Starting phenix.real_space_refine on Tue Mar 19 12:56:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vf9_31948/03_2024/7vf9_31948.pdb" } resolution = 4.04 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 86 5.16 5 C 15244 2.51 5 N 4427 2.21 5 O 4487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C ARG 725": "NH1" <-> "NH2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ARG 763": "NH1" <-> "NH2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 819": "OD1" <-> "OD2" Residue "C ARG 846": "NH1" <-> "NH2" Residue "C GLU 853": "OE1" <-> "OE2" Residue "C GLU 864": "OE1" <-> "OE2" Residue "C ARG 949": "NH1" <-> "NH2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 978": "OE1" <-> "OE2" Residue "C ASP 1057": "OD1" <-> "OD2" Residue "C ARG 1076": "NH1" <-> "NH2" Residue "C ARG 1147": "NH1" <-> "NH2" Residue "C ARG 1159": "NH1" <-> "NH2" Residue "C GLU 1168": "OE1" <-> "OE2" Residue "C ASP 1181": "OD1" <-> "OD2" Residue "C GLU 1207": "OE1" <-> "OE2" Residue "C ARG 1231": "NH1" <-> "NH2" Residue "C ASP 1255": "OD1" <-> "OD2" Residue "C ASP 1256": "OD1" <-> "OD2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "C ARG 1329": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ARG 481": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D ASP 622": "OD1" <-> "OD2" Residue "D ASP 648": "OD1" <-> "OD2" Residue "D ARG 652": "NH1" <-> "NH2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 846": "NH1" <-> "NH2" Residue "D ARG 908": "NH1" <-> "NH2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1262": "NH1" <-> "NH2" Residue "D PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1330": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F ASP 257": "OD1" <-> "OD2" Residue "F ASP 259": "OD1" <-> "OD2" Residue "F ARG 317": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24247 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1587 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1508 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 9387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 9387 Classifications: {'peptide': 1324} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 53, 'TRANS': 1270} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1243 Unresolved non-hydrogen dihedrals: 740 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 16, 'ASP:plan': 29, 'PHE:plan': 5, 'GLU:plan': 49, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 556 Chain: "D" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 9407 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 60, 'TRANS': 1278} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1019 Unresolved non-hydrogen angles: 1308 Unresolved non-hydrogen dihedrals: 803 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 22, 'TYR:plan': 5, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 49, 'ASP:plan': 41} Unresolved non-hydrogen planarities: 631 Chain: "E" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 463 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1892 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 187 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12896 SG CYS D 70 111.686 49.089 70.575 1.00 63.72 S ATOM 18908 SG CYS D 888 80.197 69.653 125.220 1.00 33.02 S ATOM 18969 SG CYS D 898 76.769 69.429 127.302 1.00 25.74 S Time building chain proxies: 12.74, per 1000 atoms: 0.53 Number of scatterers: 24247 At special positions: 0 Unit cell: (143.77, 162.068, 159.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 86 16.00 Mg 1 11.99 O 4487 8.00 N 4427 7.00 C 15244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 46 sheets defined 39.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.319A pdb=" N HIS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 50 removed outlier: 3.581A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.506A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 211 through 229 removed outlier: 4.155A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.713A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.517A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.743A pdb=" N ALA B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.897A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.138A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.892A pdb=" N ALA C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.935A pdb=" N VAL C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.551A pdb=" N ALA C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 removed outlier: 3.757A pdb=" N LEU C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.621A pdb=" N ILE C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 299 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.869A pdb=" N LEU C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.868A pdb=" N ASP C 354 " --> pdb=" O PRO C 350 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.545A pdb=" N ALA C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 395 removed outlier: 3.756A pdb=" N THR C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.583A pdb=" N LYS C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 443 removed outlier: 3.505A pdb=" N ILE C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 485 removed outlier: 3.507A pdb=" N MET C 464 " --> pdb=" O CYS C 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 472 " --> pdb=" O GLN C 468 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 4.144A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.660A pdb=" N ILE C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 511 " --> pdb=" O ILE C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.645A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.999A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.914A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 removed outlier: 3.815A pdb=" N VAL C 655 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 removed outlier: 4.117A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 removed outlier: 3.820A pdb=" N LEU C 672 " --> pdb=" O ALA C 669 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE C 673 " --> pdb=" O ALA C 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 669 through 673' Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.800A pdb=" N ASN C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 717 removed outlier: 4.023A pdb=" N ARG C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 716 " --> pdb=" O ASN C 712 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 711 through 717' Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 863 through 870 removed outlier: 3.825A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 868 " --> pdb=" O GLU C 864 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 869 " --> pdb=" O ALA C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 912 removed outlier: 3.783A pdb=" N LEU C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 912 " --> pdb=" O ARG C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 3.742A pdb=" N ILE C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 954 " --> pdb=" O ALA C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.664A pdb=" N ASP C1044 " --> pdb=" O GLN C1040 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 4.732A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1151 removed outlier: 4.178A pdb=" N ILE C1129 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C1137 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C1150 " --> pdb=" O ASN C1146 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.708A pdb=" N LYS C1160 " --> pdb=" O ALA C1156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C1165 " --> pdb=" O PHE C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1191 removed outlier: 3.828A pdb=" N ILE C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C1186 " --> pdb=" O ASN C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1194 No H-bonds generated for 'chain 'C' and resid 1192 through 1194' Processing helix chain 'C' and resid 1206 through 1217 removed outlier: 3.509A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1287 through 1296 removed outlier: 3.582A pdb=" N LEU C1293 " --> pdb=" O GLU C1289 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C1296 " --> pdb=" O ALA C1292 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1308 removed outlier: 3.642A pdb=" N LEU C1306 " --> pdb=" O LEU C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1312 through 1326 Processing helix chain 'C' and resid 1335 through 1347 removed outlier: 3.652A pdb=" N VAL C1340 " --> pdb=" O GLU C1336 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C1347 " --> pdb=" O LYS C1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.821A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.007A pdb=" N ARG D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 114 through 119 removed outlier: 4.225A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.789A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.621A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.526A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.830A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.544A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.500A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.532A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 281 removed outlier: 4.057A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.769A pdb=" N ARG D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.709A pdb=" N LEU D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.934A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.855A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.542A pdb=" N PHE D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.505A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.520A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.513A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.516A pdb=" N MET D 513 " --> pdb=" O GLY D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.587A pdb=" N ALA D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 540 " --> pdb=" O ALA D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.666A pdb=" N PHE D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.730A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 4.065A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.542A pdb=" N PHE D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.514A pdb=" N ASP D 659 " --> pdb=" O ASN D 655 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 662 " --> pdb=" O THR D 658 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 666 " --> pdb=" O LYS D 662 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 668 " --> pdb=" O ILE D 664 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 669 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 670 " --> pdb=" O SER D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.506A pdb=" N TYR D 679 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 687 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.692A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 741 removed outlier: 3.750A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.651A pdb=" N PHE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 802 removed outlier: 3.654A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.799A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 871 " --> pdb=" O LYS D 867 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET D 875 " --> pdb=" O PHE D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.751A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 4.015A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.772A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1222 removed outlier: 3.882A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1216 through 1222' Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 3.608A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.187A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.897A pdb=" N LEU D1292 " --> pdb=" O GLU D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 4.178A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.718A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.738A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D1336 " --> pdb=" O LEU D1332 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 removed outlier: 3.533A pdb=" N GLU D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D1376 " --> pdb=" O GLN D1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 3.554A pdb=" N LEU E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.579A pdb=" N LYS E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 29 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.741A pdb=" N VAL E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 removed outlier: 3.667A pdb=" N ASP E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.956A pdb=" N GLU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 removed outlier: 3.809A pdb=" N VAL F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.623A pdb=" N GLU F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.753A pdb=" N ARG F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 113 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 137 removed outlier: 3.609A pdb=" N LEU F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 163 removed outlier: 4.299A pdb=" N TRP F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 156 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN F 157 " --> pdb=" O TRP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 195 removed outlier: 3.523A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 180 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 removed outlier: 3.582A pdb=" N ILE F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.756A pdb=" N LYS F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 250 through 271 removed outlier: 3.501A pdb=" N THR F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 281 removed outlier: 3.619A pdb=" N GLU F 277 " --> pdb=" O ASP F 273 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 278 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 324 removed outlier: 3.616A pdb=" N ILE F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 312 " --> pdb=" O ARG F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 334 removed outlier: 3.722A pdb=" N PHE F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 3.639A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 4.098A pdb=" N VAL A 98 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 104 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.149A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 3.553A pdb=" N ALA A 174 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.339A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 204 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 201 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 185 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 3.998A pdb=" N GLY B 53 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS B 144 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 59 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 142 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 61 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 140 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.272A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.452A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 70 through 79 removed outlier: 6.914A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 119 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 70 through 79 removed outlier: 6.914A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.780A pdb=" N VAL C 148 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 518 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 458 removed outlier: 3.592A pdb=" N VAL C 535 " --> pdb=" O ASN C 578 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 164 removed outlier: 6.729A pdb=" N ASP C 164 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 175 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR C 176 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 192 " --> pdb=" O TYR C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.504A pdb=" N LEU C 243 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 235 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 244 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 233 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 232 " --> pdb=" O THR C 340 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 340 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 234 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 338 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 254 through 255 removed outlier: 4.205A pdb=" N ALA C 255 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 272 " --> pdb=" O ALA C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC2, first strand: chain 'C' and resid 585 through 586 removed outlier: 5.321A pdb=" N GLU C 607 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC4, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC5, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.775A pdb=" N ALA C 789 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 755 through 757 removed outlier: 6.971A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC8, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 3.574A pdb=" N ALA C1084 " --> pdb=" O LEU C1248 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 823 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE C1096 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 805 " --> pdb=" O MET C1245 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 837 through 844 removed outlier: 4.466A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 892 through 893 removed outlier: 3.510A pdb=" N THR C 893 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.571A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.571A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1284 through 1286 Processing sheet with id=AD5, first strand: chain 'C' and resid 1350 through 1352 removed outlier: 3.593A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 8.461A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.640A pdb=" N VAL D 145 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.591A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 550 through 556 removed outlier: 3.617A pdb=" N VAL D 550 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 554 " --> pdb=" O ASN D 566 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 556 " --> pdb=" O THR D 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 564 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.620A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 950 through 951 removed outlier: 6.733A pdb=" N VAL D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.866A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 981 " --> pdb=" O HIS D 961 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 974 through 975 Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 4.047A pdb=" N ILE D1124 " --> pdb=" O HIS D1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1098 through 1099 removed outlier: 3.881A pdb=" N GLY D1033 " --> pdb=" O VAL D1115 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D1115 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.852A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D1107 " --> pdb=" O ILE D1059 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 3.663A pdb=" N GLU D1202 " --> pdb=" O ILE D1163 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 3.566A pdb=" N ASP D1278 " --> pdb=" O VAL D1264 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2388 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: 10.53 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8436 1.34 - 1.46: 4435 1.46 - 1.58: 11544 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 24565 Sorted by residual: bond pdb=" CA VAL C 925 " pdb=" CB VAL C 925 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.91e-01 bond pdb=" N ILE D1357 " pdb=" CA ILE D1357 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.77e-01 bond pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.27e-02 6.20e+03 5.47e-01 bond pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 1.514 1.504 0.010 1.41e-02 5.03e+03 5.23e-01 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 4.98e-01 ... (remaining 24560 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 681 107.22 - 113.91: 14066 113.91 - 120.59: 9591 120.59 - 127.28: 8817 127.28 - 133.97: 182 Bond angle restraints: 33337 Sorted by residual: angle pdb=" N VAL D 591 " pdb=" CA VAL D 591 " pdb=" C VAL D 591 " ideal model delta sigma weight residual 112.80 109.78 3.02 1.15e+00 7.56e-01 6.90e+00 angle pdb=" N VAL D 611 " pdb=" CA VAL D 611 " pdb=" C VAL D 611 " ideal model delta sigma weight residual 111.62 109.77 1.85 7.90e-01 1.60e+00 5.46e+00 angle pdb=" C ILE D 500 " pdb=" N VAL D 501 " pdb=" CA VAL D 501 " ideal model delta sigma weight residual 119.72 123.86 -4.14 2.01e+00 2.48e-01 4.23e+00 angle pdb=" CA VAL D 592 " pdb=" C VAL D 592 " pdb=" N ASN D 593 " ideal model delta sigma weight residual 116.60 119.23 -2.63 1.45e+00 4.76e-01 3.28e+00 angle pdb=" C GLY D1137 " pdb=" N LEU D1138 " pdb=" CA LEU D1138 " ideal model delta sigma weight residual 120.09 122.28 -2.19 1.25e+00 6.40e-01 3.08e+00 ... (remaining 33332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 14307 17.43 - 34.85: 581 34.85 - 52.28: 70 52.28 - 69.71: 12 69.71 - 87.13: 12 Dihedral angle restraints: 14982 sinusoidal: 5182 harmonic: 9800 Sorted by residual: dihedral pdb=" CB GLU C1168 " pdb=" CG GLU C1168 " pdb=" CD GLU C1168 " pdb=" OE1 GLU C1168 " ideal model delta sinusoidal sigma weight residual 0.00 -87.13 87.13 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU D 225 " pdb=" CG GLU D 225 " pdb=" CD GLU D 225 " pdb=" OE1 GLU D 225 " ideal model delta sinusoidal sigma weight residual 0.00 -84.97 84.97 1 3.00e+01 1.11e-03 9.73e+00 dihedral pdb=" CB GLU F 320 " pdb=" CG GLU F 320 " pdb=" CD GLU F 320 " pdb=" OE1 GLU F 320 " ideal model delta sinusoidal sigma weight residual 0.00 84.68 -84.68 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 14979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2583 0.031 - 0.062: 1007 0.062 - 0.092: 205 0.092 - 0.123: 177 0.123 - 0.154: 4 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CB ILE D 500 " pdb=" CA ILE D 500 " pdb=" CG1 ILE D 500 " pdb=" CG2 ILE D 500 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE C 673 " pdb=" N ILE C 673 " pdb=" C ILE C 673 " pdb=" CB ILE C 673 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 821 " pdb=" N ILE C 821 " pdb=" C ILE C 821 " pdb=" CB ILE C 821 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 3973 not shown) Planarity restraints: 4392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 502 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO D 851 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO D1139 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " -0.015 5.00e-02 4.00e+02 ... (remaining 4389 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 760 2.72 - 3.27: 22809 3.27 - 3.81: 34270 3.81 - 4.36: 41716 4.36 - 4.90: 71338 Nonbonded interactions: 170893 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.176 2.170 nonbonded pdb=" O SER C 667 " pdb=" OG SER C 671 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OD1 ASP C 325 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR A 10 " pdb=" O GLN B 225 " model vdw 2.280 2.440 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.284 2.170 ... (remaining 170888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 57 or (resid 58 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 throug \ h 66 and (name N or name CA or name C or name O or name CB )) or resid 67 throug \ h 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or re \ sid 76 through 79 or (resid 80 and (name N or name CA or name C or name O or nam \ e CB )) or resid 81 through 89 or (resid 90 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or resid 91 through 92 or (resid 93 \ and (name N or name CA or name C or name O or name CB )) or resid 94 or (resid 9 \ 5 and (name N or name CA or name C or name O or name CB or name CG )) or resid 9 \ 6 through 104 or (resid 105 and (name N or name CA or name C or name O or name C \ B )) or resid 109 through 113 or (resid 114 and (name N or name CA or name C or \ name O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name \ CA or name C or name O or name CB )) or resid 120 through 134 or resid 139 throu \ gh 141 or (resid 142 and (name N or name CA or name C or name O or name CB )) or \ resid 143 through 157 or (resid 169 and (name N or name CA or name C or name O \ or name CB )) or resid 170 through 182 or (resid 183 and (name N or name CA or n \ ame C or name O or name CB )) or resid 184 through 229 or (resid 230 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 8 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or resid 15 through 25 or (resid \ 26 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2)) or resid 27 through 71 or (resid 72 and (name N or name CA or name C or name \ O or name CB )) or resid 73 through 116 or (resid 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 through 126 or (resid 127 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 128 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 141 through 151 or (resid 152 and (name N or name CA or name C or \ name O or name CB )) or resid 153 through 193 or (resid 194 through 196 and (na \ me N or name CA or name C or name O or name CB )) or resid 197 through 212 or (r \ esid 213 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 230)) } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.500 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 69.610 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.140 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 : 0.001 0.031 24565 Z= 0.094 Angle : 0.385 5.909 33337 Z= 0.228 Chirality : 0.038 0.154 3976 Planarity : 0.002 0.039 4392 Dihedral : 9.647 87.134 8652 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.11), residues: 3397 helix: -4.56 (0.05), residues: 1095 sheet: -0.99 (0.26), residues: 339 loop : -2.36 (0.11), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 187 HIS 0.001 0.000 HIS C 154 PHE 0.017 0.000 PHE D1325 TYR 0.004 0.000 TYR C1296 ARG 0.001 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 576 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable