix chain 'S' and resid 1023 through 1030 removed outlier: 4.072A pdb=" N HIS S1030 " --> pdb=" O CYS S1026 " (cutoff:3.500A) Processing helix chain 'S' and resid 1117 through 1121 Processing helix chain 'S' and resid 1129 through 1137 Processing helix chain 'S' and resid 1187 through 1192 removed outlier: 3.626A pdb=" N GLN S1192 " --> pdb=" O ALA S1189 " (cutoff:3.500A) Processing helix chain 'S' and resid 1211 through 1220 removed outlier: 3.674A pdb=" N GLU S1216 " --> pdb=" O ASN S1212 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG S1217 " --> pdb=" O GLU S1213 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU S1218 " --> pdb=" O SER S1214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU S1219 " --> pdb=" O ALA S1215 " (cutoff:3.500A) Processing helix chain 'S' and resid 1244 through 1248 removed outlier: 3.637A pdb=" N VAL S1248 " --> pdb=" O LEU S1245 " (cutoff:3.500A) Processing helix chain 'S' and resid 1266 through 1271 removed outlier: 3.980A pdb=" N PHE S1270 " --> pdb=" O CYS S1266 " (cutoff:3.500A) removed outlier: 3.755A 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 1275 through 1280 removed outlier: 3.678A pdb=" N ASN S1279 " --> pdb=" O MET S1276 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG S1280 " --> pdb=" O ARG S1277 " (cutoff:3.500A) Processing helix chain 'S' and resid 1282 through 1290 removed outlier: 3.793A pdb=" N GLU S1288 " --> pdb=" O THR S1284 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER S1290 " --> pdb=" O VAL S1286 " (cutoff:3.500A) Processing helix chain 'S' and resid 1334 through 1342 removed outlier: 3.891A pdb=" N LEU S1338 " --> pdb=" O HIS S1334 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 39 through 44 removed outlier: 3.717A pdb=" N ALA T 43 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG T 44 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 73 removed outlier: 3.547A 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 183 removed outlier: 3.646A pdb=" N PHE T 149 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR T 150 " --> pdb=" O PRO T 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS T 157 " --> pdb=" O ALA T 153 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR T 158 " --> pdb=" O GLY T 154 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA T 169 " --> pdb=" O PHE T 165 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU T 170 " --> pdb=" O GLY T 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY T 173 " --> pdb=" O ALA T 169 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL T 175 " --> pdb=" O GLU T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 196 removed outlier: 5.159A pdb=" N THR T 194 " --> pdb=" O PHE T 190 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU T 195 " --> pdb=" O ILE T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 224 removed outlier: 3.902A pdb=" N SER T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET T 216 " --> pdb=" O ASP T 212 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU T 223 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 232 removed outlier: 3.801A pdb=" N GLU T 232 " --> pdb=" O ASP T 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 252 removed outlier: 3.546A pdb=" N VAL T 241 " --> pdb=" O GLY T 237 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL T 252 " --> pdb=" O MET T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 260 removed outlier: 4.491A pdb=" N GLY T 260 " --> pdb=" O VAL T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 270 No H-bonds generated for 'chain 'T' and resid 268 through 270' Processing helix chain 'T' and resid 279 through 290 removed outlier: 4.264A pdb=" N ARG T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN T 288 " --> pdb=" O ARG T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 318 removed outlier: 3.870A pdb=" N THR T 315 " --> pdb=" O ALA T 311 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 334 removed outlier: 3.545A pdb=" N ARG T 332 " --> pdb=" O GLN T 328 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE T 333 " --> pdb=" O PHE T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 347 removed outlier: 3.503A pdb=" N LYS T 347 " --> pdb=" O VAL T 343 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 350 No H-bonds generated for 'chain 'T' and resid 348 through 350' Processing helix chain 'T' and resid 445 through 454 removed outlier: 3.991A pdb=" N ALA T 449 " --> pdb=" O GLY T 445 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS T 451 " --> pdb=" O GLN T 447 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER T 452 " --> pdb=" O ASN T 448 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE T 453 " --> pdb=" O ALA T 449 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 459 Processing helix chain 'T' and resid 461 through 472 removed outlier: 3.585A pdb=" N PHE T 472 " --> pdb=" O LEU T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 492 through 498 removed outlier: 3.500A pdb=" N PHE T 497 " --> pdb=" O LEU T 493 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 518 removed outlier: 3.501A pdb=" N LYS T 515 " --> pdb=" O ASP T 511 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU T 517 " --> pdb=" O ALA T 513 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL T 518 " --> pdb=" O GLN T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 519 through 524 removed outlier: 3.851A pdb=" N LEU T 524 " --> pdb=" O THR T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 561 through 565 removed outlier: 3.542A pdb=" N ASN T 564 " --> pdb=" O MET T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 571 through 586 removed outlier: 3.537A pdb=" N VAL T 585 " --> pdb=" O GLN T 581 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR T 586 " --> pdb=" O PHE T 582 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 605 removed outlier: 4.480A pdb=" N VAL T 599 " --> pdb=" O LEU T 595 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU T 602 " --> pdb=" O ASP T 598 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR T 603 " --> pdb=" O VAL T 599 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA T 604 " --> pdb=" O ILE T 600 " (cutoff:3.500A) Processing helix chain 'T' and resid 610 through 621 removed outlier: 3.939A pdb=" N TYR T 614 " --> pdb=" O PRO T 610 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA T 618 " --> pdb=" O TYR T 614 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET T 619 " --> pdb=" O VAL T 615 " (cutoff:3.500A) Processing helix chain 'T' and resid 624 through 630 removed outlier: 3.672A pdb=" N ASN T 630 " --> pdb=" O LYS T 626 " (cutoff:3.500A) Processing helix chain 'T' and resid 630 through 643 removed outlier: 3.855A pdb=" N ALA T 635 " --> pdb=" O MET T 631 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 636 " --> pdb=" O PRO T 632 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR T 640 " --> pdb=" O LEU T 636 " (cutoff:3.500A) Processing helix chain 'T' and resid 653 through 663 removed outlier: 3.760A pdb=" N PHE T 659 " --> pdb=" O HIS T 655 " (cutoff:3.500A) Processing helix chain 'T' and resid 670 through 695 removed outlier: 4.383A pdb=" N HIS T 676 " --> pdb=" O GLU T 672 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR T 677 " --> pdb=" O ALA T 673 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG T 678 " --> pdb=" O HIS T 674 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS T 679 " --> pdb=" O GLY T 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA T 686 " --> pdb=" O GLY T 682 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU T 691 " --> pdb=" O LEU T 687 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU T 692 " --> pdb=" O GLU T 688 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS T 693 " --> pdb=" O GLN T 689 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU T 694 " --> pdb=" O ALA T 690 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA T 695 " --> pdb=" O LEU T 691 " (cutoff:3.500A) Processing helix chain 'T' and resid 704 through 708 Processing helix chain 'T' and resid 725 through 734 removed outlier: 4.050A pdb=" N ASP T 729 " --> pdb=" O ASP T 725 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS T 733 " --> pdb=" O ASP T 729 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER T 734 " --> pdb=" O LEU T 730 " (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: 3.631A 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 769 through 776 removed outlier: 3.784A pdb=" N TYR T 774 " --> pdb=" O LEU T 770 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN T 775 " --> pdb=" O VAL T 771 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR T 776 " --> pdb=" O ASN T 772 " (cutoff:3.500A) Processing helix chain 'T' and resid 799 through 808 removed outlier: 3.748A pdb=" N GLU T 803 " --> pdb=" O ASN T 799 " (cutoff:3.500A) Processing helix chain 'T' and resid 809 through 815 removed outlier: 3.686A pdb=" N VAL T 813 " --> pdb=" O VAL T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 825 through 836 removed outlier: 3.585A pdb=" N VAL T 829 " --> pdb=" O ASP T 825 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU T 831 " --> pdb=" O GLN T 827 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR T 832 " --> pdb=" O ASN T 828 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU T 833 " --> pdb=" O VAL T 829 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR T 835 " --> pdb=" O LEU T 831 " (cutoff:3.500A) Processing helix chain 'T' and resid 836 through 841 removed outlier: 3.508A pdb=" N PHE T 840 " --> pdb=" O ASN T 836 " (cutoff:3.500A) Processing helix chain 'T' and resid 849 through 853 removed outlier: 3.711A pdb=" N LEU T 852 " --> pdb=" O ASP T 849 " (cutoff:3.500A) Processing helix chain 'T' and resid 857 through 865 removed outlier: 4.331A pdb=" N ASP T 861 " --> pdb=" O GLY T 857 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU T 863 " --> pdb=" O LEU T 859 " (cutoff:3.500A) Processing helix chain 'T' and resid 871 through 881 removed outlier: 3.554A pdb=" N VAL T 877 " --> pdb=" O ASP T 873 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU T 878 " --> pdb=" O MET T 874 " (cutoff:3.500A) Processing helix chain 'T' and resid 882 through 885 removed outlier: 3.506A 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 899 through 903 removed outlier: 3.716A pdb=" N SER T 903 " --> pdb=" O PRO T 900 " (cutoff:3.500A) Processing helix chain 'T' and resid 932 through 937 removed outlier: 4.163A pdb=" N THR T 937 " --> pdb=" O GLU T 933 " (cutoff:3.500A) Processing helix chain 'T' and resid 950 through 958 removed outlier: 4.331A pdb=" N THR T 956 " --> pdb=" O LEU T 952 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU T 957 " --> pdb=" O VAL T 953 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.834A pdb=" N GLN T 971 " --> pdb=" O LEU T 968 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN T 973 " --> pdb=" O ASN T 970 " (cutoff:3.500A) Processing helix chain 'T' and resid 992 through 1001 removed outlier: 4.467A pdb=" N ALA T 996 " --> pdb=" O LYS T 992 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 997 " --> pdb=" O SER T 993 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER T1001 " --> pdb=" O ALA T 997 " (cutoff:3.500A) Processing helix chain 'T' and resid 1005 through 1016 removed outlier: 3.552A pdb=" N SER T1010 " --> pdb=" O PRO T1006 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA T1011 " --> pdb=" O GLY T1007 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET T1012 " --> pdb=" O ALA T1008 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL T1013 " --> pdb=" O ILE T1009 " (cutoff:3.500A) Processing helix chain 'T' and resid 1023 through 1030 removed outlier: 3.720A pdb=" N GLN T1027 " --> pdb=" O SER T1023 " (cutoff:3.500A) Processing helix chain 'T' and resid 1117 through 1122 removed outlier: 3.581A 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 Processing helix chain 'T' and resid 1211 through 1221 removed outlier: 4.127A pdb=" N LEU T1218 " --> pdb=" O SER T1214 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU T1219 " --> pdb=" O ALA T1215 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP T1221 " --> pdb=" O ARG T1217 " (cutoff:3.500A) Processing helix chain 'T' and resid 1244 through 1250 Processing helix chain 'T' and resid 1265 through 1271 removed outlier: 4.462A pdb=" N PHE T1269 " --> pdb=" O PRO T1265 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE T1270 " --> pdb=" O CYS T1266 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS T1271 " --> pdb=" O ARG T1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1265 through 1271' Processing helix chain 'T' and resid 1271 through 1276 removed outlier: 3.620A pdb=" N ILE T1275 " --> pdb=" O HIS T1271 " (cutoff:3.500A) Processing helix chain 'T' and resid 1277 through 1280 removed outlier: 4.187A pdb=" N ARG T1280 " --> pdb=" O ARG T1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1277 through 1280' Processing helix chain 'T' and resid 1281 through 1290 removed outlier: 3.594A pdb=" N ASN T1287 " --> pdb=" O TYR T1283 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER T1290 " --> pdb=" O VAL T1286 " (cutoff:3.500A) Processing helix chain 'T' and resid 1319 through 1324 removed outlier: 3.571A pdb=" N LEU T1323 " --> pdb=" O PRO T1319 " (cutoff:3.500A) Processing helix chain 'T' and resid 1334 through 1344 removed outlier: 4.045A pdb=" N LEU T1338 " --> pdb=" O HIS T1334 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP T1339 " --> pdb=" O ARG T1335 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU T1340 " --> pdb=" O VAL T1336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR T1341 " --> pdb=" O MET T1337 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET T1342 " --> pdb=" O LEU T1338 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 29 removed outlier: 4.061A pdb=" N ALA W 28 " --> pdb=" O LYS W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 73 removed outlier: 3.538A pdb=" N ALA W 72 " --> pdb=" O THR W 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA W 73 " --> pdb=" O ALA W 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 69 through 73' Processing helix chain 'W' and resid 133 through 138 Processing helix chain 'W' and resid 145 through 169 removed outlier: 4.231A pdb=" N THR W 150 " --> pdb=" O PRO W 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS W 157 " --> pdb=" O ALA W 153 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR W 158 " --> pdb=" O GLY W 154 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE W 165 " --> pdb=" O SER W 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 185 removed outlier: 3.670A pdb=" N VAL W 175 " --> pdb=" O GLU W 171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU W 179 " --> pdb=" O VAL W 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG W 184 " --> pdb=" O ALA W 180 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS W 185 " --> pdb=" O VAL W 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 197 removed outlier: 4.755A pdb=" N THR W 194 " --> pdb=" O PHE W 190 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU W 195 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP W 197 " --> pdb=" O LYS W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 225 removed outlier: 3.732A pdb=" N SER W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER W 215 " --> pdb=" O SER W 211 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET W 216 " --> pdb=" O ASP W 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU W 221 " --> pdb=" O PHE W 217 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER W 225 " --> pdb=" O LEU W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 231 removed outlier: 3.574A pdb=" N ALA W 231 " --> pdb=" O PHE W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 250 Processing helix chain 'W' and resid 256 through 260 removed outlier: 4.479A pdb=" N GLY W 260 " --> pdb=" O VAL W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 270 removed outlier: 3.888A pdb=" N GLY W 269 " --> pdb=" O THR W 266 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.623A pdb=" N ARG W 284 " --> pdb=" O ASP W 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG W 285 " --> pdb=" O SER W 281 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 318 removed outlier: 3.524A pdb=" N THR W 315 " --> pdb=" O ALA W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 334 removed outlier: 3.693A pdb=" N ALA W 331 " --> pdb=" O GLU W 327 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG W 332 " --> pdb=" O GLN W 328 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE W 333 " --> pdb=" O PHE W 329 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 351 removed outlier: 4.751A pdb=" N ALA W 348 " --> pdb=" O GLU W 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA W 349 " --> pdb=" O GLY W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.567A pdb=" N GLU W 385 " --> pdb=" O ARG W 381 " (cutoff:3.500A) Processing helix chain 'W' and resid 445 through 450 removed outlier: 3.809A pdb=" N ALA W 449 " --> pdb=" O GLY W 445 " (cutoff:3.500A) Processing helix chain 'W' and resid 451 through 453 No H-bonds generated for 'chain 'W' and resid 451 through 453' Processing helix chain 'W' and resid 455 through 460 removed outlier: 4.063A pdb=" N ASN W 460 " --> pdb=" O ARG W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 461 through 472 Processing helix chain 'W' and resid 492 through 502 removed outlier: 3.704A pdb=" N THR W 496 " --> pdb=" O ASN W 492 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN W 499 " --> pdb=" O ARG W 495 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR W 500 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR W 501 " --> pdb=" O PHE W 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 510 through 516 removed outlier: 3.744A pdb=" N GLN W 514 " --> pdb=" O PRO W 510 " (cutoff:3.500A) Processing helix chain 'W' and resid 519 through 525 removed outlier: 3.558A pdb=" N LEU W 524 " --> pdb=" O THR W 520 " (cutoff:3.500A) Processing helix chain 'W' and resid 561 through 565 Processing helix chain 'W' and resid 571 through 587 removed outlier: 3.707A pdb=" N VAL W 585 " --> pdb=" O GLN W 581 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR W 586 " --> pdb=" O PHE W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 593 through 605 removed outlier: 3.748A pdb=" N ILE W 597 " --> pdb=" O ASP W 593 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP W 598 " --> pdb=" O GLN W 594 " (cutoff:3.500A) Processing helix chain 'W' and resid 610 through 621 removed outlier: 3.838A pdb=" N TYR W 614 " --> pdb=" O PRO W 610 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA W 618 " --> pdb=" O TYR W 614 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS W 621 " --> pdb=" O GLU W 617 " (cutoff:3.500A) Processing helix chain 'W' and resid 623 through 628 Processing helix chain 'W' and resid 632 through 645 removed outlier: 3.782A pdb=" N ILE W 638 " --> pdb=" O ILE W 634 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL W 643 " --> pdb=" O GLN W 639 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN W 644 " --> pdb=" O THR W 640 " (cutoff:3.500A) Processing helix chain 'W' and resid 653 through 663 removed outlier: 3.605A pdb=" N VAL W 657 " --> pdb=" O SER W 653 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS W 661 " --> pdb=" O VAL W 657 " (cutoff:3.500A) Processing helix chain 'W' and resid 670 through 695 removed outlier: 3.550A pdb=" N GLY W 675 " --> pdb=" O LYS W 671 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS W 676 " --> pdb=" O GLU W 672 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR W 677 " --> pdb=" O ALA W 673 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU W 681 " --> pdb=" O TYR W 677 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA W 686 " --> pdb=" O GLY W 682 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU W 688 " --> pdb=" O LEU W 684 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN W 689 " --> pdb=" O ILE W 685 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA W 690 " --> pdb=" O ALA W 686 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS W 693 " --> pdb=" O GLN W 689 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU W 694 " --> pdb=" O ALA W 690 " (cutoff:3.500A) Processing helix chain 'W' and resid 705 through 710 removed outlier: 4.593A pdb=" N SER W 710 " --> pdb=" O THR W 706 " (cutoff:3.500A) Processing helix chain 'W' and resid 726 through 734 removed outlier: 3.540A pdb=" N MET W 731 " --> pdb=" O PHE W 727 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN W 732 " --> pdb=" O THR W 728 " (cutoff:3.500A) Processing helix chain 'W' and resid 749 through 753 Processing helix chain 'W' and resid 769 through 779 removed outlier: 3.793A pdb=" N ILE W 773 " --> pdb=" O ASN W 769 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR W 774 " --> pdb=" O LEU W 770 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR W 776 " --> pdb=" O ASN W 772 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG W 777 " --> pdb=" O ILE W 773 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL W 778 " --> pdb=" O TYR W 774 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN W 779 " --> pdb=" O GLN W 775 " (cutoff:3.500A) Processing helix chain 'W' and resid 799 through 809 removed outlier: 3.523A pdb=" N GLU W 803 " --> pdb=" O ASN W 799 " (cutoff:3.500A) Processing helix chain 'W' and resid 809 through 815 removed outlier: 3.651A pdb=" N VAL W 813 " --> pdb=" O VAL W 809 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 834 removed outlier: 3.522A pdb=" N VAL W 829 " --> pdb=" O ASP W 825 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA W 830 " --> pdb=" O TYR W 826 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU W 831 " --> pdb=" O GLN W 827 " (cutoff:3.500A) Processing helix chain 'W' and resid 836 through 840 removed outlier: 3.695A 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 857 through 864 removed outlier: 4.073A pdb=" N ASP W 861 " --> pdb=" O GLY W 857 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE W 862 " --> pdb=" O THR W 858 " (cutoff:3.500A) Processing helix chain 'W' and resid 871 through 879 removed outlier: 3.630A pdb=" N ILE W 875 " --> pdb=" O THR W 871 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU W 878 " --> pdb=" O MET W 874 " (cutoff:3.500A) Processing helix chain 'W' and resid 880 through 885 removed outlier: 3.659A pdb=" N THR W 884 " --> pdb=" O SER W 881 " (cutoff:3.500A) Processing helix chain 'W' and resid 899 through 903 removed outlier: 3.977A pdb=" N SER W 903 " --> pdb=" O PRO W 900 " (cutoff:3.500A) Processing helix chain 'W' and resid 907 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: 4.122A pdb=" N THR W 956 " --> pdb=" O LEU W 952 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU W 957 " --> pdb=" O VAL W 953 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS W 958 " --> pdb=" O ALA W 954 " (cutoff:3.500A) Processing helix chain 'W' and resid 958 through 968 removed outlier: 3.992A pdb=" N TYR W 964 " --> pdb=" O LEU W 960 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR W 966 " --> pdb=" O ALA W 962 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU W 968 " --> pdb=" O TYR W 964 " (cutoff:3.500A) Processing helix chain 'W' and resid 969 through 972 Processing helix chain 'W' and resid 992 through 1001 removed outlier: 4.359A pdb=" N ALA W 996 " --> pdb=" O LYS W 992 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER W1001 " --> pdb=" O ALA W 997 " (cutoff:3.500A) Processing helix chain 'W' and resid 1006 through 1016 removed outlier: 3.592A pdb=" N SER W1010 " --> pdb=" O PRO W1006 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET W1012 " --> pdb=" O ALA W1008 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS W1016 " --> pdb=" O MET W1012 " (cutoff:3.500A) Processing helix chain 'W' and resid 1020 through 1031 removed outlier: 3.566A pdb=" N PHE W1024 " --> pdb=" O SER W1020 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE W1025 " --> pdb=" O ALA W1021 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS W1026 " --> pdb=" O PRO W1022 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS W1030 " --> pdb=" O CYS W1026 " (cutoff:3.500A) Processing helix chain 'W' and resid 1117 through 1122 removed outlier: 3.915A pdb=" N ILE W1121 " --> pdb=" O ASP W1117 " (cutoff:3.500A) Processing helix chain 'W' and resid 1129 through 1137 removed outlier: 3.659A pdb=" N ASP W1134 " --> pdb=" O ARG W1130 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR W1135 " --> pdb=" O GLN W1131 " (cutoff:3.500A) Processing helix chain 'W' and resid 1187 through 1191 Processing helix chain 'W' and resid 1211 through 1221 removed outlier: 3.503A pdb=" N GLU W1216 " --> pdb=" O ASN W1212 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU W1219 " --> pdb=" O ALA W1215 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP W1221 " --> pdb=" O ARG W1217 " (cutoff:3.500A) Processing helix chain 'W' and resid 1244 through 1251 removed outlier: 3.665A pdb=" N ASN W1251 " --> pdb=" O ASP W1247 " (cutoff:3.500A) Processing helix chain 'W' and resid 1264 through 1269 removed outlier: 3.520A pdb=" N ARG W1267 " --> pdb=" O SER W1264 " (cutoff:3.500A) Processing helix chain 'W' and resid 1271 through 1276 removed outlier: 3.738A pdb=" N ILE W1275 " --> pdb=" O HIS W1271 " (cutoff:3.500A) Processing helix chain 'W' and resid 1277 through 1280 removed outlier: 4.164A pdb=" N ARG W1280 " --> pdb=" O ARG W1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 1277 through 1280' Processing helix chain 'W' and resid 1281 through 1292 removed outlier: 4.019A pdb=" N SER W1290 " --> pdb=" O VAL W1286 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA W1291 " --> pdb=" O ASN W1287 " (cutoff:3.500A) Processing helix chain 'W' and resid 1334 through 1344 removed outlier: 4.402A pdb=" N LEU W1338 " --> pdb=" O HIS W1334 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP W1339 " --> pdb=" O ARG W1335 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN W1344 " --> pdb=" O GLU W1340 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 73 removed outlier: 3.784A pdb=" N ALA X 73 " --> pdb=" O ALA X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 84 No H-bonds generated for 'chain 'X' and resid 82 through 84' Processing helix chain 'X' and resid 133 through 138 removed outlier: 3.739A pdb=" N LEU X 138 " --> pdb=" O ALA X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 185 removed outlier: 3.639A pdb=" N GLY X 154 " --> pdb=" O THR X 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE X 156 " --> pdb=" O TYR X 152 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS X 157 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR X 158 " --> pdb=" O GLY X 154 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER X 161 " --> pdb=" O LYS X 157 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA X 169 " --> pdb=" O PHE X 165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU X 170 " --> pdb=" O GLY X 166 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU X 171 " --> pdb=" O MET X 167 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL X 175 " --> pdb=" O GLU X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 197 removed outlier: 5.158A pdb=" N THR X 194 " --> pdb=" O PHE X 190 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU X 195 " --> pdb=" O ILE X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 224 removed outlier: 3.890A pdb=" N SER X 211 " --> pdb=" O LYS X 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP X 212 " --> pdb=" O ALA X 208 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE X 217 " --> pdb=" O MET X 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA X 219 " --> pdb=" O SER X 215 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU X 223 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 231 Processing helix chain 'X' and resid 237 through 249 removed outlier: 4.026A pdb=" N ASP X 247 " --> pdb=" O THR X 243 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 260 removed outlier: 4.327A pdb=" N GLY X 260 " --> pdb=" O VAL X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 279 through 290 removed outlier: 4.239A pdb=" N ARG X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN X 288 " --> pdb=" O ARG X 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 309 through 318 removed outlier: 3.507A pdb=" N VAL X 314 " --> pdb=" O GLY X 310 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 334 removed outlier: 3.512A pdb=" N PHE X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG X 332 " --> pdb=" O GLN X 328 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL X 334 " --> pdb=" O MET X 330 " (cutoff:3.500A) Processing helix chain 'X' and resid 343 through 351 removed outlier: 4.154A pdb=" N ALA X 348 " --> pdb=" O GLU X 344 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA X 349 " --> pdb=" O GLY X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 379 through 384 removed outlier: 3.774A pdb=" N TYR X 383 " --> pdb=" O LEU X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 445 through 449 Processing helix chain 'X' and resid 455 through 459 Processing helix chain 'X' and resid 492 through 501 removed outlier: 3.834A pdb=" N TYR X 500 " --> pdb=" O THR X 496 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR X 501 " --> pdb=" O PHE X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 534 removed outlier: 3.896A pdb=" N LEU X 534 " --> pdb=" O ARG X 530 " (cutoff:3.500A) Processing helix chain 'X' and resid 571 through 587 removed outlier: 3.516A pdb=" N ALA X 584 " --> pdb=" O ALA X 580 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL X 585 " --> pdb=" O GLN X 581 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR X 586 " --> pdb=" O PHE X 582 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 605 removed outlier: 3.767A pdb=" N ILE X 597 " --> pdb=" O ASP X 593 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU X 602 " --> pdb=" O ASP X 598 " (cutoff:3.500A) Processing helix chain 'X' and resid 611 through 621 Processing helix chain 'X' and resid 623 through 630 removed outlier: 3.525A pdb=" N VAL X 628 " --> pdb=" O GLU X 624 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN X 630 " --> pdb=" O LYS X 626 " (cutoff:3.500A) Processing helix chain 'X' and resid 630 through 642 removed outlier: 3.608A pdb=" N ALA X 635 " --> pdb=" O MET X 631 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU X 636 " --> pdb=" O PRO X 632 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN X 639 " --> pdb=" O ALA X 635 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 664 removed outlier: 4.599A pdb=" N PHE X 659 " --> pdb=" O HIS X 655 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS X 663 " --> pdb=" O PHE X 659 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 689 removed outlier: 4.396A pdb=" N HIS X 676 " --> pdb=" O GLU X 672 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR X 677 " --> pdb=" O ALA X 673 " (cutoff:3.500A) Processing helix chain 'X' and resid 691 through 696 removed outlier: 3.715A pdb=" N GLY X 696 " --> pdb=" O LEU X 692 " (cutoff:3.500A) Processing helix chain 'X' and resid 705 through 710 removed outlier: 4.614A pdb=" N SER X 710 " --> pdb=" O THR X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 730 removed outlier: 4.085A pdb=" N ASP X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) Processing helix chain 'X' and resid 731 through 734 removed outlier: 4.060A pdb=" N SER X 734 " --> pdb=" O MET X 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 731 through 734' Processing helix chain 'X' and resid 749 through 753 Processing helix chain 'X' and resid 763 through 767 removed outlier: 3.504A pdb=" N LEU X 766 " --> pdb=" O MET X 763 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL X 767 " --> pdb=" O GLU X 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 763 through 767' Processing helix chain 'X' and resid 769 through 776 removed outlier: 4.024A pdb=" N TYR X 774 " --> pdb=" O LEU X 770 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR X 776 " --> pdb=" O ASN X 772 " (cutoff:3.500A) Processing helix chain 'X' and resid 799 through 809 removed outlier: 3.603A pdb=" N GLU X 803 " --> pdb=" O ASN X 799 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE X 806 " --> pdb=" O LEU X 802 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR X 807 " --> pdb=" O GLU X 803 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL X 809 " --> pdb=" O LEU X 805 " (cutoff:3.500A) Processing helix chain 'X' and resid 809 through 815 removed outlier: 3.764A pdb=" N VAL X 813 " --> pdb=" O VAL X 809 " (cutoff:3.500A) Processing helix chain 'X' and resid 825 through 834 removed outlier: 4.157A pdb=" N LEU X 831 " --> pdb=" O GLN X 827 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR X 832 " --> pdb=" O ASN X 828 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU X 833 " --> pdb=" O VAL X 829 " (cutoff:3.500A) Processing helix chain 'X' and resid 857 through 866 removed outlier: 3.863A pdb=" N ASP X 861 " --> pdb=" O GLY X 857 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY X 866 " --> pdb=" O ILE X 862 " (cutoff:3.500A) Processing helix chain 'X' and resid 871 through 880 removed outlier: 3.524A pdb=" N ILE X 875 " --> pdb=" O THR X 871 " (cutoff:3.500A) removed outlier: 3.521A 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 907 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: 5.191A pdb=" N THR X 956 " --> pdb=" O LEU X 952 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU X 957 " --> pdb=" O VAL X 953 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS X 958 " --> pdb=" O ALA X 954 " (cutoff:3.500A) Processing helix chain 'X' and resid 958 through 968 removed outlier: 3.696A pdb=" N THR X 966 " --> pdb=" O ALA X 962 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU X 968 " --> pdb=" O TYR X 964 " (cutoff:3.500A) Processing helix chain 'X' and resid 969 through 972 removed outlier: 3.913A pdb=" N ARG X 972 " --> pdb=" O PRO X 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 969 through 972' Processing helix chain 'X' and resid 993 through 1000 removed outlier: 3.556A pdb=" N ALA X 997 " --> pdb=" O SER X 993 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR X 998 " --> pdb=" O PRO X 994 " (cutoff:3.500A) Processing helix chain 'X' and resid 1008 through 1016 removed outlier: 3.639A pdb=" N MET X1012 " --> pdb=" O ALA X1008 " (cutoff:3.500A) Processing helix chain 'X' and resid 1024 through 1028 Processing helix chain 'X' and resid 1117 through 1122 removed outlier: 3.872A 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 1192 removed outlier: 3.747A pdb=" N PHE X1191 " --> pdb=" O ASP X1187 " (cutoff:3.500A) Processing helix chain 'X' and resid 1215 through 1220 removed outlier: 4.329A pdb=" N LEU X1219 " --> pdb=" O ALA X1215 " (cutoff:3.500A) Processing helix chain 'X' and resid 1244 through 1250 removed outlier: 3.581A pdb=" N TYR X1250 " --> pdb=" O GLY X1246 " (cutoff:3.500A) Processing helix chain 'X' and resid 1266 through 1271 removed outlier: 3.616A pdb=" N PHE X1270 " --> pdb=" O CYS X1266 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS X1271 " --> pdb=" O ARG X1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1266 through 1271' Processing helix chain 'X' and resid 1275 through 1280 removed outlier: 3.520A pdb=" N ASN X1279 " --> pdb=" O MET X1276 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG X1280 " --> pdb=" O ARG X1277 " (cutoff:3.500A) Processing helix chain 'X' and resid 1281 through 1292 removed outlier: 3.526A pdb=" N VAL X1286 " --> pdb=" O LEU X1282 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER X1290 " --> pdb=" O VAL X1286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA X1291 " --> pdb=" O ASN X1287 " (cutoff:3.500A) Processing helix chain 'X' and resid 1334 through 1342 removed outlier: 4.114A pdb=" N LEU X1338 " --> pdb=" O HIS X1334 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 18 removed outlier: 3.688A pdb=" N LEU b 11 " --> pdb=" O ASN b 7 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU b 16 " --> pdb=" O GLY b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 38 removed outlier: 3.622A pdb=" N VAL b 38 " --> pdb=" O ALA b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 57 Processing helix chain 'b' and resid 107 through 116 removed outlier: 3.576A pdb=" N MET b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY b 116 " --> pdb=" O PHE b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 122 removed outlier: 3.550A pdb=" N LYS b 121 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 132 removed outlier: 3.938A pdb=" N VAL b 128 " --> pdb=" O GLN b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 141 removed outlier: 3.640A pdb=" N ALA b 140 " --> pdb=" O GLY b 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP b 141 " --> pdb=" O SER b 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 136 through 141' Processing helix chain 'b' and resid 147 through 152 removed outlier: 3.658A pdb=" N ASP b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR b 152 " --> pdb=" O GLU b 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 147 through 152' Processing helix chain 'b' and resid 154 through 157 Processing helix chain 'b' and resid 251 through 263 removed outlier: 3.545A pdb=" N VAL b 255 " --> pdb=" O GLY b 251 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL b 256 " --> pdb=" O PHE b 252 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA b 257 " --> pdb=" O ALA b 253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS b 260 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP b 261 " --> pdb=" O ALA b 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 271 Processing helix chain 'b' and resid 272 through 276 removed outlier: 3.628A pdb=" N ARG b 275 " --> pdb=" O ILE b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 279 through 283 Processing helix chain 'c' and resid 16 through 26 removed outlier: 3.740A pdb=" N ALA c 22 " --> pdb=" O ASP c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 58 through 67 removed outlier: 3.686A 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 142 through 161 removed outlier: 4.107A pdb=" N LEU c 149 " --> pdb=" O GLY c 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE c 157 " --> pdb=" O LEU c 153 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS c 160 " --> pdb=" O HIS c 156 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE c 161 " --> pdb=" O ILE c 157 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 179 Processing helix chain 'c' and resid 197 through 215 removed outlier: 3.605A pdb=" N ARG c 202 " --> pdb=" O ARG c 198 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL c 203 " --> pdb=" O THR c 199 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU c 204 " --> pdb=" O ALA c 200 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET c 209 " --> pdb=" O ASP c 205 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS c 212 " --> pdb=" O SER c 208 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE c 213 " --> pdb=" O MET c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 220 through 230 removed outlier: 4.070A pdb=" N LEU c 226 " --> pdb=" O CYS c 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 248 through 253 removed outlier: 3.507A pdb=" N ILE c 252 " --> pdb=" O GLU c 248 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP c 253 " --> pdb=" O VAL c 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 248 through 253' Processing helix chain 'c' and resid 258 through 273 removed outlier: 3.954A pdb=" N ASP c 262 " --> pdb=" O SER c 258 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR c 264 " --> pdb=" O PRO c 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG c 267 " --> pdb=" O ILE c 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL c 268 " --> pdb=" O THR c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 274 through 278 removed outlier: 3.676A pdb=" N SER c 277 " --> pdb=" O GLN c 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 26 removed outlier: 3.589A pdb=" N LEU d 20 " --> pdb=" O PHE d 16 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA d 21 " --> pdb=" O ALA d 17 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA d 22 " --> pdb=" O ASP d 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU d 23 " --> pdb=" O GLU d 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS d 26 " --> pdb=" O ALA d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 45 removed outlier: 4.233A pdb=" N ALA d 44 " --> pdb=" O ASN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 69 removed outlier: 3.958A pdb=" N SER d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS d 68 " --> pdb=" O GLN d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 123 removed outlier: 3.577A pdb=" N SER d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) No H-bonds generated for '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: 4.059A pdb=" N LEU d 152 " --> pdb=" O ILE d 148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 169 removed outlier: 4.057A pdb=" N ASP d 168 " --> pdb=" O ALA d 165 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL d 169 " --> pdb=" O PRO d 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 165 through 169' Processing helix chain 'd' and resid 170 through 179 removed outlier: 3.767A pdb=" N TYR d 177 " --> pdb=" O GLU d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 228 removed outlier: 3.959A pdb=" N CYS d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) Proline residue: d 219 - end of helix removed outlier: 3.965A pdb=" N LEU d 223 " --> pdb=" O PRO d 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG d 224 " --> pdb=" O ARG d 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 243 removed outlier: 3.570A pdb=" N GLU d 239 " --> pdb=" O PRO d 236 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE d 241 " --> pdb=" O THR d 238 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU d 242 " --> pdb=" O GLU d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 252 removed outlier: 3.634A pdb=" N ILE d 252 " --> pdb=" O VAL d 249 " (cutoff:3.500A) Processing helix chain 'd' and resid 258 through 282 removed outlier: 3.921A pdb=" N THR d 264 " --> pdb=" O PRO d 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU d 273 " --> pdb=" O MET d 269 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER d 275 " --> pdb=" O SER d 271 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER d 278 " --> pdb=" O GLN d 274 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE d 279 " --> pdb=" O SER d 275 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 60 removed outlier: 3.990A pdb=" N GLU 5 58 " --> pdb=" O GLY 5 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA 5 59 " --> pdb=" O SER 5 55 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU 5 60 " --> pdb=" O LEU 5 56 " (cutoff:3.500A) Processing helix chain '5' and resid 78 through 80 No H-bonds generated for 'chain '5' and resid 78 through 80' Processing helix chain '5' and resid 107 through 116 removed outlier: 3.829A pdb=" N MET 5 113 " --> pdb=" O THR 5 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU 5 114 " --> pdb=" O SER 5 110 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY 5 116 " --> pdb=" O PHE 5 112 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 133 removed outlier: 3.749A pdb=" N LYS 5 127 " --> pdb=" O PRO 5 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 5 128 " --> pdb=" O GLN 5 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY 5 130 " --> pdb=" O HIS 5 126 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 141 Processing helix chain '5' and resid 148 through 153 Processing helix chain '5' and resid 251 through 263 removed outlier: 3.618A pdb=" N VAL 5 255 " --> pdb=" O GLY 5 251 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL 5 256 " --> pdb=" O PHE 5 252 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA 5 257 " --> pdb=" O ALA 5 253 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP 5 261 " --> pdb=" O ALA 5 257 " (cutoff:3.500A) Processing helix chain '5' and resid 263 through 272 removed outlier: 3.588A pdb=" N ILE 5 267 " --> pdb=" O PHE 5 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG 5 268 " --> pdb=" O THR 5 264 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR 5 269 " --> pdb=" O ASP 5 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE 5 272 " --> pdb=" O ARG 5 268 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '6' and resid 19 through 26 removed outlier: 3.623A pdb=" N LEU 6 23 " --> pdb=" O GLU 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 45 No H-bonds generated for 'chain '6' and resid 43 through 45' Processing helix chain '6' and resid 46 through 50 removed outlier: 3.553A pdb=" N CYS 6 49 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL 6 50 " --> pdb=" O LEU 6 47 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 46 through 50' Processing helix chain '6' and resid 58 through 67 removed outlier: 3.784A pdb=" N SER 6 67 " --> pdb=" O MET 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 119 through 123 removed outlier: 3.786A 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 142 through 146 removed outlier: 3.539A pdb=" N HIS 6 146 " --> pdb=" O GLN 6 142 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 142 through 146' Processing helix chain '6' and resid 146 through 161 removed outlier: 3.708A pdb=" N GLN 6 151 " --> pdb=" O ALA 6 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS 6 160 " --> pdb=" O HIS 6 156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 6 161 " --> pdb=" O ILE 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 196 through 199 removed outlier: 4.221A pdb=" N THR 6 199 " --> pdb=" O ASP 6 196 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 196 through 199' Processing helix chain '6' and resid 200 through 205 Processing helix chain '6' and resid 207 through 214 removed outlier: 3.561A pdb=" N CYS 6 212 " --> pdb=" O SER 6 208 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE 6 213 " --> pdb=" O MET 6 209 " (cutoff:3.500A) Processing helix chain '6' and resid 219 through 228 removed outlier: 3.732A pdb=" N LEU 6 226 " --> pdb=" O CYS 6 222 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR 6 227 " --> pdb=" O LEU 6 223 " (cutoff:3.500A) Processing helix chain '6' and resid 246 through 254 removed outlier: 4.024A pdb=" N THR 6 250 " --> pdb=" O PRO 6 246 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 6 254 " --> pdb=" O THR 6 250 " (cutoff:3.500A) Processing helix chain '6' and resid 265 through 273 removed outlier: 3.518A pdb=" N LEU 6 273 " --> pdb=" O MET 6 269 " (cutoff:3.500A) Processing helix chain '6' and resid 274 through 278 removed outlier: 3.659A pdb=" N SER 6 277 " --> pdb=" O GLN 6 274 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 26 removed outlier: 3.793A pdb=" N ALA 7 22 " --> pdb=" O ASP 7 18 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU 7 23 " --> pdb=" O GLU 7 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 7 25 " --> pdb=" O ALA 7 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS 7 26 " --> pdb=" O ALA 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 41 through 45 removed outlier: 3.735A pdb=" N ALA 7 44 " --> pdb=" O ASN 7 41 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU 7 45 " --> pdb=" O ILE 7 42 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 41 through 45' Processing helix chain '7' and resid 46 through 50 removed outlier: 4.071A pdb=" N CYS 7 49 " --> pdb=" O GLY 7 46 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 67 removed outlier: 4.401A pdb=" N TYR 7 65 " --> pdb=" O GLN 7 61 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER 7 67 " --> pdb=" O MET 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 123 removed outlier: 4.226A pdb=" N SER 7 123 " --> pdb=" O SER 7 119 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 119 through 123' Processing helix chain '7' and resid 142 through 162 removed outlier: 3.889A pdb=" N LEU 7 149 " --> pdb=" O GLY 7 145 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN 7 150 " --> pdb=" O HIS 7 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN 7 151 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 7 152 " --> pdb=" O ILE 7 148 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL 7 154 " --> pdb=" O GLN 7 150 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 7 157 " --> pdb=" O LEU 7 153 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 7 160 " --> pdb=" O HIS 7 156 " (cutoff:3.500A) Processing helix chain '7' and resid 165 through 169 removed outlier: 3.843A pdb=" N ASP 7 168 " --> pdb=" O ALA 7 165 " (cutoff:3.500A) Processing helix chain '7' and resid 170 through 178 removed outlier: 4.395A pdb=" N LEU 7 176 " --> pdb=" O ALA 7 172 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 206 through 214 removed outlier: 3.788A pdb=" N CYS 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 229 removed outlier: 4.182A pdb=" N ARG 7 220 " --> pdb=" O ALA 7 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU 7 223 " --> pdb=" O PRO 7 219 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU 7 226 " --> pdb=" O CYS 7 222 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 7 228 " --> pdb=" O ARG 7 224 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU 7 229 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) Processing helix chain '7' and resid 235 through 240 Processing helix chain '7' and resid 248 through 252 removed outlier: 3.514A pdb=" N ILE 7 252 " --> pdb=" O VAL 7 249 " (cutoff:3.500A) Processing helix chain '7' and resid 253 through 257 removed outlier: 3.940A pdb=" N GLN 7 256 " --> pdb=" O ASP 7 253 " (cutoff:3.500A) removed outlier: 3.687A 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 276 removed outlier: 3.795A pdb=" N VAL 7 268 " --> pdb=" O THR 7 264 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET 7 269 " --> pdb=" O ARG 7 265 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER 7 271 " --> pdb=" O ARG 7 267 " (cutoff:3.500A) Processing helix chain '0' and resid 15 through 20 removed outlier: 3.604A pdb=" N TYR 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 0 20 " --> pdb=" O ASP 0 16 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 15 through 20' Processing helix chain '0' and resid 22 through 30 removed outlier: 3.896A pdb=" N ALA 0 26 " --> pdb=" O HIS 0 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR 0 30 " --> pdb=" O ALA 0 26 " (cutoff:3.500A) Processing helix chain '0' and resid 37 through 65 removed outlier: 3.521A pdb=" N VAL 0 43 " --> pdb=" O ALA 0 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG 0 63 " --> pdb=" O GLU 0 59 " (cutoff:3.500A) Processing helix chain '0' and resid 69 through 77 removed outlier: 3.843A pdb=" N HIS 0 73 " --> pdb=" O GLN 0 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) Processing helix chain '1' and resid 15 through 20 removed outlier: 3.605A pdb=" N TYR 1 19 " --> pdb=" O LEU 1 15 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 1 20 " --> pdb=" O ASP 1 16 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 15 through 20' Processing helix chain '1' and resid 22 through 30 removed outlier: 3.896A pdb=" N ALA 1 26 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 1 30 " --> pdb=" O ALA 1 26 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 65 removed outlier: 3.521A pdb=" N VAL 1 43 " --> pdb=" O ALA 1 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG 1 63 " --> pdb=" O GLU 1 59 " (cutoff:3.500A) Processing helix chain '1' and resid 69 through 77 removed outlier: 3.844A pdb=" N HIS 1 73 " --> pdb=" O GLN 1 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR 1 76 " --> pdb=" O ASP 1 72 " (cutoff:3.500A) Processing helix chain '2' and resid 15 through 20 removed outlier: 3.604A pdb=" N TYR 2 19 " --> pdb=" O LEU 2 15 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 2 20 " --> pdb=" O ASP 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 15 through 20' Processing helix chain '2' and resid 22 through 30 removed outlier: 3.896A pdb=" N ALA 2 26 " --> pdb=" O HIS 2 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 2 30 " --> pdb=" O ALA 2 26 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 65 removed outlier: 3.522A pdb=" N VAL 2 43 " --> pdb=" O ALA 2 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 2 63 " --> pdb=" O GLU 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 77 removed outlier: 3.843A pdb=" N HIS 2 73 " --> pdb=" O GLN 2 69 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR 2 76 " --> pdb=" O ASP 2 72 " (cutoff:3.500A) Processing helix chain '3' and resid 15 through 20 removed outlier: 3.604A pdb=" N TYR 3 19 " --> pdb=" O LEU 3 15 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 3 20 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 15 through 20' Processing helix chain '3' and resid 22 through 30 removed outlier: 3.895A pdb=" N ALA 3 26 " --> pdb=" O HIS 3 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR 3 30 " --> pdb=" O ALA 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 65 removed outlier: 3.522A pdb=" N VAL 3 43 " --> pdb=" O ALA 3 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG 3 63 " --> pdb=" O GLU 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 77 removed outlier: 3.843A pdb=" N HIS 3 73 " --> pdb=" O GLN 3 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'k' and resid 62 through 64 removed outlier: 3.685A pdb=" N GLY k 78 " --> pdb=" O VAL k 64 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL k 21 " --> pdb=" O LEU k 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 57 through 59 removed outlier: 3.556A pdb=" N VAL k 59 " --> pdb=" O PHE k 41 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE k 41 " --> pdb=" O VAL k 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'k' and resid 379 through 384 removed outlier: 5.490A pdb=" N LEU k 380 " --> pdb=" O VAL k 369 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL k 369 " --> pdb=" O LEU k 380 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS k 365 " --> pdb=" O LEU k 384 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE k 435 " --> pdb=" O LEU k 427 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 51 through 53 removed outlier: 6.185A pdb=" N GLU S 51 " --> pdb=" O ALA T 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'S' and resid 56 through 58 removed outlier: 6.414A pdb=" N TYR S 57 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS T 118 " --> pdb=" O ILE T 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 76 through 78 removed outlier: 6.688A pdb=" N VAL S 76 " --> pdb=" O MET S1061 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL S1063 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR S 78 " --> pdb=" O VAL S1063 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 121 through 125 Processing sheet with id=AA8, first strand: chain 'S' and resid 112 through 117 removed outlier: 4.397A pdb=" N ARG S 112 " --> pdb=" O MET S 97 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET S 97 " --> pdb=" O ARG S 112 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN S 92 " --> pdb=" O TYR X 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 265 through 266 Processing sheet with id=AB1, first strand: chain 'S' and resid 272 through 278 removed outlier: 6.933A pdb=" N PHE S 373 " --> pdb=" O VAL S 272 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY S 274 " --> pdb=" O PHE S 373 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU S 377 " --> pdb=" O LEU S 276 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR S 278 " --> pdb=" O GLU S 377 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER S 365 " --> pdb=" O ILE S 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 1097 through 1107 removed outlier: 5.234A pdb=" N ILE S1099 " --> pdb=" O TYR S1053 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR S1053 " --> pdb=" O ILE S1099 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE S1051 " --> pdb=" O PRO S1101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU S1047 " --> pdb=" O ALA S1105 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE S1107 " --> pdb=" O GLU S1045 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU S1045 " --> pdb=" O ILE S1107 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG S 394 " --> pdb=" O ALA S1048 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP S1317 " --> pdb=" O ASN S 393 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG S 395 " --> pdb=" O ASP S1317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 1180 through 1182 removed outlier: 3.631A pdb=" N ARG S 394 " --> pdb=" O ALA S1048 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N TYR S1327 " --> pdb=" O GLN S 397 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR S 399 " --> pdb=" O TYR S1327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 432 through 435 Processing sheet with id=AB5, first strand: chain 'S' and resid 540 through 545 removed outlier: 3.701A pdb=" N SER S 553 " --> pdb=" O HIS S 545 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 739 through 741 removed outlier: 3.713A pdb=" N ARG S 893 " --> pdb=" O LYS S 741 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 757 through 759 removed outlier: 5.857A pdb=" N ASN S 758 " --> pdb=" O VAL S 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'S' and resid 922 through 924 Processing sheet with id=AB9, first strand: chain 'S' and resid 1369 through 1370 removed outlier: 3.606A pdb=" N LEU S1370 " --> pdb=" O LYS S1373 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS S1373 " --> pdb=" O LEU S1370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'T' and resid 121 through 125 removed outlier: 6.424A pdb=" N VAL T 76 " --> pdb=" O MET T1061 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL T1063 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR T 78 " --> pdb=" O VAL T1063 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.651A pdb=" N THR T1079 " --> pdb=" O ARG T1071 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 265 through 266 removed outlier: 3.687A pdb=" N THR T 265 " --> pdb=" O SER T 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 366 through 369 removed outlier: 3.521A pdb=" N ILE T 369 " --> pdb=" O LYS T 372 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE T 373 " --> pdb=" O VAL T 272 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY T 274 " --> pdb=" O PHE T 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.031A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.031A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET T1038 " --> pdb=" O VAL T 404 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N TYR T1327 " --> pdb=" O GLN T 397 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR T 399 " --> pdb=" O TYR T1327 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 432 through 435 Processing sheet with id=AC8, first strand: chain 'T' and resid 540 through 545 Processing sheet with id=AC9, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AD1, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AD2, first strand: chain 'T' and resid 757 through 759 removed outlier: 5.842A pdb=" N ASN T 758 " --> pdb=" O VAL T 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'T' and resid 922 through 924 removed outlier: 3.669A pdb=" N PHE T 922 " --> pdb=" O MET T 822 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 1109 through 1110 Processing sheet with id=AD5, first strand: chain 'T' and resid 1331 through 1332 removed outlier: 3.850A pdb=" N ALA T1331 " --> pdb=" O ILE T1358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 1368 through 1370 removed outlier: 3.518A pdb=" N LEU T1368 " --> pdb=" O VAL T1375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU T1370 " --> pdb=" O LYS T1373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS T1373 " --> pdb=" O LEU T1370 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 112 through 116 removed outlier: 4.484A pdb=" N ARG X 112 " --> pdb=" O MET X 97 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE W 50 " --> pdb=" O ILE X 87 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY X 89 " --> pdb=" O PHE W 50 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA W 52 " --> pdb=" O GLY X 89 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE X 91 " --> pdb=" O ALA W 52 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU W 54 " --> pdb=" O ILE X 91 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N PHE X 93 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL W 56 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ILE X 95 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N THR W 58 " --> pdb=" O ILE X 95 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N MET X 97 " --> pdb=" O THR W 58 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU W 51 " --> pdb=" O ALA X 322 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 121 through 127 removed outlier: 6.407A pdb=" N VAL W 76 " --> pdb=" O MET W1061 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL W1063 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR W 78 " --> pdb=" O VAL W1063 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA W 304 " --> pdb=" O ASN W 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 121 through 127 Processing sheet with id=AE1, first strand: chain 'W' and resid 90 through 95 removed outlier: 3.576A pdb=" N LYS W 118 " --> pdb=" O ILE W 91 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE W 93 " --> pdb=" O VAL W 116 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL W 116 " --> pdb=" O PHE W 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE W 95 " --> pdb=" O TYR W 114 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 130 through 132 Processing sheet with id=AE3, first strand: chain 'W' and resid 365 through 369 removed outlier: 4.392A pdb=" N SER W 365 " --> pdb=" O ILE W 376 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA W 375 " --> pdb=" O ALA W 273 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL W 275 " --> pdb=" O ALA W 375 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU W 377 " --> pdb=" O VAL W 275 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU W 277 " --> pdb=" O GLU W 377 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 297 through 300 removed outlier: 3.558A pdb=" N GLY W 299 " --> pdb=" O THR W 360 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 1101 through 1107 removed outlier: 6.742A pdb=" N LEU W1047 " --> pdb=" O ALA W1105 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE W1107 " --> pdb=" O GLU W1045 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU W1045 " --> pdb=" O ILE W1107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 1180 through 1182 removed outlier: 3.639A pdb=" N MET W1038 " --> pdb=" O VAL W 404 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 540 through 545 Processing sheet with id=AE8, first strand: chain 'W' and resid 721 through 722 removed outlier: 3.706A pdb=" N GLN W 745 " --> pdb=" O ILE W 742 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 757 through 758 Processing sheet with id=AF1, first strand: chain 'W' and resid 822 through 824 Processing sheet with id=AF2, first strand: chain 'W' and resid 1331 through 1332 removed outlier: 3.745A pdb=" N ALA W1331 " --> pdb=" O ILE W1358 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE W1358 " --> pdb=" O ALA W1331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'X' and resid 121 through 132 removed outlier: 3.577A pdb=" N ALA X 127 " --> pdb=" O ILE X1082 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL X 76 " --> pdb=" O MET X1061 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL X1063 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR X 78 " --> pdb=" O VAL X1063 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 121 through 132 removed outlier: 3.577A pdb=" N ALA X 127 " --> pdb=" O ILE X1082 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA X1077 " --> pdb=" O VAL X1073 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL X1073 " --> pdb=" O ALA X1077 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR X1079 " --> pdb=" O ARG X1071 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 265 through 266 Processing sheet with id=AF6, first strand: chain 'X' and resid 1178 through 1182 removed outlier: 3.664A pdb=" N VAL X1041 " --> pdb=" O GLU X1178 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA X 375 " --> pdb=" O ALA X 273 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL X 275 " --> pdb=" O ALA X 375 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU X 377 " --> pdb=" O VAL X 275 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU X 277 " --> pdb=" O GLU X 377 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS X 372 " --> pdb=" O ILE X 369 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE X 376 " --> pdb=" O SER X 365 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER X 365 " --> pdb=" O ILE X 376 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 1097 through 1107 removed outlier: 3.610A pdb=" N ALA X1102 " --> pdb=" O GLU X1049 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU X1049 " --> pdb=" O ALA X1102 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL X1104 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU X1047 " --> pdb=" O VAL X1104 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA X1106 " --> pdb=" O GLU X1045 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU X1045 " --> pdb=" O ALA X1106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET X1038 " --> pdb=" O VAL X 404 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N TYR X1327 " --> pdb=" O GLN X 397 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR X 399 " --> pdb=" O TYR X1327 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 1316 through 1317 removed outlier: 6.188A pdb=" N ARG X 395 " --> pdb=" O ASP X1317 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET X1038 " --> pdb=" O VAL X 404 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU X1045 " --> pdb=" O ALA X1106 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA X1106 " --> pdb=" O GLU X1045 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU X1047 " --> pdb=" O VAL X1104 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL X1104 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU X1049 " --> pdb=" O ALA X1102 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X1102 " --> pdb=" O GLU X1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 434 through 435 Processing sheet with id=AG1, first strand: chain 'X' and resid 540 through 545 Processing sheet with id=AG2, first strand: chain 'X' and resid 721 through 722 removed outlier: 3.804A pdb=" N ALA X 722 " --> pdb=" O LEU X 918 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 757 through 759 Processing sheet with id=AG4, first strand: chain 'X' and resid 922 through 924 removed outlier: 3.604A pdb=" N PHE X 922 " --> pdb=" O MET X 822 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 1331 through 1332 removed outlier: 3.788A pdb=" N ALA X1331 " --> pdb=" O ILE X1358 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 1368 through 1370 removed outlier: 3.695A pdb=" N LEU X1368 " --> pdb=" O VAL X1375 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU X1370 " --> pdb=" O LYS X1373 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS X1373 " --> pdb=" O LEU X1370 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 69 through 76 removed outlier: 3.571A pdb=" N THR b 69 " --> pdb=" O MET b 181 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA b 180 " --> pdb=" O MET b 165 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N MET b 165 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL b 162 " --> pdb=" O LEU b 90 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU b 90 " --> pdb=" O VAL b 162 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET b 104 " --> pdb=" O PHE b 93 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 185 through 186 removed outlier: 4.381A pdb=" N GLY b 185 " --> pdb=" O VAL b 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 204 through 206 removed outlier: 3.678A pdb=" N GLN b 247 " --> pdb=" O VAL b 205 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER b 248 " --> pdb=" O THR b 225 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY b 292 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA b 228 " --> pdb=" O THR b 290 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR b 290 " --> pdb=" O ALA b 228 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU b 230 " --> pdb=" O VAL b 288 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL b 288 " --> pdb=" O LEU b 230 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR b 232 " --> pdb=" O GLY b 286 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY b 286 " --> pdb=" O TYR b 232 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY b 286 " --> pdb=" O PHE b 330 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 7 through 9 removed outlier: 7.239A pdb=" N ARG c 83 " --> pdb=" O GLU c 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR c 70 " --> pdb=" O LEU c 33 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 92 through 96 removed outlier: 7.205A pdb=" N ALA c 297 " --> pdb=" O TYR c 291 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR c 291 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER c 299 " --> pdb=" O TYR c 289 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP c 301 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS c 287 " --> pdb=" O TRP c 301 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 124 through 125 Processing sheet with id=AH4, first strand: chain 'c' and resid 180 through 182 removed outlier: 3.575A pdb=" N VAL c 181 " --> pdb=" O TYR c 188 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 30 through 33 removed outlier: 7.408A pdb=" N ARG d 83 " --> pdb=" O GLU d 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL d 8 " --> pdb=" O GLN d 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 92 through 96 removed outlier: 7.103A pdb=" N ALA d 297 " --> pdb=" O TYR d 291 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR d 291 " --> pdb=" O ALA d 297 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER d 299 " --> pdb=" O TYR d 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG d 285 " --> pdb=" O SER d 303 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 124 through 127 removed outlier: 3.833A pdb=" N ILE d 134 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 180 through 183 Processing sheet with id=AH9, first strand: chain '5' and resid 71 through 76 removed outlier: 3.779A pdb=" N SER 5 179 " --> pdb=" O GLY 5 71 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR 5 178 " --> pdb=" O VAL 5 166 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '5' and resid 198 through 200 Processing sheet with id=AI2, first strand: chain '5' and resid 204 through 206 removed outlier: 3.741A pdb=" N GLN 5 247 " --> pdb=" O VAL 5 205 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE 5 246 " --> pdb=" O TYR 5 227 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY 5 292 " --> pdb=" O ILE 5 226 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA 5 228 " --> pdb=" O THR 5 290 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR 5 290 " --> pdb=" O ALA 5 228 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU 5 230 " --> pdb=" O VAL 5 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL 5 288 " --> pdb=" O LEU 5 230 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU 5 321 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '5' and resid 204 through 206 removed outlier: 3.741A pdb=" N GLN 5 247 " --> pdb=" O VAL 5 205 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE 5 246 " --> pdb=" O TYR 5 227 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY 5 292 " --> pdb=" O ILE 5 226 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA 5 228 " --> pdb=" O THR 5 290 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR 5 290 " --> pdb=" O ALA 5 228 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU 5 230 " --> pdb=" O VAL 5 288 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL 5 288 " --> pdb=" O LEU 5 230 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '6' and resid 30 through 33 removed outlier: 3.556A pdb=" N LEU 6 33 " --> pdb=" O THR 6 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR 6 70 " --> pdb=" O LEU 6 33 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG 6 83 " --> pdb=" O GLU 6 75 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL 6 77 " --> pdb=" O SER 6 81 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER 6 81 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN 6 40 " --> pdb=" O VAL 6 8 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '6' and resid 138 through 141 removed outlier: 3.953A pdb=" N LEU 6 286 " --> pdb=" O LEU 6 111 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER 6 299 " --> pdb=" O TYR 6 289 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '6' and resid 124 through 127 Processing sheet with id=AI7, first strand: chain '7' and resid 39 through 40 removed outlier: 3.727A pdb=" N GLN 7 40 " --> pdb=" O VAL 7 8 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG 7 78 " --> pdb=" O SER 7 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU 7 76 " --> pdb=" O ARG 7 83 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '7' and resid 30 through 31 Processing sheet with id=AI9, first strand: chain '7' and resid 95 through 96 removed outlier: 3.863A pdb=" N ALA 7 297 " --> pdb=" O SER 7 292 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA 7 290 " --> pdb=" O SER 7 299 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '7' and resid 138 through 141 removed outlier: 3.869A pdb=" N ARG 7 285 " --> pdb=" O SER 7 303 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '7' and resid 124 through 126 removed outlier: 3.567A pdb=" N ILE 7 134 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) 1915 hydrogen bonds defined for protein. 5208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 25.94 Time building geometry restraints manager: 19.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20659 1.34 - 1.46: 14595 1.46 - 1.59: 28198 1.59 - 1.71: 0 1.71 - 1.83: 668 Bond restraints: 64120 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 1.71e+01 bond pdb=" C SER X 993 " pdb=" N PRO X 994 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.37e+01 bond pdb=" N ASP W 849 " pdb=" CA ASP W 849 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 bond pdb=" N THR T 263 " pdb=" CA THR T 263 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.16e-02 7.43e+03 7.43e+00 bond pdb=" CB ASP b 297 " pdb=" CG ASP b 297 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.86e+00 ... (remaining 64115 not shown) Histogram of bond angle deviations from ideal: 96.06 - 104.76: 1508 104.76 - 113.47: 35983 113.47 - 122.18: 38311 122.18 - 130.89: 10978 130.89 - 139.60: 370 Bond angle restraints: 87150 Sorted by residual: angle pdb=" C SER W 262 " pdb=" N THR W 263 " pdb=" CA THR W 263 " ideal model delta sigma weight residual 121.54 134.73 -13.19 1.91e+00 2.74e-01 4.77e+01 angle pdb=" C ALA 3 20 " pdb=" N HIS 3 21 " pdb=" CA HIS 3 21 " ideal model delta sigma weight residual 121.70 133.79 -12.09 1.80e+00 3.09e-01 4.51e+01 angle pdb=" C ALA 2 20 " pdb=" N HIS 2 21 " pdb=" CA HIS 2 21 " ideal model delta sigma weight residual 121.70 133.77 -12.07 1.80e+00 3.09e-01 4.50e+01 angle pdb=" C ALA 1 20 " pdb=" N HIS 1 21 " pdb=" CA HIS 1 21 " ideal model delta sigma weight residual 121.70 133.77 -12.07 1.80e+00 3.09e-01 4.50e+01 angle pdb=" C ALA 0 20 " pdb=" N HIS 0 21 " pdb=" CA HIS 0 21 " ideal model delta sigma weight residual 121.70 133.77 -12.07 1.80e+00 3.09e-01 4.49e+01 ... (remaining 87145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 36639 15.63 - 31.25: 1547 31.25 - 46.88: 405 46.88 - 62.50: 32 62.50 - 78.13: 54 Dihedral angle restraints: 38677 sinusoidal: 15355 harmonic: 23322 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 180.00 121.97 58.03 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA PHE T 944 " pdb=" C PHE T 944 " pdb=" N ASN T 945 " pdb=" CA ASN T 945 " ideal model delta harmonic sigma weight residual -180.00 -126.85 -53.15 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA HIS T 537 " pdb=" C HIS T 537 " pdb=" N PRO T 538 " pdb=" CA PRO T 538 " ideal model delta harmonic sigma weight residual -180.00 -138.76 -41.24 0 5.00e+00 4.00e-02 6.80e+01 ... (remaining 38674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 7331 0.057 - 0.113: 2065 0.113 - 0.170: 421 0.170 - 0.226: 47 0.226 - 0.283: 9 Chirality restraints: 9873 Sorted by residual: chirality pdb=" CB ILE T 895 " pdb=" CA ILE T 895 " pdb=" CG1 ILE T 895 " pdb=" CG2 ILE T 895 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE X 125 " pdb=" CA ILE X 125 " pdb=" CG1 ILE X 125 " pdb=" CG2 ILE X 125 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+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 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 9870 not shown) Planarity restraints: 11302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR W 263 " -0.032 2.00e-02 2.50e+03 6.32e-02 3.99e+01 pdb=" C THR W 263 " 0.109 2.00e-02 2.50e+03 pdb=" O THR W 263 " -0.040 2.00e-02 2.50e+03 pdb=" N TYR W 264 " -0.037 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 1.20e-01 2.30e+01 pdb=" N PRO T 11 " 0.208 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=" C GLY S 837 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO S 838 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO S 838 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 838 " -0.044 5.00e-02 4.00e+02 ... (remaining 11299 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5339 2.74 - 3.28: 58176 3.28 - 3.82: 97131 3.82 - 4.36: 113970 4.36 - 4.90: 195278 Nonbonded interactions: 469894 Sorted by model distance: nonbonded pdb=" OH TYR W 481 " pdb=" O VAL W 979 " model vdw 2.200 2.440 nonbonded pdb=" O LEU S1169 " pdb=" OG SER T 211 " model vdw 2.220 2.440 nonbonded pdb=" OG SER S 211 " pdb=" O LEU X1169 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR X1190 " pdb=" O ASN X1196 " model vdw 2.253 2.440 nonbonded pdb=" O ARG T1071 " pdb=" OG1 THR T1079 " model vdw 2.255 2.440 ... (remaining 469889 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 '6' and (resid 2 through 52 or resid 56 through 193 or resid 201 through \ 305)) selection = (chain '7' and (resid 2 through 163 or resid 174 through 305)) selection = (chain 'c' and (resid 2 through 52 or resid 56 through 193 or resid 201 through \ 305)) selection = (chain 'd' and (resid 2 through 52 or resid 56 through 163 or resid 174 through \ 193 or resid 201 through 305)) } ncs_group { reference = (chain 'S' and (resid 56 through 547 or resid 551 through 1376)) selection = (chain 'T' and (resid 56 through 300 or resid 361 through 1141 or resid 1166 thr \ ough 1252 or resid 1262 through 1376)) selection = (chain 'W' and (resid 56 through 300 or resid 361 through 547 or resid 551 throu \ gh 1141 or resid 1166 through 1252 or resid 1262 through 1376)) selection = (chain 'X' and (resid 56 through 300 or resid 361 through 547 or resid 551 throu \ gh 1376)) } ncs_group { reference = (chain 'l' and (resid 22 through 54 or resid 62 through 104)) selection = (chain 'm' and resid 22 through 104) } ncs_group { reference = chain 'n' selection = chain 'o' } 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.990 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 124.630 Find NCS groups from input model: 3.620 Set up NCS constraints: 0.300 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.006 0.078 64120 Z= 0.369 Angle : 0.974 13.187 87150 Z= 0.530 Chirality : 0.055 0.283 9873 Planarity : 0.007 0.120 11302 Dihedral : 10.224 78.128 23570 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 1.97 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.67 % 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: -4.52 (0.07), residues: 7871 helix: -4.40 (0.04), residues: 2513 sheet: -1.79 (0.14), residues: 1133 loop : -2.41 (0.08), residues: 4225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2664 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 2643 time to evaluate : 5.575 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 2656 average time/residue: 0.6309 time to fit residues: 2758.0411 Evaluate side-chains 1535 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1531 time to evaluate : 5.143 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4269 time to fit residues: 10.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 665 optimal weight: 5.9990 chunk 597 optimal weight: 0.9980 chunk 331 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 617 optimal weight: 7.9990 chunk 239 optimal weight: 0.6980 chunk 375 optimal weight: 9.9990 chunk 459 optimal weight: 0.9980 chunk 715 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN k 31 HIS l 75 GLN l 97 ASN l 103 ASN m 64 HIS S 224 HIS S 271 GLN S 380 GLN ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 575 GLN S 630 ASN S 674 HIS S 746 ASN S 758 ASN S 782 HIS S 856 ASN S 978 ASN S1017 GLN S1084 HIS S1116 GLN S1171 HIS S1173 GLN S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1344 ASN T 113 GLN T 220 HIS T 224 HIS ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 HIS T 380 GLN ** T 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 463 GLN T 558 HIS ** T 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 663 HIS T 674 HIS T 689 GLN ** T 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 818 HIS ** T 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 920 ASN T 970 ASN T 991 HIS T1017 GLN T1133 HIS T1171 HIS T1212 ASN ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1334 HIS W 92 GLN W 102 HIS W 113 GLN W 312 ASN W 428 GLN ** W 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 655 HIS W 716 HIS W 749 ASN W 752 ASN W 827 GLN ** W 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1017 GLN W1027 GLN W1133 HIS W1171 HIS W1196 ASN W1222 HIS W1241 GLN ** W1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1334 HIS X 109 ASN X 292 GLN X 312 ASN X 384 ASN ** X 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 525 HIS X 630 ASN X 652 ASN ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 716 HIS X 775 GLN X 779 ASN X 816 ASN X 978 ASN X1027 GLN X1084 HIS X1171 HIS X1192 GLN X1222 HIS X1344 ASN X1355 GLN b 78 GLN c 40 GLN ** c 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN c 151 GLN c 156 HIS ** d 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 156 HIS d 194 ASN d 235 HIS 6 37 HIS 6 94 GLN 6 110 GLN 6 146 HIS 6 150 GLN 6 156 HIS ** 7 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 156 HIS 0 38 GLN 0 55 HIS 0 56 HIS 0 73 HIS 1 38 GLN 1 47 HIS 2 38 GLN 2 47 HIS 2 55 HIS ** 2 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 33 GLN 3 73 HIS Total number of N/Q/H flips: 106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 64120 Z= 0.197 Angle : 0.653 11.852 87150 Z= 0.336 Chirality : 0.044 0.229 9873 Planarity : 0.005 0.103 11302 Dihedral : 6.058 73.833 8713 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.03 % 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: -3.28 (0.08), residues: 7871 helix: -2.80 (0.07), residues: 2679 sheet: -1.25 (0.15), residues: 1132 loop : -1.95 (0.09), residues: 4060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1959 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1948 time to evaluate : 5.180 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 1954 average time/residue: 0.6161 time to fit residues: 2019.7156 Evaluate side-chains 1418 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1418 time to evaluate : 5.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 397 optimal weight: 0.6980 chunk 222 optimal weight: 0.0770 chunk 595 optimal weight: 6.9990 chunk 487 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 716 optimal weight: 9.9990 chunk 774 optimal weight: 0.0040 chunk 638 optimal weight: 6.9990 chunk 710 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 575 optimal weight: 9.9990 overall best weight: 2.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 16 HIS k 31 HIS ** k 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 75 GLN ** m 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN S 384 ASN ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 674 HIS S 707 HIS S 758 ASN S1090 HIS S1116 GLN S1133 HIS S1192 GLN S1318 GLN S1321 HIS ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1344 ASN T 92 GLN T 271 GLN T 312 ASN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 384 ASN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 463 GLN ** T 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 590 HIS ** T 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1305 GLN T1334 HIS W 164 GLN W 387 GLN W 397 GLN W 590 HIS W 724 HIS W 978 ASN ** W1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN X 448 ASN X 463 GLN ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 707 HIS X 902 GLN X 982 ASN X1027 GLN X1103 HIS X1114 HIS X1192 GLN X1318 GLN ** X1321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1324 GLN X1344 ASN ** c 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 281 ASN d 146 HIS ** d 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 235 HIS ** 7 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 56 HIS 2 12 GLN 2 38 GLN 2 55 HIS ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 64120 Z= 0.189 Angle : 0.609 10.992 87150 Z= 0.308 Chirality : 0.043 0.310 9873 Planarity : 0.005 0.096 11302 Dihedral : 5.569 74.613 8713 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.03 % 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: -2.52 (0.09), residues: 7871 helix: -1.85 (0.09), residues: 2670 sheet: -0.93 (0.15), residues: 1131 loop : -1.71 (0.09), residues: 4070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1812 time to evaluate : 5.193 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 1813 average time/residue: 0.6097 time to fit residues: 1858.8189 Evaluate side-chains 1405 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1405 time to evaluate : 5.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 708 optimal weight: 10.0000 chunk 538 optimal weight: 8.9990 chunk 372 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 342 optimal weight: 8.9990 chunk 481 optimal weight: 0.4980 chunk 719 optimal weight: 8.9990 chunk 761 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 chunk 681 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN k 16 HIS k 31 HIS k 227 ASN ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 970 ASN S1090 HIS S1116 GLN S1318 GLN S1344 ASN T 92 GLN T 113 GLN T 224 HIS T 271 GLN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 384 ASN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 545 HIS T 601 GLN ** T 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 737 GLN ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1114 HIS ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1268 GLN T1318 GLN W 77 ASN ** W 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 732 GLN ** W1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1268 GLN W1334 HIS X 358 GLN X 499 GLN X 644 ASN ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 902 GLN X 982 ASN ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1344 ASN X1355 GLN b 83 GLN c 151 GLN d 156 HIS ** d 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 110 GLN 6 142 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 HIS 7 110 GLN ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 69 GLN 2 22 HIS ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 64120 Z= 0.235 Angle : 0.628 11.508 87150 Z= 0.315 Chirality : 0.044 0.233 9873 Planarity : 0.004 0.093 11302 Dihedral : 5.399 73.968 8713 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.01 % 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: -2.07 (0.09), residues: 7871 helix: -1.27 (0.09), residues: 2657 sheet: -0.82 (0.15), residues: 1171 loop : -1.57 (0.09), residues: 4043 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1733 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1724 time to evaluate : 5.665 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 revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 1728 average time/residue: 0.6083 time to fit residues: 1776.0758 Evaluate side-chains 1365 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1365 time to evaluate : 5.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 634 optimal weight: 9.9990 chunk 432 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 567 optimal weight: 0.3980 chunk 314 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 526 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 10.0000 chunk 683 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN k 227 ASN l 64 HIS S 239 GLN S 380 GLN ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 827 GLN S 970 ASN S1027 GLN S1116 GLN S1171 HIS S1192 GLN S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1344 ASN T 224 HIS T 271 GLN T 380 GLN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 492 ASN T 689 GLN T 707 HIS T 737 GLN ** T 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN W 77 ASN W 164 GLN W 354 HIS ** W 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 991 HIS ** W1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN X 358 GLN ** X 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 ASN X 630 ASN ** X 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 816 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 982 ASN ** X 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1133 HIS X1192 GLN b 57 HIS b 83 GLN b 170 HIS c 110 GLN c 130 ASN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 281 ASN c 287 HIS d 130 ASN d 156 HIS ** d 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 281 ASN 6 110 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 HIS 6 194 ASN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 22 HIS 1 69 GLN ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 64120 Z= 0.349 Angle : 0.713 13.419 87150 Z= 0.360 Chirality : 0.048 0.255 9873 Planarity : 0.005 0.086 11302 Dihedral : 5.671 71.867 8713 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.03 % 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: -2.02 (0.09), residues: 7871 helix: -1.09 (0.09), residues: 2677 sheet: -0.91 (0.15), residues: 1190 loop : -1.61 (0.09), residues: 4004 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1670 time to evaluate : 5.302 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 1672 average time/residue: 0.6527 time to fit residues: 1843.9067 Evaluate side-chains 1306 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1304 time to evaluate : 5.224 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5587 time to fit residues: 10.0138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 256 optimal weight: 5.9990 chunk 685 optimal weight: 0.0030 chunk 150 optimal weight: 6.9990 chunk 447 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 762 optimal weight: 30.0000 chunk 632 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 400 optimal weight: 30.0000 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 227 ASN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 786 HIS S 856 ASN S 970 ASN ** S1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1192 GLN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN S1344 ASN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 384 ASN ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 463 GLN ** T 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1268 GLN T1318 GLN W 77 ASN W 397 GLN W 746 ASN W 752 ASN W1116 GLN ** W1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1251 ASN ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 358 GLN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1192 GLN b 302 HIS c 130 ASN c 151 GLN c 281 ASN ** d 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 ASN 6 142 GLN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 ASN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 69 GLN 2 38 GLN ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 64120 Z= 0.284 Angle : 0.660 12.794 87150 Z= 0.331 Chirality : 0.046 0.194 9873 Planarity : 0.005 0.080 11302 Dihedral : 5.517 74.378 8713 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.01 % 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: -1.90 (0.09), residues: 7871 helix: -0.93 (0.10), residues: 2714 sheet: -0.87 (0.15), residues: 1188 loop : -1.58 (0.09), residues: 3969 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1638 time to evaluate : 5.131 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 outliers start: 3 outliers final: 0 residues processed: 1639 average time/residue: 0.6117 time to fit residues: 1684.4288 Evaluate side-chains 1295 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1295 time to evaluate : 5.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 735 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 434 optimal weight: 0.5980 chunk 556 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 641 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 759 optimal weight: 30.0000 chunk 475 optimal weight: 9.9990 chunk 463 optimal weight: 20.0000 chunk 350 optimal weight: 2.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN k 16 HIS k 333 HIS ** o2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 970 ASN S1171 HIS S1192 GLN S1236 ASN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1212 ASN ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN W 77 ASN W 732 GLN W 746 ASN ** W 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 915 GLN ** W1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1251 ASN ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 358 GLN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 ASN ** X 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 674 HIS ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 982 ASN ** X 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1192 GLN X1321 HIS b 83 GLN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 ASN c 151 GLN c 281 ASN d 156 HIS ** d 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 HIS 6 232 HIS 7 110 GLN ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 56 HIS ** 1 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 64120 Z= 0.316 Angle : 0.688 12.796 87150 Z= 0.345 Chirality : 0.047 0.272 9873 Planarity : 0.005 0.075 11302 Dihedral : 5.577 80.187 8713 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.67 % Favored : 94.32 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.03 % 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: -1.87 (0.09), residues: 7871 helix: -0.87 (0.10), residues: 2692 sheet: -0.87 (0.15), residues: 1202 loop : -1.58 (0.10), residues: 3977 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1590 time to evaluate : 5.561 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 1594 average time/residue: 0.6205 time to fit residues: 1669.4555 Evaluate side-chains 1290 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1290 time to evaluate : 5.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 469 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 453 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 482 optimal weight: 9.9990 chunk 517 optimal weight: 8.9990 chunk 375 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 596 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN ** k 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 970 ASN S1192 GLN S1236 ASN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1344 ASN T 271 GLN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 463 GLN ** T 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN ** T 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1212 ASN ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN W 77 ASN W 601 GLN W 746 ASN ** W 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN X 358 GLN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 428 GLN ** X 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 ASN X 674 HIS ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 782 HIS X 799 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 991 HIS ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1192 GLN ** c 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 194 ASN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 ASN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 151 GLN 7 110 GLN ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 56 HIS 2 38 GLN 3 21 HIS ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 64120 Z= 0.245 Angle : 0.660 13.330 87150 Z= 0.329 Chirality : 0.045 0.219 9873 Planarity : 0.005 0.076 11302 Dihedral : 5.453 83.083 8713 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.07 % Allowed : 1.65 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.04 % 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: -1.73 (0.09), residues: 7871 helix: -0.72 (0.10), residues: 2706 sheet: -0.81 (0.15), residues: 1191 loop : -1.51 (0.10), residues: 3974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1591 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1586 time to evaluate : 5.349 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 1590 average time/residue: 0.6241 time to fit residues: 1676.8952 Evaluate side-chains 1285 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1285 time to evaluate : 5.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 690 optimal weight: 5.9990 chunk 727 optimal weight: 4.9990 chunk 663 optimal weight: 20.0000 chunk 707 optimal weight: 8.9990 chunk 425 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 555 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 639 optimal weight: 0.8980 chunk 669 optimal weight: 0.8980 chunk 705 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 16 HIS k 333 HIS S 380 GLN ** S 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 970 ASN S1236 ASN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1344 ASN T 92 GLN ** T 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN T 716 HIS ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN W 601 GLN W 746 ASN ** W 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1310 ASN ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 358 GLN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 ASN X 674 HIS ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 737 GLN X 799 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 991 HIS ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1192 GLN b 83 GLN c 281 ASN d 24 GLN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 ASN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 ASN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 38 GLN 3 55 HIS 3 73 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64120 Z= 0.226 Angle : 0.653 12.219 87150 Z= 0.325 Chirality : 0.045 0.212 9873 Planarity : 0.005 0.072 11302 Dihedral : 5.366 85.074 8713 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.07 % Allowed : 0.71 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.04 % 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: -1.60 (0.09), residues: 7871 helix: -0.58 (0.10), residues: 2684 sheet: -0.74 (0.15), residues: 1202 loop : -1.46 (0.10), residues: 3985 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1566 time to evaluate : 5.209 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 revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 1570 average time/residue: 0.6208 time to fit residues: 1647.1839 Evaluate side-chains 1296 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1295 time to evaluate : 5.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4666 time to fit residues: 8.2066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 464 optimal weight: 20.0000 chunk 748 optimal weight: 20.0000 chunk 456 optimal weight: 5.9990 chunk 355 optimal weight: 30.0000 chunk 520 optimal weight: 0.7980 chunk 785 optimal weight: 8.9990 chunk 722 optimal weight: 1.9990 chunk 625 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 482 optimal weight: 4.9990 chunk 383 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN ** k 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 970 ASN ** S1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1192 GLN S1236 ASN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN S1344 ASN ** T 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1236 ASN ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN W 601 GLN W 746 ASN ** W 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN X 358 GLN ** X 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 ASN ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 799 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1103 HIS X1192 GLN X1324 GLN b 83 GLN c 281 ASN d 24 GLN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 ASN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS 3 21 HIS ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 73 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 64120 Z= 0.255 Angle : 0.664 12.129 87150 Z= 0.330 Chirality : 0.046 0.220 9873 Planarity : 0.005 0.082 11302 Dihedral : 5.357 87.015 8713 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.04 % 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: -1.56 (0.09), residues: 7871 helix: -0.54 (0.10), residues: 2674 sheet: -0.70 (0.15), residues: 1176 loop : -1.45 (0.10), residues: 4021 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15742 Ramachandran restraints generated. 7871 Oldfield, 0 Emsley, 7871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1532 time to evaluate : 5.288 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1535 average time/residue: 0.6462 time to fit residues: 1678.3816 Evaluate side-chains 1270 residues out of total 6854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1268 time to evaluate : 5.220 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4936 time to fit residues: 9.1185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 496 optimal weight: 7.9990 chunk 665 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 576 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 626 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 642 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN k 333 HIS ** k 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 380 GLN ** S 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1236 ASN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1318 GLN ** S1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 689 GLN T 752 ASN ** T 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 970 ASN ** T1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1236 ASN ** T1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1318 GLN ** T1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN W 746 ASN ** W 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 782 HIS W 915 GLN W1128 GLN ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 397 GLN X 448 ASN ** X 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1192 GLN b 83 GLN c 281 ASN d 24 GLN ** 5 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 ASN ** 7 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 17 HIS 2 21 HIS 2 38 GLN 3 73 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109684 restraints weight = 103359.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110297 restraints weight = 82804.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.111100 restraints weight = 64813.343| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 64120 Z= 0.263 Angle : 0.668 12.161 87150 Z= 0.331 Chirality : 0.046 0.200 9873 Planarity : 0.005 0.076 11302 Dihedral : 5.364 89.607 8713 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.22 % Twisted General : 0.04 % 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: -1.54 (0.09), residues: 7871 helix: -0.49 (0.10), residues: 2684 sheet: -0.70 (0.15), residues: 1183 loop : -1.46 (0.10), residues: 4004 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23088.20 seconds wall clock time: 400 minutes 40.59 seconds (24040.59 seconds total)