Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 02:07:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pph_20436/10_2023/6pph_20436.pdb" } resolution = 3.8 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= 0.005 sd= 0.009 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 477 5.16 5 C 46759 2.51 5 N 12791 2.21 5 O 13475 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 "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" Residue "b ARG 238": "NH1" <-> "NH2" Residue "c TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "d ARG 231": "NH1" <-> "NH2" Residue "4 ARG 106": "NH1" <-> "NH2" Residue "4 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 702": "NH1" <-> "NH2" Residue "4 ARG 753": "NH1" <-> "NH2" Residue "4 TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 106": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "S PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 572": "NH1" <-> "NH2" Residue "S ARG 702": "NH1" <-> "NH2" Residue "S ARG 753": "NH1" <-> "NH2" Residue "S ARG 1070": "NH1" <-> "NH2" Residue "S TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 106": "NH1" <-> "NH2" Residue "T PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 702": "NH1" <-> "NH2" Residue "T ARG 753": "NH1" <-> "NH2" Residue "T TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X ARG 106": "NH1" <-> "NH2" Residue "X ARG 112": "NH1" <-> "NH2" Residue "X TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 309": "NH1" <-> "NH2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 572": "NH1" <-> "NH2" Residue "X ARG 702": "NH1" <-> "NH2" Residue "X ARG 753": "NH1" <-> "NH2" Residue "X TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 106": "NH1" <-> "NH2" Residue "W PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 702": "NH1" <-> "NH2" Residue "W ARG 753": "NH1" <-> "NH2" Residue "W TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 73502 Number of models: 1 Model: "" Number of chains: 21 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: "5" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2428 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 291} Chain breaks: 2 Chain: "6" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2382 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 284} 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: "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: "4" Number of atoms: 9634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1222, 9634 Classifications: {'peptide': 1222} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 68, 'TRANS': 1152} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 380 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "S" Number of atoms: 10061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 10061 Classifications: {'peptide': 1281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 73, 'TRANS': 1207} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "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: "1" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 10519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10519 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 1265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "0" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 666 Classifications: {'peptide': 78} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain: "W" Number of atoms: 10622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1354, 10622 Classifications: {'peptide': 1354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 27.96, per 1000 atoms: 0.38 Number of scatterers: 73502 At special positions: 0 Unit cell: (218.36, 206, 224.54, 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 477 16.00 O 13475 8.00 N 12791 7.00 C 46759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS k 365 " - pdb=" SG CYS k 389 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 212 " - pdb=" SG CYS 7 222 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 222 " - pdb=" SG CYS 7 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 212 " - pdb=" SG CYS d 222 " distance=2.02 Simple disulfide: pdb=" SG CYS c 222 " - pdb=" SG CYS d 212 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.52 Conformation dependent library (CDL) restraints added in 7.9 seconds 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17686 Finding SS restraints... Secondary structure from input PDB file: 392 helices and 106 sheets defined 40.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'k' and resid 1 through 11 removed outlier: 4.321A pdb=" N ALA k 5 " --> pdb=" O MET k 1 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN k 7 " --> pdb=" O ALA k 3 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG k 9 " --> pdb=" O ALA k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 15 Processing helix chain 'k' and resid 25 through 32 removed outlier: 3.682A pdb=" N HIS k 30 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS k 31 " --> pdb=" O PHE k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 91 removed outlier: 4.048A 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: 3.942A pdb=" N PHE k 284 " --> pdb=" O PRO k 280 " (cutoff:3.500A) Processing helix chain 'k' and resid 289 through 309 removed outlier: 3.676A pdb=" N ASP k 299 " --> pdb=" O CYS k 295 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR k 300 " --> pdb=" O ASP k 296 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS k 305 " --> pdb=" O LEU k 301 " (cutoff:3.500A) Processing helix chain 'k' and resid 323 through 344 removed outlier: 3.554A pdb=" N ALA k 327 " --> pdb=" O ASP k 323 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS k 331 " --> pdb=" O ALA k 327 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER k 332 " --> pdb=" O ASP k 328 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE k 334 " --> pdb=" O VAL k 330 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG k 342 " --> pdb=" O CYS k 338 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY k 343 " --> pdb=" O LEU k 339 " (cutoff:3.500A) Processing helix chain 'k' and resid 349 through 356 Processing helix chain 'k' and resid 371 through 375 removed outlier: 3.638A pdb=" N GLU k 374 " --> pdb=" O GLY k 371 " (cutoff:3.500A) Processing helix chain 'k' and resid 392 through 394 No H-bonds generated for 'chain 'k' and resid 392 through 394' Processing helix chain 'k' and resid 395 through 401 removed outlier: 3.534A pdb=" N ILE k 399 " --> pdb=" O ASP k 395 " (cutoff:3.500A) Processing helix chain 'k' and resid 404 through 411 Processing helix chain 'k' and resid 442 through 453 removed outlier: 3.503A pdb=" N VAL k 447 " --> pdb=" O LYS k 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG k 452 " --> pdb=" O PHE k 448 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 97 removed outlier: 3.587A pdb=" N THR l 42 " --> pdb=" O THR l 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL l 45 " --> pdb=" O GLU l 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY l 48 " --> pdb=" O ARG l 44 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU l 53 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN l 56 " --> pdb=" O GLN l 52 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG l 59 " --> pdb=" O ARG l 55 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA l 63 " --> pdb=" O ARG l 59 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU l 65 " --> pdb=" O THR l 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU l 66 " --> pdb=" O LYS l 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER l 67 " --> pdb=" O ALA l 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER l 79 " --> pdb=" O GLN l 75 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL l 83 " --> pdb=" O SER l 79 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.743A pdb=" N GLU m 41 " --> pdb=" O PRO m 37 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 63 through 103 removed outlier: 3.505A pdb=" N GLU m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU m 70 " --> pdb=" O LEU m 66 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL m 74 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN m 75 " --> pdb=" O ASP m 71 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER m 79 " --> pdb=" O GLN m 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA m 86 " --> pdb=" O ARG m 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS m 92 " --> pdb=" O ILE m 88 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN m 93 " --> pdb=" O ASP m 89 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY m 96 " --> pdb=" O LYS m 92 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR m 99 " --> pdb=" O ILE m 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP m 100 " --> pdb=" O GLY m 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER m 101 " --> pdb=" O ASN m 97 " (cutoff:3.500A) Processing helix chain 'n' and resid 2597 through 2605 removed outlier: 3.678A pdb=" N ALA n2601 " --> pdb=" O ASP n2597 " (cutoff:3.500A) Processing helix chain 'n' and resid 2606 through 2635 removed outlier: 3.573A pdb=" N ILE n2612 " --> pdb=" O PHE n2608 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS n2615 " --> pdb=" O ARG n2611 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA n2617 " --> pdb=" O LYS n2613 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA n2618 " --> pdb=" O GLN n2614 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU n2619 " --> pdb=" O LYS n2615 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER n2620 " --> pdb=" O VAL n2616 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP n2628 " --> pdb=" O ALA n2624 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS n2631 " --> pdb=" O VAL n2627 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS n2632 " --> pdb=" O ASP n2628 " (cutoff:3.500A) Processing helix chain 'o' and resid 2597 through 2605 removed outlier: 3.679A pdb=" N ALA o2601 " --> pdb=" O ASP o2597 " (cutoff:3.500A) Processing helix chain 'o' and resid 2606 through 2635 removed outlier: 3.573A pdb=" N ILE o2612 " --> pdb=" O PHE o2608 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS o2615 " --> pdb=" O ARG o2611 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA o2617 " --> pdb=" O LYS o2613 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA o2618 " --> pdb=" O GLN o2614 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU o2619 " --> pdb=" O LYS o2615 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER o2620 " --> pdb=" O VAL o2616 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP o2628 " --> pdb=" O ALA o2624 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS o2631 " --> pdb=" O VAL o2627 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS o2632 " --> pdb=" O ASP o2628 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 16 removed outlier: 3.781A pdb=" N ARG 5 13 " --> pdb=" O ALA 5 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN 5 14 " --> pdb=" O ARG 5 10 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU 5 16 " --> pdb=" O GLY 5 12 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 46 removed outlier: 3.532A pdb=" N ALA 5 35 " --> pdb=" O GLY 5 31 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG 5 36 " --> pdb=" O PRO 5 32 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 5 37 " --> pdb=" O GLU 5 33 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 5 41 " --> pdb=" O GLY 5 37 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS 5 44 " --> pdb=" O ASP 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 52 through 58 Processing helix chain '5' and resid 107 through 116 removed outlier: 4.722A pdb=" N MET 5 113 " --> pdb=" O THR 5 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 5 114 " --> pdb=" O SER 5 110 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY 5 116 " --> pdb=" O PHE 5 112 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 132 removed outlier: 4.463A pdb=" N LYS 5 127 " --> pdb=" O PRO 5 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL 5 128 " --> pdb=" O GLN 5 124 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 141 Processing helix chain '5' and resid 251 through 263 removed outlier: 3.727A pdb=" N VAL 5 256 " --> pdb=" O PHE 5 252 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA 5 257 " --> pdb=" O ALA 5 253 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP 5 261 " --> pdb=" O ALA 5 257 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS 5 262 " --> pdb=" O MET 5 258 " (cutoff:3.500A) Processing helix chain '5' and resid 263 through 272 removed outlier: 3.742A pdb=" N THR 5 269 " --> pdb=" O ASP 5 265 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 284 removed outlier: 4.150A pdb=" N VAL 5 284 " --> pdb=" O ASN 5 281 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 26 removed outlier: 3.676A pdb=" N ALA 6 21 " --> pdb=" O ALA 6 17 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS 6 26 " --> pdb=" O ALA 6 22 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 45 removed outlier: 3.913A pdb=" N ALA 6 44 " --> pdb=" O ASN 6 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 6 45 " --> pdb=" O ILE 6 42 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 41 through 45' Processing helix chain '6' and resid 46 through 50 removed outlier: 3.723A pdb=" N CYS 6 49 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.713A pdb=" N SER 6 67 " --> pdb=" O MET 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 119 through 124 removed outlier: 3.570A pdb=" N SER 6 123 " --> pdb=" O SER 6 119 " (cutoff:3.500A) Processing helix chain '6' and resid 142 through 165 removed outlier: 3.912A pdb=" N ALA 6 147 " --> pdb=" O GLN 6 143 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU 6 149 " --> pdb=" O GLY 6 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 6 153 " --> pdb=" O LEU 6 149 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS 6 160 " --> pdb=" O HIS 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 170 through 179 removed outlier: 3.755A pdb=" N LEU 6 176 " --> pdb=" O ALA 6 172 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR 6 177 " --> pdb=" O GLU 6 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR 6 179 " --> pdb=" O ASP 6 175 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 217 removed outlier: 3.811A pdb=" N VAL 6 203 " --> pdb=" O THR 6 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 6 204 " --> pdb=" O ALA 6 200 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET 6 209 " --> pdb=" O ASP 6 205 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 6 210 " --> pdb=" O ASP 6 206 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS 6 212 " --> pdb=" O SER 6 208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE 6 213 " --> pdb=" O MET 6 209 " (cutoff:3.500A) Processing helix chain '6' and resid 219 through 228 removed outlier: 3.520A pdb=" N LEU 6 223 " --> pdb=" O PRO 6 219 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 6 226 " --> pdb=" O CYS 6 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR 6 227 " --> pdb=" O LEU 6 223 " (cutoff:3.500A) Processing helix chain '6' and resid 246 through 251 removed outlier: 3.899A pdb=" N THR 6 250 " --> pdb=" O PRO 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 258 through 261 Processing helix chain '6' and resid 262 through 274 removed outlier: 3.841A pdb=" N VAL 6 268 " --> pdb=" O THR 6 264 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 279 Processing helix chain '7' and resid 16 through 26 removed outlier: 3.916A pdb=" N ALA 7 21 " --> pdb=" O ALA 7 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA 7 22 " --> pdb=" O ASP 7 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 7 23 " --> pdb=" O GLU 7 19 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER 7 25 " --> pdb=" O ALA 7 21 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS 7 26 " --> pdb=" O ALA 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 41 through 45 removed outlier: 3.702A pdb=" N ALA 7 44 " --> pdb=" O ASN 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 46 through 50 removed outlier: 4.287A pdb=" N CYS 7 49 " --> pdb=" O GLY 7 46 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 removed outlier: 3.717A pdb=" N TYR 7 65 " --> pdb=" O GLN 7 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 7 67 " --> pdb=" O MET 7 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS 7 68 " --> pdb=" O GLN 7 64 " (cutoff:3.500A) Processing helix chain '7' and resid 142 through 151 removed outlier: 3.523A pdb=" N ALA 7 147 " --> pdb=" O GLN 7 143 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU 7 149 " --> pdb=" O GLY 7 145 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN 7 151 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) Processing helix chain '7' and resid 151 through 165 removed outlier: 3.872A pdb=" N LYS 7 160 " --> pdb=" O HIS 7 156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA 7 163 " --> pdb=" O SER 7 159 " (cutoff:3.500A) Processing helix chain '7' and resid 166 through 169 removed outlier: 3.875A pdb=" N VAL 7 169 " --> pdb=" O PRO 7 166 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 166 through 169' Processing helix chain '7' and resid 170 through 178 removed outlier: 3.886A pdb=" N LEU 7 176 " --> pdb=" O ALA 7 172 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 212 Processing helix chain '7' and resid 216 through 229 removed outlier: 4.248A pdb=" N ARG 7 220 " --> pdb=" O ALA 7 216 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU 7 223 " --> pdb=" O PRO 7 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 7 228 " --> pdb=" O ARG 7 224 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.575A pdb=" N ILE 7 252 " --> pdb=" O VAL 7 249 " (cutoff:3.500A) Processing helix chain '7' and resid 258 through 264 removed outlier: 4.020A pdb=" N THR 7 264 " --> pdb=" O PRO 7 260 " (cutoff:3.500A) Processing helix chain '7' and resid 266 through 279 removed outlier: 3.581A pdb=" N SER 7 271 " --> pdb=" O ARG 7 267 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU 7 276 " --> pdb=" O TYR 7 272 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE 7 279 " --> pdb=" O SER 7 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 18 removed outlier: 3.610A pdb=" N ARG b 10 " --> pdb=" O GLU b 6 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU b 11 " --> pdb=" O ASN b 7 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU b 16 " --> pdb=" O GLY b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 31 removed outlier: 3.511A pdb=" N ARG b 30 " --> pdb=" O SER b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 38 removed outlier: 3.547A 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 109 through 116 removed outlier: 3.714A pdb=" N MET b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 122 removed outlier: 3.557A pdb=" N LYS b 121 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 133 removed outlier: 3.769A pdb=" N VAL b 128 " --> pdb=" O GLN b 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL b 131 " --> pdb=" O LYS b 127 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR b 133 " --> pdb=" O ALA b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 152 removed outlier: 3.709A pdb=" N ASP b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) removed outlier: 3.548A 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: 3.692A pdb=" N VAL b 256 " --> pdb=" O PHE b 252 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA b 257 " --> pdb=" O ALA b 253 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP b 261 " --> pdb=" O ALA b 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 272 Processing helix chain 'b' and resid 273 through 276 Processing helix chain 'b' and resid 279 through 284 removed outlier: 4.073A pdb=" N VAL b 284 " --> pdb=" O ASN b 281 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 26 removed outlier: 3.683A pdb=" N ALA c 22 " --> pdb=" O ASP c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.619A pdb=" N ALA c 44 " --> pdb=" O ASN c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 67 removed outlier: 3.693A pdb=" N SER c 67 " --> pdb=" O MET c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 119 through 123 Processing helix chain 'c' and resid 141 through 161 removed outlier: 4.136A pdb=" N LEU c 149 " --> pdb=" O GLY c 145 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS c 160 " --> pdb=" O HIS c 156 " (cutoff:3.500A) Processing helix chain 'c' and resid 201 through 214 removed outlier: 3.869A pdb=" N CYS c 212 " --> pdb=" O SER c 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE c 213 " --> pdb=" O MET c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 230 removed outlier: 3.519A pdb=" N LEU c 223 " --> pdb=" O PRO c 219 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU c 226 " --> pdb=" O CYS c 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 248 through 253 removed outlier: 3.547A pdb=" N ILE c 252 " --> pdb=" O GLU c 248 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.743A pdb=" N ASP c 262 " --> pdb=" O SER c 258 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR c 264 " --> pdb=" O PRO c 260 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL c 268 " --> pdb=" O THR c 264 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU c 273 " --> pdb=" O MET c 269 " (cutoff:3.500A) Processing helix chain 'c' and resid 274 through 278 removed outlier: 3.669A pdb=" N SER c 277 " --> pdb=" O GLN c 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 26 removed outlier: 3.631A pdb=" N LEU d 20 " --> pdb=" O PHE d 16 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA d 21 " --> pdb=" O ALA d 17 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA d 22 " --> pdb=" O ASP d 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU d 23 " --> pdb=" O GLU d 19 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS d 26 " --> pdb=" O ALA d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 45 removed outlier: 4.176A pdb=" N ALA d 44 " --> pdb=" O ASN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 69 removed outlier: 3.657A pdb=" N TYR d 65 " --> pdb=" O GLN d 61 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS d 68 " --> pdb=" O GLN d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 123 Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 149 through 163 removed outlier: 3.536A pdb=" N ILE d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 169 removed outlier: 4.076A pdb=" N ASP d 168 " --> pdb=" O ALA d 165 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.604A pdb=" N TYR d 177 " --> pdb=" O GLU d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 228 removed outlier: 3.759A pdb=" N CYS d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) Proline residue: d 219 - end of helix removed outlier: 3.860A pdb=" N LEU d 223 " --> pdb=" O PRO d 219 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG d 224 " --> pdb=" O ARG d 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 239 through 244 removed outlier: 3.760A pdb=" N GLU d 242 " --> pdb=" O GLU d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 252 removed outlier: 3.527A pdb=" N ARG d 251 " --> pdb=" O GLU d 248 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE d 252 " --> pdb=" O VAL d 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 248 through 252' Processing helix chain 'd' and resid 258 through 282 removed outlier: 4.175A pdb=" N THR d 264 " --> pdb=" O PRO d 260 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU d 273 " --> pdb=" O MET d 269 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER d 275 " --> pdb=" O SER d 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER d 278 " --> pdb=" O GLN d 274 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE d 279 " --> pdb=" O SER d 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE d 280 " --> pdb=" O LEU d 276 " (cutoff:3.500A) Processing helix chain '4' and resid 69 through 73 removed outlier: 3.520A pdb=" N ALA 4 73 " --> pdb=" O ALA 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 82 through 86 removed outlier: 4.198A pdb=" N ARG 4 85 " --> pdb=" O ASP 4 82 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET 4 86 " --> pdb=" O LEU 4 83 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 82 through 86' Processing helix chain '4' and resid 133 through 139 Processing helix chain '4' and resid 148 through 185 removed outlier: 3.792A pdb=" N GLY 4 154 " --> pdb=" O THR 4 150 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 4 155 " --> pdb=" O GLU 4 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR 4 158 " --> pdb=" O GLY 4 154 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE 4 165 " --> pdb=" O SER 4 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 4 170 " --> pdb=" O GLY 4 166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY 4 173 " --> pdb=" O ALA 4 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 4 178 " --> pdb=" O LEU 4 174 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 4 184 " --> pdb=" O ALA 4 180 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS 4 185 " --> pdb=" O VAL 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 196 removed outlier: 3.531A pdb=" N LEU 4 192 " --> pdb=" O PRO 4 188 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR 4 194 " --> pdb=" O PHE 4 190 " (cutoff:3.500A) Processing helix chain '4' and resid 198 through 203 removed outlier: 3.967A pdb=" N GLU 4 202 " --> pdb=" O PRO 4 198 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG 4 203 " --> pdb=" O VAL 4 199 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 198 through 203' Processing helix chain '4' and resid 206 through 225 removed outlier: 3.647A pdb=" N LYS 4 210 " --> pdb=" O LYS 4 206 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL 4 214 " --> pdb=" O LYS 4 210 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER 4 215 " --> pdb=" O SER 4 211 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS 4 220 " --> pdb=" O MET 4 216 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU 4 223 " --> pdb=" O ALA 4 219 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER 4 225 " --> pdb=" O LEU 4 221 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 231 Processing helix chain '4' and resid 236 through 252 removed outlier: 3.608A pdb=" N TYR 4 240 " --> pdb=" O ARG 4 236 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET 4 248 " --> pdb=" O MET 4 244 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL 4 252 " --> pdb=" O MET 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 270 No H-bonds generated for 'chain '4' and resid 268 through 270' Processing helix chain '4' and resid 279 through 290 removed outlier: 3.796A pdb=" N ARG 4 284 " --> pdb=" O ASP 4 280 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 336 removed outlier: 3.820A pdb=" N ARG 4 332 " --> pdb=" O GLN 4 328 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE 4 333 " --> pdb=" O PHE 4 329 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL 4 334 " --> pdb=" O MET 4 330 " (cutoff:3.500A) Processing helix chain '4' and resid 380 through 385 Processing helix chain '4' and resid 445 through 450 Processing helix chain '4' and resid 451 through 453 No H-bonds generated for 'chain '4' and resid 451 through 453' Processing helix chain '4' and resid 461 through 472 removed outlier: 3.672A pdb=" N GLN 4 470 " --> pdb=" O GLN 4 466 " (cutoff:3.500A) Processing helix chain '4' and resid 493 through 501 removed outlier: 3.812A pdb=" N PHE 4 497 " --> pdb=" O LEU 4 493 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS 4 498 " --> pdb=" O PHE 4 494 " (cutoff:3.500A) Processing helix chain '4' and resid 512 through 518 removed outlier: 3.506A pdb=" N ALA 4 516 " --> pdb=" O VAL 4 512 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 4 518 " --> pdb=" O GLN 4 514 " (cutoff:3.500A) Processing helix chain '4' and resid 521 through 525 removed outlier: 3.778A pdb=" N HIS 4 525 " --> pdb=" O ASP 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 561 through 565 Processing helix chain '4' and resid 571 through 585 removed outlier: 3.731A pdb=" N GLN 4 575 " --> pdb=" O PRO 4 571 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN 4 581 " --> pdb=" O SER 4 577 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 4 585 " --> pdb=" O GLN 4 581 " (cutoff:3.500A) Processing helix chain '4' and resid 596 through 604 removed outlier: 4.053A pdb=" N GLU 4 602 " --> pdb=" O ASP 4 598 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA 4 604 " --> pdb=" O ILE 4 600 " (cutoff:3.500A) Processing helix chain '4' and resid 615 through 620 Processing helix chain '4' and resid 624 through 629 Processing helix chain '4' and resid 637 through 645 removed outlier: 3.650A pdb=" N TRP 4 642 " --> pdb=" O ILE 4 638 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL 4 643 " --> pdb=" O GLN 4 639 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN 4 644 " --> pdb=" O THR 4 640 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER 4 645 " --> pdb=" O TYR 4 641 " (cutoff:3.500A) Processing helix chain '4' and resid 653 through 663 removed outlier: 3.931A pdb=" N VAL 4 657 " --> pdb=" O SER 4 653 " (cutoff:3.500A) Processing helix chain '4' and resid 674 through 689 removed outlier: 4.387A pdb=" N ARG 4 678 " --> pdb=" O HIS 4 674 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU 4 683 " --> pdb=" O LYS 4 679 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU 4 684 " --> pdb=" O ILE 4 680 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE 4 685 " --> pdb=" O LEU 4 681 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA 4 686 " --> pdb=" O GLY 4 682 " (cutoff:3.500A) Processing helix chain '4' and resid 704 through 709 removed outlier: 3.678A pdb=" N LEU 4 708 " --> pdb=" O ILE 4 705 " (cutoff:3.500A) Processing helix chain '4' and resid 726 through 734 removed outlier: 4.471A pdb=" N GLN 4 732 " --> pdb=" O THR 4 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER 4 734 " --> pdb=" O LEU 4 730 " (cutoff:3.500A) Processing helix chain '4' and resid 767 through 777 Processing helix chain '4' and resid 794 through 798 removed outlier: 3.541A pdb=" N ASP 4 797 " --> pdb=" O ASP 4 794 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR 4 798 " --> pdb=" O GLU 4 795 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 794 through 798' Processing helix chain '4' and resid 800 through 802 No H-bonds generated for 'chain '4' and resid 800 through 802' Processing helix chain '4' and resid 803 through 808 removed outlier: 3.785A pdb=" N TYR 4 807 " --> pdb=" O GLU 4 803 " (cutoff:3.500A) Processing helix chain '4' and resid 810 through 815 Processing helix chain '4' and resid 829 through 833 Processing helix chain '4' and resid 861 through 866 Processing helix chain '4' and resid 871 through 873 No H-bonds generated for 'chain '4' and resid 871 through 873' Processing helix chain '4' and resid 874 through 881 removed outlier: 3.729A pdb=" N LEU 4 878 " --> pdb=" O MET 4 874 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS 4 879 " --> pdb=" O ILE 4 875 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR 4 880 " --> pdb=" O ARG 4 876 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER 4 881 " --> pdb=" O VAL 4 877 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 874 through 881' Processing helix chain '4' and resid 882 through 885 removed outlier: 3.554A pdb=" N CYS 4 885 " --> pdb=" O PHE 4 882 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 882 through 885' Processing helix chain '4' and resid 931 through 936 Processing helix chain '4' and resid 958 through 968 removed outlier: 3.759A pdb=" N VAL 4 965 " --> pdb=" O LEU 4 961 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR 4 966 " --> pdb=" O ALA 4 962 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU 4 968 " --> pdb=" O TYR 4 964 " (cutoff:3.500A) Processing helix chain '4' and resid 969 through 972 removed outlier: 4.014A pdb=" N ARG 4 972 " --> pdb=" O PRO 4 969 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 969 through 972' Processing helix chain '4' and resid 992 through 999 Processing helix chain '4' and resid 1005 through 1014 removed outlier: 3.807A pdb=" N SER 41010 " --> pdb=" O PRO 41006 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET 41012 " --> pdb=" O ALA 41008 " (cutoff:3.500A) Processing helix chain '4' and resid 1021 through 1030 removed outlier: 4.465A pdb=" N GLN 41027 " --> pdb=" O SER 41023 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 41028 " --> pdb=" O PHE 41024 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS 41029 " --> pdb=" O ILE 41025 " (cutoff:3.500A) Processing helix chain '4' and resid 1117 through 1122 removed outlier: 3.811A pdb=" N ILE 41121 " --> pdb=" O ASP 41117 " (cutoff:3.500A) Processing helix chain '4' and resid 1132 through 1137 removed outlier: 3.579A pdb=" N LYS 41137 " --> pdb=" O HIS 41133 " (cutoff:3.500A) Processing helix chain '4' and resid 1138 through 1141 removed outlier: 4.001A pdb=" N GLY 41141 " --> pdb=" O MET 41138 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 1138 through 1141' Processing helix chain '4' and resid 1214 through 1220 Processing helix chain '4' and resid 1244 through 1251 Processing helix chain '4' and resid 1266 through 1271 removed outlier: 3.812A pdb=" N PHE 41270 " --> pdb=" O CYS 41266 " (cutoff:3.500A) Processing helix chain '4' and resid 1271 through 1293 removed outlier: 3.610A pdb=" N MET 41276 " --> pdb=" O LYS 41272 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG 41277 " --> pdb=" O GLU 41273 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR 41278 " --> pdb=" O ASP 41274 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 41280 " --> pdb=" O MET 41276 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY 41281 " --> pdb=" O ARG 41277 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 41282 " --> pdb=" O TYR 41278 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR 41284 " --> pdb=" O ARG 41280 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU 41288 " --> pdb=" O THR 41284 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR 41289 " --> pdb=" O LEU 41285 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER 41290 " --> pdb=" O VAL 41286 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA 41291 " --> pdb=" O ASN 41287 " (cutoff:3.500A) Processing helix chain '4' and resid 1319 through 1324 Processing helix chain '4' and resid 1335 through 1344 removed outlier: 3.898A pdb=" N ASP 41339 " --> pdb=" O ARG 41335 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN 41344 " --> pdb=" O GLU 41340 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 38 through 63 removed outlier: 3.625A pdb=" N LEU A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain '2' and resid 14 through 20 removed outlier: 3.855A pdb=" N ASP 2 18 " --> pdb=" O ARG 2 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 2 19 " --> pdb=" O LEU 2 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 2 20 " --> pdb=" O ASP 2 16 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 14 through 20' Processing helix chain '2' and resid 22 through 30 removed outlier: 3.948A pdb=" N ALA 2 26 " --> pdb=" O HIS 2 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR 2 30 " --> pdb=" O ALA 2 26 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 65 removed outlier: 3.542A pdb=" N VAL 2 43 " --> pdb=" O ALA 2 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE 2 51 " --> pdb=" O HIS 2 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG 2 63 " --> pdb=" O GLU 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 77 removed outlier: 3.654A pdb=" N HIS 2 73 " --> pdb=" O GLN 2 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 2 76 " --> pdb=" O ASP 2 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 3.994A pdb=" N ALA S 28 " --> pdb=" O LYS S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 65 through 75 removed outlier: 6.526A pdb=" N ALA S 70 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU S 71 " --> pdb=" O GLU S 68 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA S 72 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 141 removed outlier: 3.916A pdb=" N LEU S 138 " --> pdb=" O ALA S 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU S 139 " --> pdb=" O ASP S 135 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE S 140 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA S 141 " --> pdb=" O GLU S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 160 removed outlier: 3.919A pdb=" N GLY S 154 " --> pdb=" O THR S 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 158 " --> pdb=" O GLY S 154 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR S 160 " --> pdb=" O ILE S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 162 through 184 removed outlier: 3.998A pdb=" N GLY S 166 " --> pdb=" O ALA S 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU S 170 " --> pdb=" O GLY S 166 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU S 171 " --> pdb=" O MET S 167 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL S 175 " --> pdb=" O GLU S 171 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL S 181 " --> pdb=" O THR S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 197 removed outlier: 4.675A pdb=" N THR S 194 " --> pdb=" O PHE S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 215 removed outlier: 3.590A pdb=" N SER S 211 " --> pdb=" O LYS S 207 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 224 removed outlier: 3.544A pdb=" N ILE S 222 " --> pdb=" O LYS S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 Processing helix chain 'S' and resid 232 through 234 No H-bonds generated for 'chain 'S' and resid 232 through 234' Processing helix chain 'S' and resid 237 through 246 removed outlier: 3.520A pdb=" N LEU S 242 " --> pdb=" O LYS S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 251 removed outlier: 3.793A pdb=" N ALA S 250 " --> pdb=" O SER S 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA S 251 " --> pdb=" O ASP S 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 246 through 251' Processing helix chain 'S' and resid 279 through 284 Processing helix chain 'S' and resid 284 through 289 removed outlier: 3.683A pdb=" N ASN S 288 " --> pdb=" O ARG S 284 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU S 289 " --> pdb=" O ARG S 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 284 through 289' Processing helix chain 'S' and resid 380 through 385 Processing helix chain 'S' and resid 447 through 452 removed outlier: 3.568A pdb=" N LEU S 450 " --> pdb=" O GLN S 447 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS S 451 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 3.993A 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 467 through 472 removed outlier: 3.541A pdb=" N PHE S 472 " --> pdb=" O LEU S 468 " (cutoff:3.500A) Processing helix chain 'S' and resid 492 through 501 removed outlier: 3.540A pdb=" N THR S 496 " --> pdb=" O ASN S 492 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR S 500 " --> pdb=" O THR S 496 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR S 501 " --> pdb=" O PHE S 497 " (cutoff:3.500A) Processing helix chain 'S' and resid 528 through 533 removed outlier: 3.877A pdb=" N LEU S 532 " --> pdb=" O SER S 528 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 587 removed outlier: 4.250A pdb=" N GLN S 581 " --> pdb=" O SER S 577 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA S 584 " --> pdb=" O ALA S 580 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL S 585 " --> pdb=" O GLN S 581 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR S 586 " --> pdb=" O PHE S 582 " (cutoff:3.500A) Processing helix chain 'S' and resid 593 through 605 removed outlier: 3.927A pdb=" N VAL S 599 " --> pdb=" O LEU S 595 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU S 602 " --> pdb=" O ASP S 598 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR S 603 " --> pdb=" O VAL S 599 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA S 604 " --> pdb=" O ILE S 600 " (cutoff:3.500A) Processing helix chain 'S' and resid 611 through 621 removed outlier: 3.544A pdb=" N VAL S 615 " --> pdb=" O LEU S 611 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU S 617 " --> pdb=" O CYS S 613 " (cutoff:3.500A) Processing helix chain 'S' and resid 623 through 629 removed outlier: 3.500A pdb=" N PHE S 627 " --> pdb=" O GLN S 623 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL S 628 " --> pdb=" O GLU S 624 " (cutoff:3.500A) Processing helix chain 'S' and resid 630 through 638 removed outlier: 3.692A pdb=" N ALA S 635 " --> pdb=" O MET S 631 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU S 636 " --> pdb=" O PRO S 632 " (cutoff:3.500A) Processing helix chain 'S' and resid 638 through 643 Processing helix chain 'S' and resid 653 through 664 removed outlier: 3.808A pdb=" N VAL S 657 " --> pdb=" O SER S 653 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET S 664 " --> pdb=" O ILE S 660 " (cutoff:3.500A) Processing helix chain 'S' and resid 670 through 695 removed outlier: 3.890A pdb=" N HIS S 676 " --> pdb=" O GLU S 672 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR S 677 " --> pdb=" O ALA S 673 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE S 680 " --> pdb=" O HIS S 676 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU S 681 " --> pdb=" O TYR S 677 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE S 685 " --> pdb=" O LEU S 681 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA S 690 " --> pdb=" O ALA S 686 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU S 692 " --> pdb=" O GLU S 688 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS S 693 " --> pdb=" O GLN S 689 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU S 694 " --> pdb=" O ALA S 690 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA S 695 " --> pdb=" O LEU S 691 " (cutoff:3.500A) Processing helix chain 'S' and resid 725 through 732 removed outlier: 3.678A pdb=" N ASP S 729 " --> pdb=" O ASP S 725 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET S 731 " --> pdb=" O PHE S 727 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN S 732 " --> pdb=" O THR S 728 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 756 removed outlier: 3.588A pdb=" N PHE S 756 " --> pdb=" O ASN S 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 752 through 756' Processing helix chain 'S' and resid 770 through 779 removed outlier: 3.795A pdb=" N TYR S 774 " --> pdb=" O LEU S 770 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 776 " --> pdb=" O ASN S 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG S 777 " --> pdb=" O ILE S 773 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL S 778 " --> pdb=" O TYR S 774 " (cutoff:3.500A) Processing helix chain 'S' and resid 799 through 808 removed outlier: 3.755A pdb=" N GLU S 803 " --> pdb=" O ASN S 799 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR S 808 " --> pdb=" O LYS S 804 " (cutoff:3.500A) Processing helix chain 'S' and resid 810 through 815 Processing helix chain 'S' and resid 825 through 834 removed outlier: 4.106A pdb=" N THR S 832 " --> pdb=" O ASN S 828 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU S 833 " --> pdb=" O VAL S 829 " (cutoff:3.500A) Processing helix chain 'S' and resid 858 through 863 Processing helix chain 'S' and resid 871 through 880 removed outlier: 3.663A pdb=" N ILE S 875 " --> pdb=" O THR S 871 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL S 877 " --> pdb=" O ASP S 873 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR S 880 " --> pdb=" O ARG S 876 " (cutoff:3.500A) Processing helix chain 'S' and resid 881 through 883 No H-bonds generated for 'chain 'S' and resid 881 through 883' Processing helix chain 'S' and resid 907 through 910 Processing helix chain 'S' and resid 931 through 936 Processing helix chain 'S' and resid 958 through 968 removed outlier: 3.699A pdb=" N LEU S 968 " --> pdb=" O TYR S 964 " (cutoff:3.500A) Processing helix chain 'S' and resid 969 through 972 removed outlier: 3.756A pdb=" N ARG S 972 " --> pdb=" O PRO S 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 969 through 972' Processing helix chain 'S' and resid 993 through 999 removed outlier: 3.747A pdb=" N TYR S 998 " --> pdb=" O PRO S 994 " (cutoff:3.500A) Processing helix chain 'S' and resid 1000 through 1002 No H-bonds generated for 'chain 'S' and resid 1000 through 1002' Processing helix chain 'S' and resid 1005 through 1014 removed outlier: 3.665A pdb=" N SER S1010 " --> pdb=" O PRO S1006 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S1012 " --> pdb=" O ALA S1008 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER S1014 " --> pdb=" O SER S1010 " (cutoff:3.500A) Processing helix chain 'S' and resid 1023 through 1030 removed outlier: 4.317A pdb=" N HIS S1030 " --> pdb=" O CYS S1026 " (cutoff:3.500A) Processing helix chain 'S' and resid 1132 through 1141 removed outlier: 3.753A pdb=" N MET S1138 " --> pdb=" O ASP S1134 " (cutoff:3.500A) Processing helix chain 'S' and resid 1211 through 1221 removed outlier: 4.452A pdb=" N ARG S1217 " --> pdb=" O GLU S1213 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU S1218 " --> pdb=" O SER S1214 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU S1219 " --> pdb=" O ALA S1215 " (cutoff:3.500A) Processing helix chain 'S' and resid 1236 through 1241 removed outlier: 4.293A pdb=" N GLN S1241 " --> pdb=" O PRO S1237 " (cutoff:3.500A) Processing helix chain 'S' and resid 1244 through 1250 Processing helix chain 'S' and resid 1266 through 1271 removed outlier: 3.537A pdb=" N PHE S1270 " --> pdb=" O CYS S1266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS S1271 " --> pdb=" O ARG S1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1266 through 1271' Processing helix chain 'S' and resid 1271 through 1276 Processing helix chain 'S' and resid 1277 through 1280 removed outlier: 4.208A pdb=" N ARG S1280 " --> pdb=" O ARG S1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 1277 through 1280' Processing helix chain 'S' and resid 1285 through 1290 removed outlier: 4.579A pdb=" N SER S1290 " --> pdb=" O VAL S1286 " (cutoff:3.500A) Processing helix chain 'S' and resid 1334 through 1342 removed outlier: 3.932A pdb=" N LEU S1338 " --> pdb=" O HIS S1334 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET S1342 " --> pdb=" O LEU S1338 " (cutoff:3.500A) Processing helix chain '3' and resid 14 through 20 removed outlier: 3.856A pdb=" N ASP 3 18 " --> pdb=" O ARG 3 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 3 19 " --> pdb=" O LEU 3 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 3 20 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 14 through 20' Processing helix chain '3' and resid 22 through 30 removed outlier: 3.948A pdb=" N ALA 3 26 " --> pdb=" O HIS 3 22 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR 3 30 " --> pdb=" O ALA 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 65 removed outlier: 3.542A pdb=" N VAL 3 43 " --> pdb=" O ALA 3 39 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE 3 51 " --> pdb=" O HIS 3 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG 3 63 " --> pdb=" O GLU 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 77 removed outlier: 3.655A pdb=" N HIS 3 73 " --> pdb=" O GLN 3 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 39 through 44 removed outlier: 3.707A pdb=" N ALA T 43 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG T 44 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 73 removed outlier: 3.764A 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 146 through 151 Processing helix chain 'T' and resid 152 through 183 removed outlier: 3.619A pdb=" N LYS T 157 " --> pdb=" O ALA T 153 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR T 158 " --> pdb=" O GLY T 154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER T 161 " --> pdb=" O LYS T 157 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY T 166 " --> pdb=" O ALA T 162 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU T 170 " --> pdb=" O GLY T 166 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY T 173 " --> pdb=" O ALA T 169 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU T 174 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL T 175 " --> pdb=" O GLU T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 193 Processing helix chain 'T' and resid 206 through 224 removed outlier: 3.578A pdb=" N LYS T 210 " --> pdb=" O LYS T 206 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET T 216 " --> pdb=" O ASP T 212 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 252 removed outlier: 3.622A pdb=" N LEU T 242 " --> pdb=" O LYS T 238 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP T 247 " --> pdb=" O THR T 243 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL T 252 " --> pdb=" O MET T 248 " (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: 3.953A pdb=" N ARG T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN T 288 " --> pdb=" O ARG T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 310 through 319 removed outlier: 3.989A pdb=" N VAL T 314 " --> pdb=" O GLY T 310 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR T 315 " --> pdb=" O ALA T 311 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 334 removed outlier: 3.755A pdb=" N ARG T 332 " --> pdb=" O GLN T 328 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE T 333 " --> pdb=" O PHE T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 351 removed outlier: 3.667A pdb=" N LEU T 350 " --> pdb=" O ASP T 346 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 454 removed outlier: 3.859A pdb=" N ALA T 449 " --> pdb=" O GLY T 445 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS T 451 " --> pdb=" O GLN T 447 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER T 452 " --> pdb=" O ASN T 448 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE T 453 " --> pdb=" O ALA T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 461 through 472 Processing helix chain 'T' and resid 497 through 502 removed outlier: 3.713A pdb=" N TYR T 501 " --> pdb=" O PHE T 497 " (cutoff:3.500A) Processing helix chain 'T' and resid 510 through 516 Processing helix chain 'T' and resid 519 through 525 removed outlier: 4.145A pdb=" N LEU T 524 " --> pdb=" O THR T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 571 through 587 removed outlier: 3.597A pdb=" N THR T 586 " --> pdb=" O PHE T 582 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN T 587 " --> pdb=" O ASP T 583 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 595 No H-bonds generated for 'chain 'T' and resid 593 through 595' Processing helix chain 'T' and resid 596 through 605 removed outlier: 3.763A pdb=" N ILE T 600 " --> pdb=" O THR T 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU T 602 " --> pdb=" O ASP T 598 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR T 603 " --> pdb=" O VAL T 599 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA T 604 " --> pdb=" O ILE T 600 " (cutoff:3.500A) Processing helix chain 'T' and resid 610 through 621 removed outlier: 3.762A pdb=" N TYR T 614 " --> pdb=" O PRO T 610 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA T 618 " --> pdb=" O TYR T 614 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET T 619 " --> pdb=" O VAL T 615 " (cutoff:3.500A) Processing helix chain 'T' and resid 624 through 630 removed outlier: 3.532A pdb=" N VAL T 628 " --> pdb=" O GLU T 624 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN T 630 " --> pdb=" O LYS T 626 " (cutoff:3.500A) Processing helix chain 'T' and resid 630 through 643 removed outlier: 3.763A pdb=" N ALA T 635 " --> pdb=" O MET T 631 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU T 636 " --> pdb=" O PRO T 632 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR T 640 " --> pdb=" O LEU T 636 " (cutoff:3.500A) Processing helix chain 'T' and resid 653 through 663 removed outlier: 3.765A pdb=" N VAL T 657 " --> pdb=" O SER T 653 " (cutoff:3.500A) Processing helix chain 'T' and resid 670 through 695 removed outlier: 4.160A pdb=" N HIS T 676 " --> pdb=" O GLU T 672 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR T 677 " --> pdb=" O ALA T 673 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS T 679 " --> pdb=" O GLY T 675 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA T 686 " --> pdb=" O GLY T 682 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU T 688 " --> pdb=" O LEU T 684 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU T 692 " --> pdb=" O GLU T 688 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS T 693 " --> pdb=" O GLN T 689 " (cutoff:3.500A) removed outlier: 3.772A 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 726 through 733 removed outlier: 3.604A pdb=" N LYS T 733 " --> pdb=" O ASP T 729 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 751 No H-bonds generated for 'chain 'T' and resid 749 through 751' Processing helix chain 'T' and resid 752 through 756 removed outlier: 3.697A pdb=" N PHE T 756 " --> pdb=" O ASN T 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 752 through 756' Processing helix chain 'T' and resid 764 through 768 removed outlier: 3.922A pdb=" N VAL T 767 " --> pdb=" O GLU T 764 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN T 768 " --> pdb=" O ASP T 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 764 through 768' Processing helix chain 'T' and resid 769 through 779 removed outlier: 3.774A pdb=" N TYR T 774 " --> pdb=" O LEU T 770 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN T 775 " --> pdb=" O VAL T 771 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR T 776 " --> pdb=" O ASN T 772 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG T 777 " --> pdb=" O ILE T 773 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL T 778 " --> pdb=" O TYR T 774 " (cutoff:3.500A) Processing helix chain 'T' and resid 799 through 808 removed outlier: 3.660A pdb=" N GLU T 803 " --> pdb=" O ASN T 799 " (cutoff:3.500A) Processing helix chain 'T' and resid 809 through 815 removed outlier: 3.721A pdb=" N VAL T 813 " --> pdb=" O VAL T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 825 through 834 removed outlier: 3.898A pdb=" N LEU T 831 " --> pdb=" O GLN T 827 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR T 832 " --> pdb=" O ASN T 828 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU T 833 " --> pdb=" O VAL T 829 " (cutoff:3.500A) Processing helix chain 'T' and resid 836 through 841 removed outlier: 3.672A pdb=" N PHE T 840 " --> pdb=" O ASN T 836 " (cutoff:3.500A) Processing helix chain 'T' and resid 849 through 853 Processing helix chain 'T' and resid 857 through 865 removed outlier: 4.194A pdb=" N ASP T 861 " --> pdb=" O GLY T 857 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA T 865 " --> pdb=" O ASP T 861 " (cutoff:3.500A) Processing helix chain 'T' and resid 871 through 880 removed outlier: 3.528A pdb=" N ILE T 875 " --> pdb=" O THR T 871 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL T 877 " --> pdb=" O ASP T 873 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU T 878 " --> pdb=" O MET T 874 " (cutoff:3.500A) Processing helix chain 'T' and resid 881 through 885 removed outlier: 3.536A pdb=" N CYS T 885 " --> pdb=" O PHE T 882 " (cutoff:3.500A) Processing helix chain 'T' and resid 950 through 958 removed outlier: 4.217A pdb=" N THR T 956 " --> pdb=" O LEU T 952 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU T 957 " --> pdb=" O VAL T 953 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS T 958 " --> pdb=" O ALA T 954 " (cutoff:3.500A) Processing helix chain 'T' and resid 958 through 968 removed outlier: 3.611A pdb=" N THR T 966 " --> pdb=" O ALA T 962 " (cutoff:3.500A) Processing helix chain 'T' and resid 969 through 973 removed outlier: 3.601A pdb=" N ARG T 972 " --> pdb=" O PRO T 969 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN T 973 " --> pdb=" O ASN T 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 969 through 973' Processing helix chain 'T' and resid 992 through 1000 removed outlier: 4.367A pdb=" N ALA T 996 " --> pdb=" O LYS T 992 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR T 998 " --> pdb=" O PRO T 994 " (cutoff:3.500A) Processing helix chain 'T' and resid 1008 through 1014 removed outlier: 3.723A pdb=" N MET T1012 " --> pdb=" O ALA T1008 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T1013 " --> pdb=" O ILE T1009 " (cutoff:3.500A) Processing helix chain 'T' and resid 1015 through 1017 No H-bonds generated for 'chain 'T' and resid 1015 through 1017' Processing helix chain 'T' and resid 1020 through 1031 removed outlier: 3.683A pdb=" N PHE T1024 " --> pdb=" O SER T1020 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE T1025 " --> pdb=" O ALA T1021 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS T1026 " --> pdb=" O PRO T1022 " (cutoff:3.500A) Processing helix chain 'T' and resid 1117 through 1122 removed outlier: 3.675A pdb=" N ILE T1121 " --> pdb=" O ASP T1117 " (cutoff:3.500A) Processing helix chain 'T' and resid 1129 through 1141 removed outlier: 3.530A pdb=" N LYS T1139 " --> pdb=" O TYR T1135 " (cutoff:3.500A) Processing helix chain 'T' and resid 1187 through 1191 removed outlier: 3.593A pdb=" N TYR T1190 " --> pdb=" O ASP T1187 " (cutoff:3.500A) Processing helix chain 'T' and resid 1211 through 1220 Processing helix chain 'T' and resid 1244 through 1250 Processing helix chain 'T' and resid 1266 through 1271 removed outlier: 3.528A pdb=" N PHE T1270 " --> pdb=" O CYS T1266 " (cutoff:3.500A) Processing helix chain 'T' and resid 1271 through 1276 Processing helix chain 'T' and resid 1277 through 1279 No H-bonds generated for 'chain 'T' and resid 1277 through 1279' Processing helix chain 'T' and resid 1281 through 1290 removed outlier: 3.662A pdb=" N GLU T1288 " --> pdb=" O THR T1284 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER T1290 " --> pdb=" O VAL T1286 " (cutoff:3.500A) Processing helix chain 'T' and resid 1319 through 1324 Processing helix chain 'T' and resid 1334 through 1344 removed outlier: 3.819A pdb=" N LEU T1338 " --> pdb=" O HIS T1334 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP T1339 " --> pdb=" O ARG T1335 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR T1341 " --> pdb=" O MET T1337 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET T1342 " --> pdb=" O LEU T1338 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 20 removed outlier: 3.856A pdb=" N ASP 1 18 " --> pdb=" O ARG 1 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 1 19 " --> pdb=" O LEU 1 15 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA 1 20 " --> pdb=" O ASP 1 16 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 14 through 20' Processing helix chain '1' and resid 22 through 30 removed outlier: 3.947A pdb=" N ALA 1 26 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR 1 30 " --> pdb=" O ALA 1 26 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 65 removed outlier: 3.542A pdb=" N VAL 1 43 " --> pdb=" O ALA 1 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE 1 51 " --> pdb=" O HIS 1 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG 1 63 " --> pdb=" O GLU 1 59 " (cutoff:3.500A) Processing helix chain '1' and resid 69 through 77 removed outlier: 3.655A pdb=" N HIS 1 73 " --> pdb=" O GLN 1 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 1 76 " --> pdb=" O ASP 1 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 18 removed outlier: 3.564A pdb=" N THR X 15 " --> pdb=" O PRO X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 24 Processing helix chain 'X' and resid 65 through 73 removed outlier: 3.506A pdb=" N THR X 69 " --> pdb=" O PHE X 66 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA X 70 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU X 71 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA X 72 " --> pdb=" O THR X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 137 Processing helix chain 'X' and resid 145 through 185 removed outlier: 3.902A pdb=" N THR X 150 " --> pdb=" O PRO X 146 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY X 154 " --> pdb=" O THR X 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA X 155 " --> pdb=" O GLU X 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS X 157 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR X 158 " --> pdb=" O GLY X 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY X 173 " --> pdb=" O ALA X 169 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL X 175 " --> pdb=" O GLU X 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS X 185 " --> pdb=" O VAL X 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 196 removed outlier: 4.860A pdb=" N THR X 194 " --> pdb=" O PHE X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 224 removed outlier: 3.677A pdb=" N SER X 211 " --> pdb=" O LYS X 207 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP X 212 " --> pdb=" O ALA X 208 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET X 216 " --> pdb=" O ASP X 212 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA X 219 " --> pdb=" O SER X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 231 Processing helix chain 'X' and resid 237 through 246 removed outlier: 3.510A pdb=" N THR X 243 " --> pdb=" O GLN X 239 " (cutoff:3.500A) Processing helix chain 'X' and resid 247 through 252 removed outlier: 3.987A pdb=" N VAL X 252 " --> pdb=" O MET X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 260 removed outlier: 4.523A pdb=" N GLY X 260 " --> pdb=" O VAL X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 279 through 290 removed outlier: 4.123A pdb=" N ARG X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN X 288 " --> pdb=" O ARG X 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 318 removed outlier: 3.804A pdb=" N THR X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 334 removed outlier: 3.667A pdb=" N PHE X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL X 334 " --> pdb=" O MET X 330 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 351 Processing helix chain 'X' and resid 379 through 384 removed outlier: 3.918A pdb=" N TYR X 383 " --> pdb=" O LEU X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 454 removed outlier: 3.765A pdb=" N ILE X 453 " --> pdb=" O ALA X 449 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS X 454 " --> pdb=" O LEU X 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 449 through 454' Processing helix chain 'X' and resid 463 through 468 removed outlier: 4.001A pdb=" N ALA X 467 " --> pdb=" O GLN X 463 " (cutoff:3.500A) Processing helix chain 'X' and resid 494 through 501 removed outlier: 3.937A pdb=" N TYR X 500 " --> pdb=" O THR X 496 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR X 501 " --> pdb=" O PHE X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 528 through 534 removed outlier: 3.953A pdb=" N LEU X 532 " --> pdb=" O SER X 528 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU X 534 " --> pdb=" O ARG X 530 " (cutoff:3.500A) Processing helix chain 'X' and resid 571 through 587 removed outlier: 4.046A pdb=" N GLN X 581 " --> pdb=" O SER X 577 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR X 586 " --> pdb=" O PHE X 582 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 605 removed outlier: 3.708A pdb=" N ILE X 597 " --> pdb=" O ASP X 593 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU X 602 " --> pdb=" O ASP X 598 " (cutoff:3.500A) Processing helix chain 'X' and resid 611 through 621 removed outlier: 3.532A pdb=" N VAL X 615 " --> pdb=" O LEU X 611 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU X 617 " --> pdb=" O CYS X 613 " (cutoff:3.500A) Processing helix chain 'X' and resid 623 through 629 removed outlier: 3.684A pdb=" N VAL X 628 " --> pdb=" O GLU X 624 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET X 629 " --> pdb=" O GLU X 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 630 through 643 removed outlier: 3.534A pdb=" N ALA X 635 " --> pdb=" O MET X 631 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU X 636 " --> pdb=" O PRO X 632 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN X 639 " --> pdb=" O ALA X 635 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 664 removed outlier: 3.786A pdb=" N VAL X 657 " --> pdb=" O SER X 653 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS X 661 " --> pdb=" O VAL X 657 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET X 664 " --> pdb=" O ILE X 660 " (cutoff:3.500A) Processing helix chain 'X' and resid 670 through 695 removed outlier: 3.805A pdb=" N HIS X 676 " --> pdb=" O GLU X 672 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR X 677 " --> pdb=" O ALA X 673 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE X 680 " --> pdb=" O HIS X 676 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU X 681 " --> pdb=" O TYR X 677 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU X 692 " --> pdb=" O GLU X 688 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS X 693 " --> pdb=" O GLN X 689 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU X 694 " --> pdb=" O ALA X 690 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA X 695 " --> pdb=" O LEU X 691 " (cutoff:3.500A) Processing helix chain 'X' and resid 705 through 710 removed outlier: 4.621A pdb=" N SER X 710 " --> pdb=" O THR X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 725 through 732 removed outlier: 3.785A pdb=" N ASP X 729 " --> pdb=" O ASP X 725 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET X 731 " --> pdb=" O PHE X 727 " (cutoff:3.500A) Processing helix chain 'X' and resid 749 through 751 No H-bonds generated for 'chain 'X' and resid 749 through 751' Processing helix chain 'X' and resid 752 through 756 removed outlier: 3.824A pdb=" N PHE X 756 " --> pdb=" O ASN X 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 752 through 756' Processing helix chain 'X' and resid 770 through 779 removed outlier: 3.904A pdb=" N TYR X 774 " --> pdb=" O LEU X 770 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR X 776 " --> pdb=" O ASN X 772 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL X 778 " --> pdb=" O TYR X 774 " (cutoff:3.500A) Processing helix chain 'X' and resid 799 through 808 removed outlier: 3.930A pdb=" N GLU X 803 " --> pdb=" O ASN X 799 " (cutoff:3.500A) Processing helix chain 'X' and resid 809 through 815 removed outlier: 3.638A pdb=" N VAL X 813 " --> pdb=" O VAL X 809 " (cutoff:3.500A) Processing helix chain 'X' and resid 825 through 835 removed outlier: 3.510A pdb=" N VAL X 829 " --> pdb=" O ASP X 825 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA X 830 " --> pdb=" O TYR X 826 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU X 831 " --> pdb=" O GLN X 827 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR X 832 " --> pdb=" O ASN X 828 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU X 833 " --> pdb=" O VAL X 829 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR X 835 " --> pdb=" O LEU X 831 " (cutoff:3.500A) Processing helix chain 'X' and resid 858 through 867 Processing helix chain 'X' and resid 871 through 881 removed outlier: 3.701A pdb=" N ILE X 875 " --> pdb=" O THR X 871 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR X 880 " --> pdb=" O ARG X 876 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER X 881 " --> pdb=" O VAL X 877 " (cutoff:3.500A) Processing helix chain 'X' and resid 908 through 910 No H-bonds generated for 'chain 'X' and resid 908 through 910' Processing helix chain 'X' and resid 931 through 936 Processing helix chain 'X' and resid 950 through 958 removed outlier: 4.557A pdb=" N THR X 956 " --> pdb=" O LEU X 952 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU X 957 " --> pdb=" O VAL X 953 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS X 958 " --> pdb=" O ALA X 954 " (cutoff:3.500A) Processing helix chain 'X' and resid 958 through 968 removed outlier: 3.585A pdb=" N LEU X 968 " --> pdb=" O TYR X 964 " (cutoff:3.500A) Processing helix chain 'X' and resid 969 through 973 removed outlier: 3.773A pdb=" N ARG X 972 " --> pdb=" O PRO X 969 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN X 973 " --> pdb=" O ASN X 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 969 through 973' Processing helix chain 'X' and resid 998 through 1002 removed outlier: 3.874A pdb=" N CYS X1002 " --> pdb=" O ALA X 999 " (cutoff:3.500A) Processing helix chain 'X' and resid 1005 through 1014 removed outlier: 3.879A pdb=" N SER X1010 " --> pdb=" O PRO X1006 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET X1012 " --> pdb=" O ALA X1008 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL X1013 " --> pdb=" O ILE X1009 " (cutoff:3.500A) Processing helix chain 'X' and resid 1020 through 1029 removed outlier: 3.713A pdb=" N PHE X1024 " --> pdb=" O SER X1020 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE X1025 " --> pdb=" O ALA X1021 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS X1026 " --> pdb=" O PRO X1022 " (cutoff:3.500A) Processing helix chain 'X' and resid 1117 through 1122 removed outlier: 4.104A 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 1211 through 1220 removed outlier: 3.621A pdb=" N GLU X1216 " --> pdb=" O ASN X1212 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG X1217 " --> pdb=" O GLU X1213 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU X1218 " --> pdb=" O SER X1214 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU X1219 " --> pdb=" O ALA X1215 " (cutoff:3.500A) Processing helix chain 'X' and resid 1236 through 1241 removed outlier: 4.321A pdb=" N GLN X1241 " --> pdb=" O PRO X1237 " (cutoff:3.500A) Processing helix chain 'X' and resid 1244 through 1250 Processing helix chain 'X' and resid 1266 through 1271 removed outlier: 3.670A pdb=" N HIS X1271 " --> pdb=" O ARG X1267 " (cutoff:3.500A) Processing helix chain 'X' and resid 1271 through 1276 Processing helix chain 'X' and resid 1277 through 1280 removed outlier: 4.194A pdb=" N ARG X1280 " --> pdb=" O ARG X1277 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1277 through 1280' Processing helix chain 'X' and resid 1281 through 1292 removed outlier: 3.578A pdb=" N VAL X1286 " --> pdb=" O LEU X1282 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER X1290 " --> pdb=" O VAL X1286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA X1291 " --> pdb=" O ASN X1287 " (cutoff:3.500A) Processing helix chain 'X' and resid 1319 through 1324 removed outlier: 3.700A pdb=" N LEU X1323 " --> pdb=" O PRO X1319 " (cutoff:3.500A) Processing helix chain 'X' and resid 1334 through 1344 removed outlier: 3.991A pdb=" N LEU X1338 " --> pdb=" O HIS X1334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET X1342 " --> pdb=" O LEU X1338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER X1343 " --> pdb=" O ASP X1339 " (cutoff:3.500A) Processing helix chain '0' and resid 14 through 20 removed outlier: 3.855A pdb=" N ASP 0 18 " --> pdb=" O ARG 0 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 0 20 " --> pdb=" O ASP 0 16 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 14 through 20' Processing helix chain '0' and resid 22 through 30 removed outlier: 3.947A pdb=" N ALA 0 26 " --> pdb=" O HIS 0 22 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR 0 30 " --> pdb=" O ALA 0 26 " (cutoff:3.500A) Processing helix chain '0' and resid 37 through 65 removed outlier: 3.542A pdb=" N VAL 0 43 " --> pdb=" O ALA 0 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE 0 51 " --> pdb=" O HIS 0 47 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG 0 63 " --> pdb=" O GLU 0 59 " (cutoff:3.500A) Processing helix chain '0' and resid 69 through 77 removed outlier: 3.654A pdb=" N HIS 0 73 " --> pdb=" O GLN 0 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 29 removed outlier: 3.768A pdb=" N ALA W 28 " --> pdb=" O LYS W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 43 removed outlier: 3.667A pdb=" N ALA W 43 " --> pdb=" O GLY W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 73 removed outlier: 3.557A pdb=" N ALA W 72 " --> pdb=" O THR W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 138 Processing helix chain 'W' and resid 145 through 153 removed outlier: 3.839A pdb=" N THR W 150 " --> pdb=" O PRO W 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU W 151 " --> pdb=" O LEU W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 169 removed outlier: 3.573A pdb=" N PHE W 165 " --> pdb=" O SER W 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 185 removed outlier: 3.610A pdb=" N VAL W 175 " --> pdb=" O GLU W 171 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS W 185 " --> pdb=" O VAL W 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 197 removed outlier: 4.557A pdb=" N THR W 194 " --> pdb=" O PHE W 190 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU W 195 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP W 197 " --> pdb=" O LYS W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 225 removed outlier: 3.694A pdb=" N SER W 215 " --> pdb=" O SER W 211 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET W 216 " --> pdb=" O ASP W 212 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA W 219 " --> pdb=" O SER W 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER W 225 " --> pdb=" O LEU W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 231 Processing helix chain 'W' and resid 237 through 246 removed outlier: 3.658A pdb=" N LEU W 242 " --> pdb=" O LYS W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 270 removed outlier: 3.883A pdb=" N GLY W 269 " --> pdb=" O THR W 266 " (cutoff:3.500A) removed outlier: 3.667A 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: 3.568A pdb=" N ARG W 284 " --> pdb=" O ASP W 280 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG W 285 " --> pdb=" O SER W 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN W 288 " --> pdb=" O ARG W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 318 removed outlier: 3.595A pdb=" N THR W 315 " --> pdb=" O ALA W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 334 removed outlier: 3.722A pdb=" N ALA W 331 " --> pdb=" O GLU W 327 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG W 332 " --> pdb=" O GLN W 328 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE W 333 " --> pdb=" O PHE W 329 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 351 removed outlier: 4.854A pdb=" N ALA W 348 " --> pdb=" O GLU W 344 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA W 349 " --> pdb=" O GLY W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.543A pdb=" N GLU W 385 " --> pdb=" O ARG W 381 " (cutoff:3.500A) Processing helix chain 'W' and resid 461 through 472 removed outlier: 3.558A pdb=" N ALA W 471 " --> pdb=" O ALA W 467 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE W 472 " --> pdb=" O LEU W 468 " (cutoff:3.500A) Processing helix chain 'W' and resid 494 through 502 removed outlier: 3.527A pdb=" N GLN W 499 " --> pdb=" O ARG W 495 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR W 500 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR W 501 " --> pdb=" O PHE W 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 512 through 516 Processing helix chain 'W' and resid 519 through 525 removed outlier: 3.657A 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: 3.565A pdb=" N GLN W 581 " --> pdb=" O SER W 577 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL W 585 " --> pdb=" O GLN W 581 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR W 586 " --> pdb=" O PHE W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 593 through 605 removed outlier: 3.699A pdb=" N ILE W 597 " --> pdb=" O ASP W 593 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP W 598 " --> pdb=" O GLN W 594 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL W 599 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing helix chain 'W' and resid 611 through 621 removed outlier: 3.796A pdb=" N ALA W 618 " --> pdb=" O TYR W 614 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS W 621 " --> pdb=" O GLU W 617 " (cutoff:3.500A) Processing helix chain 'W' and resid 623 through 630 removed outlier: 3.662A pdb=" N VAL W 628 " --> pdb=" O GLU W 624 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET W 629 " --> pdb=" O GLU W 625 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN W 630 " --> pdb=" O LYS W 626 " (cutoff:3.500A) Processing helix chain 'W' and resid 630 through 645 removed outlier: 3.579A pdb=" N ALA W 635 " --> pdb=" O MET W 631 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL W 643 " --> pdb=" O GLN W 639 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER W 645 " --> pdb=" O TYR W 641 " (cutoff:3.500A) Processing helix chain 'W' and resid 653 through 663 removed outlier: 3.603A pdb=" N VAL W 657 " --> pdb=" O SER W 653 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS W 661 " --> pdb=" O VAL W 657 " (cutoff:3.500A) Processing helix chain 'W' and resid 670 through 695 removed outlier: 4.328A pdb=" N HIS W 676 " --> pdb=" O GLU W 672 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR W 677 " --> pdb=" O ALA W 673 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA W 686 " --> pdb=" O GLY W 682 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU W 688 " --> pdb=" O LEU W 684 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA W 690 " --> pdb=" O ALA W 686 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA W 695 " --> pdb=" O LEU W 691 " (cutoff:3.500A) Processing helix chain 'W' and resid 705 through 710 removed outlier: 4.552A pdb=" N SER W 710 " --> pdb=" O THR W 706 " (cutoff:3.500A) Processing helix chain 'W' and resid 726 through 734 removed outlier: 3.663A pdb=" N GLN W 732 " --> pdb=" O THR W 728 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS W 733 " --> pdb=" O ASP W 729 " (cutoff:3.500A) Processing helix chain 'W' and resid 749 through 753 Processing helix chain 'W' and resid 769 through 779 removed outlier: 4.180A pdb=" N ARG W 777 " --> pdb=" O ILE W 773 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL W 778 " --> pdb=" O TYR W 774 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN W 779 " --> pdb=" O GLN W 775 " (cutoff:3.500A) Processing helix chain 'W' and resid 799 through 809 removed outlier: 3.832A pdb=" N GLU W 803 " --> pdb=" O ASN W 799 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL W 809 " --> pdb=" O LEU W 805 " (cutoff:3.500A) Processing helix chain 'W' and resid 809 through 815 removed outlier: 3.680A pdb=" N VAL W 813 " --> pdb=" O VAL W 809 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS W 814 " --> pdb=" O LEU W 810 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 834 removed outlier: 3.530A pdb=" N ALA W 830 " --> pdb=" O TYR W 826 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU W 831 " --> pdb=" O GLN W 827 " (cutoff:3.500A) Processing helix chain 'W' and resid 836 through 840 removed outlier: 3.545A pdb=" N VAL W 839 " --> pdb=" O ASN W 836 " (cutoff:3.500A) Processing helix chain 'W' and resid 849 through 853 Processing helix chain 'W' and resid 858 through 864 Processing helix chain 'W' and resid 871 through 879 removed outlier: 3.620A pdb=" N ILE W 875 " --> pdb=" O THR W 871 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU W 878 " --> pdb=" O MET W 874 " (cutoff:3.500A) Processing helix chain 'W' and resid 880 through 885 removed outlier: 3.744A pdb=" N THR W 884 " --> pdb=" O SER W 881 " (cutoff:3.500A) Processing helix chain 'W' and resid 908 through 910 No H-bonds generated for 'chain 'W' and resid 908 through 910' Processing helix chain 'W' and resid 950 through 958 removed outlier: 4.431A pdb=" N THR W 956 " --> pdb=" O LEU W 952 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU W 957 " --> pdb=" O VAL W 953 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS W 958 " --> pdb=" O ALA W 954 " (cutoff:3.500A) Processing helix chain 'W' and resid 958 through 968 removed outlier: 3.852A pdb=" N TYR W 964 " --> pdb=" O LEU W 960 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR W 966 " --> pdb=" O ALA W 962 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU W 968 " --> pdb=" O TYR W 964 " (cutoff:3.500A) Processing helix chain 'W' and resid 969 through 973 removed outlier: 3.693A pdb=" N ARG W 972 " --> pdb=" O PRO W 969 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN W 973 " --> pdb=" O ASN W 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 969 through 973' Processing helix chain 'W' and resid 992 through 1001 removed outlier: 4.251A pdb=" N ALA W 996 " --> pdb=" O LYS W 992 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER W1001 " --> pdb=" O ALA W 997 " (cutoff:3.500A) Processing helix chain 'W' and resid 1006 through 1014 removed outlier: 3.588A pdb=" N SER W1010 " --> pdb=" O PRO W1006 " (cutoff:3.500A) Processing helix chain 'W' and resid 1015 through 1017 No H-bonds generated for 'chain 'W' and resid 1015 through 1017' Processing helix chain 'W' and resid 1020 through 1031 removed outlier: 3.749A pdb=" N PHE W1024 " --> pdb=" O SER W1020 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE W1025 " --> pdb=" O ALA W1021 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS W1026 " --> pdb=" O PRO W1022 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS W1030 " --> pdb=" O CYS W1026 " (cutoff:3.500A) Processing helix chain 'W' and resid 1117 through 1122 removed outlier: 3.819A pdb=" N ILE W1121 " --> pdb=" O ASP W1117 " (cutoff:3.500A) Processing helix chain 'W' and resid 1132 through 1141 removed outlier: 3.683A pdb=" N MET W1138 " --> pdb=" O ASP W1134 " (cutoff:3.500A) Processing helix chain 'W' and resid 1211 through 1221 removed outlier: 3.671A pdb=" N LEU W1219 " --> pdb=" O ALA W1215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP W1221 " --> pdb=" O ARG W1217 " (cutoff:3.500A) Processing helix chain 'W' and resid 1244 through 1251 removed outlier: 3.536A pdb=" N ASN W1251 " --> pdb=" O ASP W1247 " (cutoff:3.500A) Processing helix chain 'W' and resid 1264 through 1269 removed outlier: 3.524A pdb=" N GLN W1268 " --> pdb=" O PRO W1265 " (cutoff:3.500A) Processing helix chain 'W' and resid 1271 through 1276 Processing helix chain 'W' and resid 1277 through 1280 removed outlier: 4.188A 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: 4.151A pdb=" N SER W1290 " --> pdb=" O VAL W1286 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA W1291 " --> pdb=" O ASN W1287 " (cutoff:3.500A) Processing helix chain 'W' and resid 1334 through 1344 removed outlier: 4.301A pdb=" N LEU W1338 " --> pdb=" O HIS W1334 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP W1339 " --> pdb=" O ARG W1335 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET W1342 " --> pdb=" O LEU W1338 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN W1344 " --> pdb=" O GLU W1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'k' and resid 62 through 63 removed outlier: 4.487A pdb=" N HIS k 20 " --> pdb=" O CYS k 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 40 through 46 removed outlier: 3.819A pdb=" N SER k 103 " --> pdb=" O ILE k 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'k' and resid 320 through 321 removed outlier: 3.682A pdb=" N ILE k 320 " --> pdb=" O TRP l 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 379 through 384 removed outlier: 5.219A pdb=" N LEU k 380 " --> pdb=" O VAL k 369 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL k 369 " --> pdb=" O LEU k 380 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS k 365 " --> pdb=" O LEU k 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 70 through 76 removed outlier: 5.805A pdb=" N ALA 5 180 " --> pdb=" O MET 5 165 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET 5 165 " --> pdb=" O ALA 5 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 104 through 105 removed outlier: 4.660A pdb=" N MET 5 104 " --> pdb=" O PHE 5 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR 5 160 " --> pdb=" O SER 5 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 183 through 184 removed outlier: 3.567A pdb=" N GLY 5 183 " --> pdb=" O ALA 5 322 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE 5 226 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR 5 293 " --> pdb=" O VAL 5 224 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL 5 224 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR 5 225 " --> pdb=" O SER 5 248 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER 5 248 " --> pdb=" O THR 5 225 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN 5 247 " --> pdb=" O VAL 5 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 183 through 184 removed outlier: 3.567A pdb=" N GLY 5 183 " --> pdb=" O ALA 5 322 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY 5 286 " --> pdb=" O PHE 5 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 198 through 200 Processing sheet with id=AB1, first strand: chain '5' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain '6' and resid 30 through 33 removed outlier: 3.583A pdb=" N THR 6 70 " --> pdb=" O LEU 6 33 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG 6 83 " --> pdb=" O GLU 6 75 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL 6 77 " --> pdb=" O SER 6 81 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER 6 81 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '6' and resid 91 through 92 removed outlier: 3.756A pdb=" N ASP 6 91 " --> pdb=" O TYR 6 302 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL 6 288 " --> pdb=" O THR 6 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR 6 109 " --> pdb=" O VAL 6 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 95 through 96 removed outlier: 3.626A pdb=" N ALA 6 290 " --> pdb=" O SER 6 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '6' and resid 125 through 127 removed outlier: 3.629A pdb=" N ILE 6 125 " --> pdb=" O ILE 6 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '6' and resid 180 through 182 Processing sheet with id=AB7, first strand: chain '7' and resid 8 through 9 removed outlier: 6.535A pdb=" N VAL 7 8 " --> pdb=" O GLN 7 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '7' and resid 30 through 33 removed outlier: 7.108A pdb=" N ARG 7 83 " --> pdb=" O GLU 7 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '7' and resid 92 through 96 removed outlier: 7.216A pdb=" N ALA 7 297 " --> pdb=" O TYR 7 291 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR 7 291 " --> pdb=" O ALA 7 297 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER 7 299 " --> pdb=" O TYR 7 289 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 7 285 " --> pdb=" O SER 7 303 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL 7 113 " --> pdb=" O PRO 7 284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '7' and resid 124 through 126 Processing sheet with id=AC2, first strand: chain '7' and resid 180 through 183 Processing sheet with id=AC3, first strand: chain 'b' and resid 44 through 46 Processing sheet with id=AC4, first strand: chain 'b' and resid 44 through 46 removed outlier: 6.400A pdb=" N VAL W 76 " --> pdb=" O MET W1061 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL W1063 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR W 78 " --> pdb=" O VAL W1063 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 69 through 76 removed outlier: 5.537A pdb=" N ALA b 180 " --> pdb=" O MET b 165 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET b 165 " --> pdb=" O ALA b 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 104 through 105 removed outlier: 4.561A pdb=" N MET b 104 " --> pdb=" O PHE b 93 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR b 160 " --> pdb=" O SER b 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 204 through 206 removed outlier: 3.673A pdb=" N GLN b 247 " --> pdb=" O VAL b 205 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY b 292 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA b 228 " --> pdb=" O THR b 290 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR b 290 " --> pdb=" O ALA b 228 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU b 230 " --> pdb=" O VAL b 288 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL b 288 " --> pdb=" O LEU b 230 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR b 232 " --> pdb=" O GLY b 286 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY b 286 " --> pdb=" O TYR b 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 303 through 305 Processing sheet with id=AC9, first strand: chain 'c' and resid 30 through 33 removed outlier: 3.814A pdb=" N THR c 70 " --> pdb=" O LEU c 33 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU c 71 " --> pdb=" O MET c 87 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG c 83 " --> pdb=" O GLU c 75 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN c 40 " --> pdb=" O VAL c 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 92 through 93 removed outlier: 7.028A pdb=" N SER c 299 " --> pdb=" O TYR c 289 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP c 301 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS c 287 " --> pdb=" O TRP c 301 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 124 through 125 Processing sheet with id=AD3, first strand: chain 'c' and resid 180 through 182 Processing sheet with id=AD4, first strand: chain 'd' and resid 31 through 33 removed outlier: 7.411A pdb=" N ARG d 83 " --> pdb=" O GLU d 75 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL d 8 " --> pdb=" O GLN d 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 92 through 96 removed outlier: 7.005A pdb=" N ALA d 297 " --> pdb=" O TYR d 291 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR d 291 " --> pdb=" O ALA d 297 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER d 299 " --> pdb=" O TYR d 289 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG d 285 " --> pdb=" O SER d 303 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR d 109 " --> pdb=" O VAL d 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 124 through 127 removed outlier: 3.699A pdb=" N ILE d 134 " --> pdb=" O ILE d 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 180 through 183 Processing sheet with id=AD8, first strand: chain '4' and resid 121 through 123 removed outlier: 6.470A pdb=" N VAL 4 76 " --> pdb=" O MET 41061 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '4' and resid 91 through 96 removed outlier: 3.642A pdb=" N LYS 4 118 " --> pdb=" O ILE 4 91 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL 4 116 " --> pdb=" O PHE 4 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4' and resid 126 through 132 removed outlier: 3.745A pdb=" N THR 41079 " --> pdb=" O ARG 41071 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER 41067 " --> pdb=" O THR 41083 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '4' and resid 265 through 266 Processing sheet with id=AE3, first strand: chain '4' and resid 368 through 369 removed outlier: 7.651A pdb=" N ALA 4 375 " --> pdb=" O ALA 4 273 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL 4 275 " --> pdb=" O ALA 4 375 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU 4 377 " --> pdb=" O VAL 4 275 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU 4 277 " --> pdb=" O GLU 4 377 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL 41041 " --> pdb=" O GLU 41178 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '4' and resid 1097 through 1104 removed outlier: 5.368A pdb=" N GLU 41049 " --> pdb=" O ALA 41102 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL 41104 " --> pdb=" O LEU 41047 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU 41047 " --> pdb=" O VAL 41104 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '4' and resid 307 through 309 removed outlier: 5.665A pdb=" N LYS X 33 " --> pdb=" O LEU X 54 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU X 54 " --> pdb=" O LYS X 33 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE X 35 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA X 52 " --> pdb=" O PHE X 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '4' and resid 433 through 435 Processing sheet with id=AE7, first strand: chain '4' and resid 542 through 544 Processing sheet with id=AE8, first strand: chain '4' and resid 740 through 741 Processing sheet with id=AE9, first strand: chain '4' and resid 822 through 823 Processing sheet with id=AF1, first strand: chain '4' and resid 896 through 897 removed outlier: 3.607A pdb=" N THR 4 896 " --> pdb=" O VAL 4 913 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 1331 through 1332 Processing sheet with id=AF3, first strand: chain 'S' and resid 13 through 14 removed outlier: 7.242A pdb=" N ALA W 52 " --> pdb=" O ILE X 87 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY X 89 " --> pdb=" O ALA W 52 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU W 54 " --> pdb=" O GLY X 89 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE X 91 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL W 56 " --> pdb=" O ILE X 91 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE X 93 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR W 58 " --> pdb=" O PHE X 93 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE X 95 " --> pdb=" O THR W 58 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG X 112 " --> pdb=" O MET X 97 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 13 through 14 Processing sheet with id=AF5, first strand: chain 'S' and resid 51 through 52 removed outlier: 6.287A pdb=" N GLU S 51 " --> pdb=" O ALA T 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'W' and resid 13 through 15 removed outlier: 7.600A pdb=" N VAL S 56 " --> pdb=" O LEU W 13 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR W 15 " --> pdb=" O VAL S 56 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR S 58 " --> pdb=" O THR W 15 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN S 59 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 76 through 77 Processing sheet with id=AF8, first strand: chain 'S' and resid 76 through 77 removed outlier: 6.846A pdb=" N THR S1079 " --> pdb=" O ARG S1071 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG S1071 " --> pdb=" O THR S1079 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 90 through 97 removed outlier: 4.548A pdb=" N ARG S 112 " --> pdb=" O MET S 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 265 through 266 Processing sheet with id=AG2, first strand: chain 'S' and resid 1180 through 1182 removed outlier: 6.757A pdb=" N PHE S 373 " --> pdb=" O VAL S 272 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY S 274 " --> pdb=" O PHE S 373 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER S 365 " --> pdb=" O ILE S 376 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 1097 through 1106 removed outlier: 7.057A pdb=" N SER S1097 " --> pdb=" O SER S1055 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER S1055 " --> pdb=" O SER S1097 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE S1099 " --> pdb=" O TYR S1053 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR S1053 " --> pdb=" O ILE S1099 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE S1051 " --> pdb=" O PRO S1101 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU S1047 " --> pdb=" O ALA S1105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 1316 through 1317 removed outlier: 6.666A pdb=" N LEU S1047 " --> pdb=" O ALA S1105 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE S1051 " --> pdb=" O PRO S1101 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR S1053 " --> pdb=" O ILE S1099 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE S1099 " --> pdb=" O TYR S1053 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER S1055 " --> pdb=" O SER S1097 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER S1097 " --> pdb=" O SER S1055 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 432 through 435 removed outlier: 3.751A pdb=" N THR S 432 " --> pdb=" O PHE S 444 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 540 through 545 Processing sheet with id=AG7, first strand: chain 'S' and resid 721 through 722 removed outlier: 3.624A pdb=" N GLN S 745 " --> pdb=" O ILE S 742 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 757 through 759 Processing sheet with id=AG9, first strand: chain 'S' and resid 922 through 924 Processing sheet with id=AH1, first strand: chain 'S' and resid 1109 through 1110 Processing sheet with id=AH2, first strand: chain 'S' and resid 1368 through 1370 removed outlier: 3.635A pdb=" N VAL S1375 " --> pdb=" O LEU S1368 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU S1370 " --> pdb=" O LYS S1373 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS S1373 " --> pdb=" O LEU S1370 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'T' and resid 121 through 125 removed outlier: 6.343A pdb=" N VAL T 76 " --> pdb=" O MET T1061 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL T1063 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR T 78 " --> pdb=" O VAL T1063 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 129 through 132 removed outlier: 3.733A pdb=" N ILE T 129 " --> pdb=" O PHE T1080 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA T1077 " --> pdb=" O VAL T1073 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL T1073 " --> pdb=" O ALA T1077 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR T1079 " --> pdb=" O ARG T1071 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 265 through 266 Processing sheet with id=AH6, first strand: chain 'T' and resid 366 through 369 removed outlier: 5.842A pdb=" N ALA T 375 " --> pdb=" O ALA T 273 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL T 275 " --> pdb=" O ALA T 375 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU T 377 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU T 277 " --> pdb=" O GLU T 377 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.130A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'T' and resid 1101 through 1107 removed outlier: 6.130A pdb=" N VAL T1104 " --> pdb=" O GLU T1049 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU T1049 " --> pdb=" O VAL T1104 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA T1106 " --> pdb=" O LEU T1047 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'T' and resid 432 through 435 removed outlier: 3.623A pdb=" N THR T 432 " --> pdb=" O PHE T 444 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'T' and resid 540 through 545 Processing sheet with id=AI2, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AI3, first strand: chain 'T' and resid 721 through 722 Processing sheet with id=AI4, first strand: chain 'T' and resid 757 through 759 removed outlier: 5.786A pdb=" N ASN T 758 " --> pdb=" O VAL T 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'T' and resid 922 through 924 removed outlier: 3.671A pdb=" N PHE T 922 " --> pdb=" O MET T 822 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'T' and resid 1109 through 1110 Processing sheet with id=AI7, first strand: chain 'T' and resid 1331 through 1332 removed outlier: 3.514A pdb=" N ALA T1331 " --> pdb=" O ILE T1358 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'T' and resid 1368 through 1370 removed outlier: 3.682A pdb=" N LYS T1373 " --> pdb=" O LEU T1370 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'X' and resid 121 through 132 removed outlier: 6.188A pdb=" N VAL X 76 " --> pdb=" O MET X1061 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL X1063 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR X 78 " --> pdb=" O VAL X1063 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR X 306 " --> pdb=" O GLU X 79 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'X' and resid 121 through 132 Processing sheet with id=AJ2, first strand: chain 'X' and resid 265 through 266 Processing sheet with id=AJ3, first strand: chain 'X' and resid 1178 through 1182 removed outlier: 6.806A pdb=" N PHE X 373 " --> pdb=" O VAL X 272 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY X 274 " --> pdb=" O PHE X 373 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR X 278 " --> pdb=" O GLU X 377 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'X' and resid 1097 through 1107 removed outlier: 7.234A pdb=" N SER X1097 " --> pdb=" O SER X1055 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER X1055 " --> pdb=" O SER X1097 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE X1099 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR X1053 " --> pdb=" O ILE X1099 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE X1051 " --> pdb=" O PRO X1101 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU X1047 " --> pdb=" O ALA X1105 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE X1107 " --> pdb=" O GLU X1045 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLU X1045 " --> pdb=" O ILE X1107 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N TYR X1327 " --> pdb=" O GLN X 397 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR X 399 " --> pdb=" O TYR X1327 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'X' and resid 1316 through 1317 removed outlier: 6.461A pdb=" N ARG X 395 " --> pdb=" O ASP X1317 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLU X1045 " --> pdb=" O ILE X1107 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE X1107 " --> pdb=" O GLU X1045 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU X1047 " --> pdb=" O ALA X1105 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE X1051 " --> pdb=" O PRO X1101 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR X1053 " --> pdb=" O ILE X1099 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE X1099 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER X1055 " --> pdb=" O SER X1097 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER X1097 " --> pdb=" O SER X1055 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'X' and resid 432 through 435 removed outlier: 3.501A pdb=" N THR X 432 " --> pdb=" O PHE X 444 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'X' and resid 540 through 545 Processing sheet with id=AJ8, first strand: chain 'X' and resid 721 through 722 removed outlier: 3.520A pdb=" N ALA X 722 " --> pdb=" O LEU X 918 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG X 893 " --> pdb=" O LYS X 741 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN X 745 " --> pdb=" O ILE X 742 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'X' and resid 721 through 722 removed outlier: 3.520A pdb=" N ALA X 722 " --> pdb=" O LEU X 918 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'X' and resid 757 through 759 Processing sheet with id=AK2, first strand: chain 'X' and resid 922 through 924 Processing sheet with id=AK3, first strand: chain 'X' and resid 1331 through 1332 removed outlier: 3.542A pdb=" N ALA X1331 " --> pdb=" O ILE X1358 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'X' and resid 1368 through 1369 Processing sheet with id=AK5, first strand: chain 'W' and resid 90 through 95 removed outlier: 3.678A pdb=" N VAL W 116 " --> pdb=" O PHE W 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE W 95 " --> pdb=" O TYR W 114 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'W' and resid 130 through 132 removed outlier: 7.185A pdb=" N ALA W1077 " --> pdb=" O VAL W1073 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL W1073 " --> pdb=" O ALA W1077 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR W1079 " --> pdb=" O ARG W1071 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'W' and resid 365 through 369 removed outlier: 4.484A pdb=" N SER W 365 " --> pdb=" O ILE W 376 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA W 375 " --> pdb=" O ALA W 273 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL W 275 " --> pdb=" O ALA W 375 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU W 377 " --> pdb=" O VAL W 275 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU W 277 " --> pdb=" O GLU W 377 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'W' and resid 297 through 300 removed outlier: 3.696A pdb=" N GLY W 299 " --> pdb=" O THR W 360 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'W' and resid 1101 through 1107 removed outlier: 6.641A pdb=" N LEU W1047 " --> pdb=" O ALA W1105 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE W1107 " --> pdb=" O GLU W1045 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU W1045 " --> pdb=" O ILE W1107 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'W' and resid 1180 through 1182 Processing sheet with id=AL2, first strand: chain 'W' and resid 432 through 434 removed outlier: 3.562A pdb=" N THR W 432 " --> pdb=" O PHE W 444 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'W' and resid 540 through 545 Processing sheet with id=AL4, first strand: chain 'W' and resid 721 through 722 removed outlier: 3.535A pdb=" N ARG W 893 " --> pdb=" O LYS W 741 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'W' and resid 757 through 758 Processing sheet with id=AL6, first strand: chain 'W' and resid 922 through 924 removed outlier: 3.791A pdb=" N PHE W 922 " --> pdb=" O MET W 822 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY W 821 " --> pdb=" O VAL W 942 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'W' and resid 1331 through 1332 removed outlier: 3.644A pdb=" N ALA W1331 " --> pdb=" O ILE W1358 " (cutoff:3.500A) 2291 hydrogen bonds defined for protein. 6297 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: 32.16 Time building geometry restraints manager: 23.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19948 1.33 - 1.45: 14219 1.45 - 1.58: 40246 1.58 - 1.70: 0 1.70 - 1.82: 793 Bond restraints: 75206 Sorted by residual: bond pdb=" N THR W 263 " pdb=" CA THR W 263 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.29e-02 6.01e+03 1.79e+01 bond pdb=" C SER S 993 " pdb=" N PRO S 994 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.08e-02 8.57e+03 1.55e+01 bond pdb=" N THR T 263 " pdb=" CA THR T 263 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" C SER X 993 " pdb=" N PRO X 994 " ideal model delta sigma weight residual 1.336 1.374 -0.039 1.08e-02 8.57e+03 1.28e+01 bond pdb=" N ASP W 849 " pdb=" CA ASP W 849 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 75201 not shown) Histogram of bond angle deviations from ideal: 96.05 - 105.08: 1903 105.08 - 114.11: 43436 114.11 - 123.13: 52144 123.13 - 132.16: 4638 132.16 - 141.18: 81 Bond angle restraints: 102202 Sorted by residual: angle pdb=" C TYR 4 798 " pdb=" N ASN 4 799 " pdb=" CA ASN 4 799 " ideal model delta sigma weight residual 121.70 134.73 -13.03 1.80e+00 3.09e-01 5.24e+01 angle pdb=" N GLY W 421 " pdb=" CA GLY W 421 " pdb=" C GLY W 421 " ideal model delta sigma weight residual 112.49 120.69 -8.20 1.21e+00 6.83e-01 4.59e+01 angle pdb=" N VAL T1113 " pdb=" CA VAL T1113 " pdb=" CB VAL T1113 " ideal model delta sigma weight residual 112.33 104.53 7.80 1.19e+00 7.06e-01 4.30e+01 angle pdb=" C ALA 0 20 " pdb=" N HIS 0 21 " pdb=" CA HIS 0 21 " ideal model delta sigma weight residual 121.70 133.22 -11.52 1.80e+00 3.09e-01 4.09e+01 angle pdb=" C ALA 1 20 " pdb=" N HIS 1 21 " pdb=" CA HIS 1 21 " ideal model delta sigma weight residual 121.70 133.22 -11.52 1.80e+00 3.09e-01 4.09e+01 ... (remaining 102197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 43031 16.30 - 32.61: 1801 32.61 - 48.91: 437 48.91 - 65.21: 21 65.21 - 81.51: 59 Dihedral angle restraints: 45349 sinusoidal: 18001 harmonic: 27348 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 180.00 121.72 58.28 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA ASP 4 842 " pdb=" C ASP 4 842 " pdb=" N VAL 4 843 " pdb=" CA VAL 4 843 " ideal model delta harmonic sigma weight residual -180.00 -124.40 -55.60 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA LEU 4 313 " pdb=" C LEU 4 313 " pdb=" N VAL 4 314 " pdb=" CA VAL 4 314 " ideal model delta harmonic sigma weight residual -180.00 -126.50 -53.50 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 45346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 9471 0.070 - 0.141: 1824 0.141 - 0.211: 228 0.211 - 0.282: 28 0.282 - 0.352: 4 Chirality restraints: 11555 Sorted by residual: chirality pdb=" CG LEU 4 788 " pdb=" CB LEU 4 788 " pdb=" CD1 LEU 4 788 " pdb=" CD2 LEU 4 788 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.10e+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 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL X 422 " pdb=" CA VAL X 422 " pdb=" CG1 VAL X 422 " pdb=" CG2 VAL X 422 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 11552 not shown) Planarity restraints: 13262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR W 263 " -0.033 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C THR W 263 " 0.113 2.00e-02 2.50e+03 pdb=" O THR W 263 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR W 264 " -0.038 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 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO S 838 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO S 838 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO S 838 " -0.048 5.00e-02 4.00e+02 ... (remaining 13259 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 12388 2.76 - 3.30: 64807 3.30 - 3.83: 114670 3.83 - 4.37: 135434 4.37 - 4.90: 233669 Nonbonded interactions: 560968 Sorted by model distance: nonbonded pdb=" OH TYR W 481 " pdb=" O VAL W 979 " model vdw 2.230 2.440 nonbonded pdb=" O ARG W1071 " pdb=" OG1 THR W1079 " model vdw 2.236 2.440 nonbonded pdb=" O ARG T1071 " pdb=" OG1 THR T1079 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR T 306 " pdb=" O MET T 323 " model vdw 2.244 2.440 nonbonded pdb=" OD2 ASP X 729 " pdb=" OH TYR X 798 " model vdw 2.246 2.440 ... (remaining 560963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' } ncs_group { reference = (chain '4' and (resid 47 through 300 or resid 361 through 547 or resid 551 throu \ gh 1252 or resid 1262 through 1376)) selection = (chain 'S' and (resid 47 through 253 or resid 263 through 409 or resid 427 throu \ gh 547 or resid 551 through 1141 or resid 1175 through 1293 or resid 1314 throug \ h 1344 or resid 1351 through 1376)) selection = (chain 'T' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 1141 or resid 1175 through 1252 or resid 1262 throug \ h 1293 or resid 1314 through 1344 or resid 1351 through 1376)) selection = (chain 'W' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 547 or resid 551 through 1141 or resid 1175 through \ 1252 or resid 1262 through 1293 or resid 1314 through 1344 or resid 1351 through \ 1376)) selection = (chain 'X' and (resid 47 through 253 or resid 263 through 300 or resid 361 throu \ gh 409 or resid 427 through 547 or resid 551 through 1141 or resid 1175 through \ 1293 or resid 1314 through 1344 or resid 1351 through 1376)) } ncs_group { reference = chain '5' selection = (chain 'b' and (resid 6 through 208 or resid 217 through 331)) } ncs_group { reference = (chain '6' and (resid 4 through 52 or resid 56 through 163 or resid 174 through \ 193 or resid 201 through 305)) selection = (chain '7' and (resid 4 through 163 or resid 174 through 305)) selection = (chain 'c' and (resid 4 through 52 or resid 56 through 193 or resid 201 through \ 305)) selection = (chain 'd' and (resid 4 through 52 or resid 56 through 163 or resid 174 through \ 193 or resid 201 through 305)) } 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 14.600 Check model and map are aligned: 0.830 Set scattering table: 0.520 Process input model: 147.730 Find NCS groups from input model: 4.480 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: 175.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.089 75206 Z= 0.445 Angle : 1.072 19.233 102202 Z= 0.582 Chirality : 0.057 0.352 11555 Planarity : 0.007 0.120 13262 Dihedral : 10.476 81.513 27648 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 0.49 % Allowed : 2.18 % Favored : 97.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.77 % Twisted General : 0.26 % 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: 9228 helix: -4.53 (0.04), residues: 3035 sheet: -1.74 (0.13), residues: 1379 loop : -2.28 (0.08), residues: 4814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2429 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 2390 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 9 residues processed: 2418 average time/residue: 0.7419 time to fit residues: 2954.8682 Evaluate side-chains 1412 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1403 time to evaluate : 6.128 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.5504 time to fit residues: 18.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 781 optimal weight: 10.0000 chunk 701 optimal weight: 0.9990 chunk 389 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 374 optimal weight: 0.3980 chunk 725 optimal weight: 6.9990 chunk 280 optimal weight: 0.3980 chunk 441 optimal weight: 2.9990 chunk 540 optimal weight: 3.9990 chunk 840 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 88 HIS k 333 HIS l 103 ASN m 52 GLN n2614 GLN 5 24 HIS 5 95 GLN 5 126 HIS 5 273 GLN 5 276 HIS 5 302 HIS ** 6 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 142 GLN 6 150 GLN 6 151 GLN 6 156 HIS 6 281 ASN 7 92 ASN 7 97 ASN 7 256 GLN b 281 ASN b 303 GLN b 319 ASN c 40 GLN c 110 GLN ** c 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN c 156 HIS d 94 GLN d 108 ASN d 130 ASN d 156 HIS d 194 ASN d 232 HIS ** d 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 325 ASN 4 384 ASN 4 397 GLN 4 407 HIS 4 428 GLN 4 469 ASN 4 498 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 567 GLN 4 590 HIS 4 652 ASN 4 655 HIS ** 4 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 769 ASN 4 978 ASN 41016 HIS 41090 HIS 41196 ASN ** 41241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41251 ASN ** 41355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN A 44 GLN A 47 HIS 2 17 HIS ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 38 GLN 2 47 HIS S 109 ASN ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 HIS S 239 GLN S 384 ASN ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN S 459 HIS ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 575 GLN S 590 HIS S 601 GLN S 630 ASN S 674 HIS S 716 HIS S 746 ASN S 749 ASN S 768 ASN S 786 HIS S 978 ASN S1114 HIS S1133 HIS S1171 HIS S1173 GLN S1235 ASN S1344 ASN 3 17 HIS ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 224 HIS T 239 GLN T 312 ASN T 325 ASN ** T 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 460 ASN ** T 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 581 GLN T 724 HIS T 745 GLN T 746 ASN T 853 HIS ** T 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 978 ASN T1027 GLN T1133 HIS T1171 HIS T1212 ASN T1305 GLN T1344 ASN T1372 ASN 1 17 HIS 1 47 HIS X 224 HIS X 312 ASN X 328 GLN X 384 ASN X 397 GLN X 463 GLN X 575 GLN X 590 HIS X 652 ASN X 663 HIS X 716 HIS X 746 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1027 GLN X1128 GLN X1192 GLN X1235 ASN X1268 GLN X1318 GLN X1344 ASN 0 17 HIS 0 47 HIS 0 73 HIS ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 HIS W 224 HIS W 270 GLN W 292 GLN W 448 ASN W 463 GLN ** W 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 545 HIS W 575 GLN W 590 HIS W 707 HIS W 746 ASN W 772 ASN ** W 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 853 HIS W 902 GLN W 920 ASN W 978 ASN W1027 GLN W1173 GLN W1268 GLN W1334 HIS W1344 ASN Total number of N/Q/H flips: 144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 75206 Z= 0.197 Angle : 0.676 13.063 102202 Z= 0.348 Chirality : 0.045 0.212 11555 Planarity : 0.005 0.103 13262 Dihedral : 6.488 79.772 10220 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 2.92 % Allowed : 10.61 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.14 % 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: -3.42 (0.07), residues: 9228 helix: -3.14 (0.06), residues: 3174 sheet: -1.24 (0.13), residues: 1402 loop : -1.87 (0.08), residues: 4652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1818 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1584 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 234 outliers final: 133 residues processed: 1730 average time/residue: 0.7537 time to fit residues: 2214.6051 Evaluate side-chains 1472 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1339 time to evaluate : 6.249 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 133 outliers final: 2 residues processed: 133 average time/residue: 0.5719 time to fit residues: 152.9198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 467 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 699 optimal weight: 10.0000 chunk 572 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 842 optimal weight: 8.9990 chunk 910 optimal weight: 8.9990 chunk 750 optimal weight: 0.9990 chunk 835 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 675 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 HIS m 103 ASN ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 130 ASN 7 156 HIS 7 281 ASN b 319 ASN d 150 GLN d 232 HIS d 235 HIS 4 384 ASN 4 498 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 581 GLN 4 655 HIS ** 4 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 752 ASN 41016 HIS 41355 GLN ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 73 HIS ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 239 GLN ** S 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN S 470 GLN S 505 ASN ** S 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 575 GLN S 707 HIS S 768 ASN S 971 GLN S1173 GLN ** 3 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 239 GLN T 397 GLN T 498 HIS T 558 HIS T 630 ASN T 674 HIS ** T 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 745 GLN T 799 ASN T 902 GLN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1196 ASN T1305 GLN T1318 GLN T1372 ASN 1 38 GLN X 102 HIS X 124 HIS X 354 HIS X 397 GLN X 558 HIS X 575 GLN X 630 ASN X 737 GLN X 775 GLN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 991 HIS X1030 HIS ** X1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1348 HIS X1352 HIS 0 22 HIS 0 38 GLN W 288 ASN W 463 GLN W 498 HIS W 630 ASN W 828 ASN ** W 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 853 HIS W 971 GLN W1027 GLN W1192 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 75206 Z= 0.367 Angle : 0.724 13.812 102202 Z= 0.367 Chirality : 0.048 0.201 11555 Planarity : 0.005 0.096 13262 Dihedral : 6.196 77.734 10220 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 3.58 % Allowed : 12.70 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.08 % 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: -2.73 (0.08), residues: 9228 helix: -2.23 (0.08), residues: 3198 sheet: -1.10 (0.13), residues: 1395 loop : -1.64 (0.09), residues: 4635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1722 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1435 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 287 outliers final: 155 residues processed: 1618 average time/residue: 0.7239 time to fit residues: 1988.8965 Evaluate side-chains 1429 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1274 time to evaluate : 6.139 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 155 outliers final: 2 residues processed: 155 average time/residue: 0.5817 time to fit residues: 179.0823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 832 optimal weight: 5.9990 chunk 633 optimal weight: 8.9990 chunk 437 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 402 optimal weight: 0.1980 chunk 565 optimal weight: 2.9990 chunk 845 optimal weight: 2.9990 chunk 895 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 chunk 801 optimal weight: 0.4980 chunk 241 optimal weight: 9.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 274 GLN ** 7 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 126 HIS b 319 ASN c 43 GLN d 24 GLN d 232 HIS 4 498 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 564 ASN 4 655 HIS ** 4 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 41016 HIS 41114 HIS A 29 ASN ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 397 GLN S 902 GLN S1173 GLN S1344 ASN 3 22 HIS 3 38 GLN ** T 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 466 GLN T 674 HIS T 745 GLN T 853 HIS T 902 GLN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1030 HIS ** T1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1305 GLN T1348 HIS X 707 HIS ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 978 ASN X 991 HIS W 239 GLN W 397 GLN W 587 ASN W 707 HIS W 828 ASN W1116 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 75206 Z= 0.166 Angle : 0.610 14.015 102202 Z= 0.306 Chirality : 0.043 0.206 11555 Planarity : 0.004 0.093 13262 Dihedral : 5.709 75.959 10220 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 2.07 % Allowed : 14.91 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.08), residues: 9228 helix: -1.62 (0.08), residues: 3192 sheet: -0.82 (0.14), residues: 1388 loop : -1.50 (0.09), residues: 4648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1379 time to evaluate : 6.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 69 residues processed: 1488 average time/residue: 0.7249 time to fit residues: 1832.4718 Evaluate side-chains 1332 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1263 time to evaluate : 6.225 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 69 outliers final: 2 residues processed: 69 average time/residue: 0.5854 time to fit residues: 83.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 745 optimal weight: 10.0000 chunk 508 optimal weight: 0.2980 chunk 13 optimal weight: 20.0000 chunk 666 optimal weight: 0.9980 chunk 369 optimal weight: 20.0000 chunk 763 optimal weight: 9.9990 chunk 618 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 457 optimal weight: 0.0030 chunk 803 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 overall best weight: 3.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 319 ASN d 232 HIS 4 397 GLN ** 4 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 498 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 567 GLN 4 652 ASN ** 4 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 818 HIS ** 4 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41016 HIS 41114 HIS 41222 HIS ** 2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 35 ASN ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 239 GLN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1084 HIS ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 239 GLN T 466 GLN T 674 HIS T 902 GLN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1305 GLN X 775 GLN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 971 GLN X1084 HIS ** X1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 397 GLN W 707 HIS ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 75206 Z= 0.250 Angle : 0.630 12.745 102202 Z= 0.315 Chirality : 0.045 0.189 11555 Planarity : 0.005 0.088 13262 Dihedral : 5.579 72.349 10220 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 2.44 % Allowed : 16.10 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % Twisted General : 0.05 % 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: -1.99 (0.08), residues: 9228 helix: -1.25 (0.09), residues: 3214 sheet: -0.80 (0.14), residues: 1401 loop : -1.46 (0.09), residues: 4613 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1328 time to evaluate : 6.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 113 residues processed: 1433 average time/residue: 0.7327 time to fit residues: 1781.4676 Evaluate side-chains 1373 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1260 time to evaluate : 6.129 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 113 outliers final: 2 residues processed: 113 average time/residue: 0.5576 time to fit residues: 127.0891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 301 optimal weight: 9.9990 chunk 806 optimal weight: 8.9990 chunk 176 optimal weight: 0.5980 chunk 525 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 895 optimal weight: 3.9990 chunk 743 optimal weight: 9.9990 chunk 414 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 HIS ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 146 HIS 7 281 ASN b 126 HIS b 145 ASN b 223 ASN b 319 ASN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 232 HIS 4 59 ASN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 746 ASN ** 4 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN 2 22 HIS ** S 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 21 HIS T 466 GLN T 498 HIS ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1165 ASN X 384 ASN X 630 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1133 HIS X1171 HIS ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 707 HIS W 828 ASN ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1212 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 75206 Z= 0.229 Angle : 0.609 12.344 102202 Z= 0.304 Chirality : 0.044 0.226 11555 Planarity : 0.004 0.082 13262 Dihedral : 5.444 75.736 10220 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 1.83 % Allowed : 17.22 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.08), residues: 9228 helix: -0.96 (0.09), residues: 3225 sheet: -0.71 (0.14), residues: 1400 loop : -1.40 (0.09), residues: 4603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1489 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1342 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 147 outliers final: 80 residues processed: 1423 average time/residue: 0.7201 time to fit residues: 1740.6975 Evaluate side-chains 1353 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1273 time to evaluate : 6.062 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 80 outliers final: 2 residues processed: 80 average time/residue: 0.5804 time to fit residues: 94.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 863 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 510 optimal weight: 50.0000 chunk 654 optimal weight: 5.9990 chunk 506 optimal weight: 5.9990 chunk 754 optimal weight: 10.0000 chunk 500 optimal weight: 9.9990 chunk 892 optimal weight: 0.0370 chunk 558 optimal weight: 6.9990 chunk 544 optimal weight: 4.9990 chunk 412 optimal weight: 4.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 103 ASN ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 319 ASN c 94 GLN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 564 ASN 4 594 GLN ** 4 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 41334 HIS A 29 ASN ** 2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 HIS S 239 GLN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN S1173 GLN ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 HIS T 466 GLN T 498 HIS T 745 GLN T 853 HIS T 902 GLN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1318 GLN 0 55 HIS ** W 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1196 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 75206 Z= 0.262 Angle : 0.630 12.864 102202 Z= 0.314 Chirality : 0.045 0.203 11555 Planarity : 0.004 0.078 13262 Dihedral : 5.422 76.630 10220 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 1.61 % Allowed : 17.75 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % Twisted General : 0.05 % 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: -1.65 (0.08), residues: 9228 helix: -0.80 (0.09), residues: 3209 sheet: -0.72 (0.14), residues: 1411 loop : -1.36 (0.09), residues: 4608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1311 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 129 outliers final: 69 residues processed: 1378 average time/residue: 0.7347 time to fit residues: 1714.8585 Evaluate side-chains 1342 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1273 time to evaluate : 6.126 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 69 outliers final: 2 residues processed: 69 average time/residue: 0.5588 time to fit residues: 81.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 552 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 533 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 567 optimal weight: 7.9990 chunk 608 optimal weight: 10.0000 chunk 441 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 701 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 291 ASN ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 HIS ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 170 HIS b 319 ASN c 94 GLN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 156 HIS 4 428 GLN ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 41334 HIS A 29 ASN ** 2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 ASN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 991 HIS ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 HIS T 466 GLN ** T 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 845 ASN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1116 GLN T1344 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 991 HIS W 639 GLN ** W 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 689 GLN W 828 ASN ** W 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 902 GLN W1305 GLN W1318 GLN W1321 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 75206 Z= 0.363 Angle : 0.694 14.661 102202 Z= 0.348 Chirality : 0.047 0.202 11555 Planarity : 0.005 0.078 13262 Dihedral : 5.662 78.680 10220 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 1.53 % Allowed : 18.24 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % 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: -1.79 (0.08), residues: 9228 helix: -0.89 (0.09), residues: 3231 sheet: -0.82 (0.14), residues: 1406 loop : -1.46 (0.09), residues: 4591 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1290 time to evaluate : 6.172 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 123 outliers final: 73 residues processed: 1353 average time/residue: 0.7388 time to fit residues: 1690.0051 Evaluate side-chains 1311 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1238 time to evaluate : 6.161 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 73 outliers final: 2 residues processed: 73 average time/residue: 0.5565 time to fit residues: 85.6172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 811 optimal weight: 4.9990 chunk 855 optimal weight: 7.9990 chunk 780 optimal weight: 3.9990 chunk 831 optimal weight: 0.9990 chunk 854 optimal weight: 6.9990 chunk 500 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 751 optimal weight: 7.9990 chunk 786 optimal weight: 40.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 319 ASN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 232 HIS ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 ASN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1173 GLN ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 336 HIS T 466 GLN T 529 HIS ** T 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 836 ASN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1344 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 55 HIS W 22 GLN W 587 ASN W 836 ASN W1318 GLN W1321 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 75206 Z= 0.245 Angle : 0.637 16.813 102202 Z= 0.318 Chirality : 0.045 0.220 11555 Planarity : 0.004 0.077 13262 Dihedral : 5.467 77.205 10220 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 0.79 % Allowed : 19.20 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % 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: -1.59 (0.08), residues: 9228 helix: -0.69 (0.09), residues: 3206 sheet: -0.75 (0.14), residues: 1411 loop : -1.36 (0.09), residues: 4611 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1292 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 63 outliers final: 37 residues processed: 1323 average time/residue: 0.7877 time to fit residues: 1775.4136 Evaluate side-chains 1287 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1250 time to evaluate : 6.121 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 0.5865 time to fit residues: 48.9222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 828 optimal weight: 9.9990 chunk 546 optimal weight: 2.9990 chunk 879 optimal weight: 0.2980 chunk 536 optimal weight: 20.0000 chunk 417 optimal weight: 0.6980 chunk 611 optimal weight: 5.9990 chunk 922 optimal weight: 8.9990 chunk 849 optimal weight: 0.4980 chunk 734 optimal weight: 20.0000 chunk 76 optimal weight: 0.5980 chunk 567 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 126 HIS ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 319 ASN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 590 HIS 4 746 ASN ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 958 HIS A 29 ASN ** 2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 55 HIS S 514 GLN S 796 ASN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN ** S1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 288 ASN ** T 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 836 ASN T 853 HIS ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 971 GLN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 55 HIS W 769 ASN W 782 HIS W 828 ASN W1318 GLN W1321 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 75206 Z= 0.155 Angle : 0.592 14.575 102202 Z= 0.295 Chirality : 0.043 0.184 11555 Planarity : 0.004 0.072 13262 Dihedral : 5.115 73.969 10220 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 0.39 % Allowed : 19.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % 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: -1.27 (0.09), residues: 9228 helix: -0.35 (0.09), residues: 3217 sheet: -0.55 (0.14), residues: 1364 loop : -1.24 (0.09), residues: 4647 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18456 Ramachandran restraints generated. 9228 Oldfield, 0 Emsley, 9228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1342 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 1354 average time/residue: 0.7456 time to fit residues: 1699.5350 Evaluate side-chains 1264 residues out of total 8021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1253 time to evaluate : 6.110 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU 4 947 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU T 947 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.5571 time to fit residues: 20.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 926 random chunks: chunk 450 optimal weight: 4.9990 chunk 583 optimal weight: 7.9990 chunk 782 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 677 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 735 optimal weight: 10.0000 chunk 307 optimal weight: 30.0000 chunk 755 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 7 ASN ** n2614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 281 ASN b 319 ASN c 64 GLN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 746 ASN ** 4 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN A 44 GLN S 514 GLN ** S 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 971 GLN S1279 ASN ** S1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 288 ASN ** T 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 836 ASN ** T 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1165 ASN ** X 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.148278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.127198 restraints weight = 94517.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.124355 restraints weight = 192079.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.125262 restraints weight = 180988.389| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 75206 Z= 0.234 Angle : 0.618 17.990 102202 Z= 0.307 Chirality : 0.044 0.234 11555 Planarity : 0.004 0.075 13262 Dihedral : 5.138 74.146 10220 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 0.62 % Allowed : 20.03 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.08 % Twisted Proline : 0.19 % 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: -1.21 (0.09), residues: 9228 helix: -0.28 (0.09), residues: 3200 sheet: -0.53 (0.14), residues: 1376 loop : -1.21 (0.09), residues: 4652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25307.48 seconds wall clock time: 439 minutes 45.01 seconds (26385.01 seconds total)