Starting phenix.real_space_refine on Sat Oct 12 12:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wa0_37387/10_2024/8wa0_37387.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 50 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 P 19 5.49 5 Mg 1 5.21 5 S 248 5.16 5 C 38569 2.51 5 N 10876 2.21 5 O 11412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 61128 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2164 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "a" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2377 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 14, 'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE%COO:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 7296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7296 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 42, 'TRANS': 930} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 280 Chain: "C" Number of atoms: 4738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 4738 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 34, 'TRANS': 626} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 816 Unresolved non-hydrogen dihedrals: 542 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 364 Chain: "c" Number of atoms: 8108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 8108 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 364} Link IDs: {'PTRANS': 54, 'TRANS': 1121} Chain breaks: 6 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1275 Unresolved non-hydrogen angles: 1614 Unresolved non-hydrogen dihedrals: 1050 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 30, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 16, 'GLU:plan': 21, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 666 Chain: "D" Number of atoms: 4772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 4772 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 621} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 218 Chain: "E" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 4483 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 18, 'TRANS': 681} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1450 Unresolved non-hydrogen dihedrals: 948 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 650 Chain: "F" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4185 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 33, 'TRANS': 510} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 245 Chain: "G" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2099 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2924 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 21, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "i" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2887 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 354} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3358 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 24, 'TRANS': 396} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1656 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 187} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1702 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 15, 'TRANS': 219} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "M" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 931 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 822 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "N" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 2987 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 352} Link IDs: {'PTRANS': 23, 'TRANS': 513} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1214 Unresolved non-hydrogen angles: 1553 Unresolved non-hydrogen dihedrals: 971 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 34, 'PHE:plan': 14, 'GLU:plan': 38, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 649 Chain: "O" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "P" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 761 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "R" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "S" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.49, per 1000 atoms: 0.42 Number of scatterers: 61128 At special positions: 0 Unit cell: (230.88, 250.12, 160.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 248 16.00 P 19 15.00 Mg 1 11.99 O 11412 8.00 N 10876 7.00 C 38569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS m 101 " - pdb=" SG CYS m 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 11.48 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 536 " 16568 Ramachandran restraints generated. 8284 Oldfield, 0 Emsley, 8284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15614 Finding SS restraints... Secondary structure from input PDB file: 345 helices and 67 sheets defined 46.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 removed outlier: 4.073A pdb=" N THR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.560A pdb=" N GLU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.546A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.591A pdb=" N LEU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.668A pdb=" N MET A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 removed outlier: 3.786A pdb=" N TYR A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 54 removed outlier: 3.894A pdb=" N THR a 44 " --> pdb=" O GLY a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 92 Processing helix chain 'a' and resid 210 through 227 Processing helix chain 'a' and resid 228 through 231 Processing helix chain 'a' and resid 251 through 264 removed outlier: 3.877A pdb=" N LYS a 264 " --> pdb=" O LEU a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 272 removed outlier: 3.962A pdb=" N SER a 271 " --> pdb=" O ILE a 267 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE a 272 " --> pdb=" O ALA a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 272' Processing helix chain 'a' and resid 280 through 290 Processing helix chain 'a' and resid 294 through 301 Processing helix chain 'a' and resid 302 through 309 removed outlier: 3.533A pdb=" N MET a 307 " --> pdb=" O GLN a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 328 removed outlier: 3.659A pdb=" N LYS a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 Processing helix chain 'B' and resid 28 through 38 removed outlier: 3.754A pdb=" N LYS B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.743A pdb=" N PHE B 204 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 282 through 298 removed outlier: 4.151A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 316 through 347 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.573A pdb=" N VAL B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.618A pdb=" N THR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.745A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.614A pdb=" N ASP B 412 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 4.029A pdb=" N TYR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 491 through 494 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.737A pdb=" N ILE B 531 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.676A pdb=" N ALA B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 576 removed outlier: 4.465A pdb=" N GLY B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 835 through 839 Processing helix chain 'B' and resid 855 through 861 removed outlier: 4.210A pdb=" N SER B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 879 removed outlier: 3.695A pdb=" N PHE B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 870 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.559A pdb=" N ARG B 890 " --> pdb=" O PHE B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 911 Processing helix chain 'B' and resid 913 through 917 removed outlier: 3.574A pdb=" N VAL B 916 " --> pdb=" O ASN B 913 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 917 " --> pdb=" O PRO B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 917' Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 986 through 997 Processing helix chain 'B' and resid 998 through 1007 Processing helix chain 'B' and resid 1012 through 1026 removed outlier: 3.873A pdb=" N LEU B1020 " --> pdb=" O ARG B1016 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1048 Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.552A pdb=" N ALA C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.662A pdb=" N TYR C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 4.039A pdb=" N LEU C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 237 through 265 removed outlier: 3.502A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 297 through 320 removed outlier: 3.736A pdb=" N ARG C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 345 removed outlier: 3.730A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 333 " --> pdb=" O MET C 329 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 406 through 413 removed outlier: 3.632A pdb=" N GLU C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 429 through 439 removed outlier: 3.566A pdb=" N LYS C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 removed outlier: 4.197A pdb=" N TRP C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 446 " --> pdb=" O PRO C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 489 through 494 removed outlier: 3.521A pdb=" N PHE C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 540 through 551 Processing helix chain 'C' and resid 591 through 601 removed outlier: 3.832A pdb=" N ALA C 595 " --> pdb=" O ASN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 removed outlier: 3.618A pdb=" N ILE C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 670 " --> pdb=" O HIS C 666 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 31 Processing helix chain 'c' and resid 31 through 54 removed outlier: 3.589A pdb=" N HIS c 37 " --> pdb=" O ALA c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 62 removed outlier: 3.588A pdb=" N LEU c 62 " --> pdb=" O ILE c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 88 Processing helix chain 'c' and resid 92 through 123 removed outlier: 3.508A pdb=" N TRP c 104 " --> pdb=" O SER c 100 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 135 removed outlier: 3.749A pdb=" N GLY c 135 " --> pdb=" O MET c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 148 Processing helix chain 'c' and resid 174 through 210 removed outlier: 3.712A pdb=" N TYR c 183 " --> pdb=" O ILE c 179 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY c 184 " --> pdb=" O ILE c 180 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA c 185 " --> pdb=" O SER c 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER c 197 " --> pdb=" O ALA c 193 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY c 200 " --> pdb=" O THR c 196 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 210 " --> pdb=" O LEU c 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 245 Processing helix chain 'c' and resid 268 through 279 Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.716A pdb=" N CYS c 291 " --> pdb=" O PRO c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 303 Processing helix chain 'c' and resid 317 through 328 removed outlier: 3.537A pdb=" N ILE c 321 " --> pdb=" O ALA c 317 " (cutoff:3.500A) Processing helix chain 'c' and resid 329 through 332 Processing helix chain 'c' and resid 485 through 492 removed outlier: 3.543A pdb=" N SER c 490 " --> pdb=" O LEU c 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE c 491 " --> pdb=" O VAL c 487 " (cutoff:3.500A) Processing helix chain 'c' and resid 563 through 568 Processing helix chain 'c' and resid 616 through 620 Processing helix chain 'c' and resid 907 through 916 Processing helix chain 'c' and resid 931 through 935 removed outlier: 4.345A pdb=" N LYS c 935 " --> pdb=" O ASN c 932 " (cutoff:3.500A) Processing helix chain 'c' and resid 993 through 997 removed outlier: 4.158A pdb=" N HIS c 996 " --> pdb=" O SER c 993 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU c 997 " --> pdb=" O SER c 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 993 through 997' Processing helix chain 'c' and resid 1004 through 1009 removed outlier: 3.989A pdb=" N TYR c1008 " --> pdb=" O LEU c1004 " (cutoff:3.500A) Processing helix chain 'c' and resid 1146 through 1154 Processing helix chain 'c' and resid 1157 through 1162 removed outlier: 3.885A pdb=" N ILE c1161 " --> pdb=" O SER c1157 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER c1162 " --> pdb=" O VAL c1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1157 through 1162' Processing helix chain 'c' and resid 1162 through 1180 removed outlier: 3.943A pdb=" N THR c1177 " --> pdb=" O ASN c1173 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG c1178 " --> pdb=" O LYS c1174 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE c1179 " --> pdb=" O CYS c1175 " (cutoff:3.500A) Processing helix chain 'c' and resid 1181 through 1212 removed outlier: 4.369A pdb=" N PHE c1186 " --> pdb=" O ILE c1182 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU c1187 " --> pdb=" O PRO c1183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL c1208 " --> pdb=" O LYS c1204 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN c1212 " --> pdb=" O VAL c1208 " (cutoff:3.500A) Processing helix chain 'c' and resid 1217 through 1229 removed outlier: 4.092A pdb=" N LEU c1221 " --> pdb=" O HIS c1217 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE c1224 " --> pdb=" O HIS c1220 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN c1227 " --> pdb=" O ILE c1223 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE c1228 " --> pdb=" O ILE c1224 " (cutoff:3.500A) Processing helix chain 'c' and resid 1251 through 1261 Processing helix chain 'c' and resid 1273 through 1280 removed outlier: 3.643A pdb=" N SER c1278 " --> pdb=" O ILE c1274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU c1279 " --> pdb=" O THR c1275 " (cutoff:3.500A) Processing helix chain 'c' and resid 1292 through 1304 Processing helix chain 'c' and resid 1311 through 1318 removed outlier: 3.840A pdb=" N ASN c1315 " --> pdb=" O GLY c1311 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU c1318 " --> pdb=" O GLU c1314 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 83 removed outlier: 3.539A pdb=" N GLU D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 100 removed outlier: 3.518A pdb=" N VAL D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.824A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.839A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 173 through 187 removed outlier: 3.546A pdb=" N VAL D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 224 through 239 removed outlier: 3.601A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.541A pdb=" N PHE D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 253 " --> pdb=" O CYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.749A pdb=" N PHE D 264 " --> pdb=" O PRO D 260 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 336 through 350 removed outlier: 3.753A pdb=" N ALA D 340 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 347 " --> pdb=" O HIS D 343 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 removed outlier: 3.695A pdb=" N VAL D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 377 Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.631A pdb=" N ALA D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 415 removed outlier: 4.561A pdb=" N TRP D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 439 Processing helix chain 'D' and resid 458 through 462 Processing helix chain 'D' and resid 473 through 496 removed outlier: 3.573A pdb=" N LEU D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.925A pdb=" N ILE D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 514 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 606 through 616 removed outlier: 3.665A pdb=" N TRP D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 745 Processing helix chain 'D' and resid 749 through 753 Processing helix chain 'D' and resid 755 through 760 Processing helix chain 'D' and resid 764 through 771 removed outlier: 4.390A pdb=" N ILE D 768 " --> pdb=" O TRP D 764 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 769 " --> pdb=" O GLU D 765 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 771 " --> pdb=" O GLU D 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 764 through 771' Processing helix chain 'D' and resid 777 through 796 Processing helix chain 'D' and resid 800 through 814 removed outlier: 4.000A pdb=" N ALA D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 830 removed outlier: 4.097A pdb=" N PHE D 820 " --> pdb=" O MET D 816 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 821 " --> pdb=" O PRO D 817 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 822 " --> pdb=" O SER D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 850 removed outlier: 3.808A pdb=" N TYR D 839 " --> pdb=" O GLY D 835 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 842 " --> pdb=" O LEU D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 866 Processing helix chain 'D' and resid 870 through 885 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.876A pdb=" N ARG E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 149 Processing helix chain 'E' and resid 151 through 161 Processing helix chain 'E' and resid 170 through 184 removed outlier: 3.527A pdb=" N TYR E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 205 through 220 Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 241 through 256 removed outlier: 3.906A pdb=" N CYS E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 4.280A pdb=" N MET E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.573A pdb=" N LYS E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.620A pdb=" N LEU E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 326 Processing helix chain 'E' and resid 328 through 342 Processing helix chain 'E' and resid 346 through 361 removed outlier: 4.248A pdb=" N TYR E 350 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 375 removed outlier: 3.599A pdb=" N GLU E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 395 removed outlier: 3.796A pdb=" N GLY E 395 " --> pdb=" O VAL E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 412 removed outlier: 3.597A pdb=" N PHE E 405 " --> pdb=" O VAL E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 451 through 466 removed outlier: 4.510A pdb=" N TYR E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA E 465 " --> pdb=" O ALA E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 482 Processing helix chain 'E' and resid 486 through 499 removed outlier: 3.632A pdb=" N PHE E 490 " --> pdb=" O MET E 486 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS E 495 " --> pdb=" O ASN E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 517 removed outlier: 3.616A pdb=" N GLU E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 517 " --> pdb=" O MET E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 535 removed outlier: 3.579A pdb=" N PHE E 525 " --> pdb=" O ASN E 521 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 551 removed outlier: 4.491A pdb=" N ILE E 542 " --> pdb=" O PHE E 538 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 543 " --> pdb=" O GLU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 567 removed outlier: 3.965A pdb=" N TYR E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 587 Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.879A pdb=" N MET E 597 " --> pdb=" O ILE E 593 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 620 removed outlier: 3.585A pdb=" N VAL E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 630 removed outlier: 3.802A pdb=" N VAL E 629 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 654 removed outlier: 4.211A pdb=" N TYR E 649 " --> pdb=" O GLN E 645 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 650 " --> pdb=" O MET E 646 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 654 " --> pdb=" O VAL E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'E' and resid 661 through 675 removed outlier: 3.658A pdb=" N TRP E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 683 Processing helix chain 'E' and resid 684 through 693 removed outlier: 4.089A pdb=" N GLU E 688 " --> pdb=" O ARG E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 736 removed outlier: 4.204A pdb=" N ALA E 718 " --> pdb=" O TRP E 714 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 720 " --> pdb=" O GLY E 716 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS E 734 " --> pdb=" O GLU E 730 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 735 " --> pdb=" O GLU E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 754 removed outlier: 3.903A pdb=" N LYS E 754 " --> pdb=" O GLN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 757 through 760 Processing helix chain 'E' and resid 761 through 775 removed outlier: 4.198A pdb=" N ALA E 766 " --> pdb=" O PRO E 762 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR E 768 " --> pdb=" O ALA E 764 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER E 769 " --> pdb=" O LYS E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 793 through 801 removed outlier: 3.797A pdb=" N ILE E 799 " --> pdb=" O GLN E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 84 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.723A pdb=" N PHE F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.530A pdb=" N ARG F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.627A pdb=" N TYR F 144 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE F 149 " --> pdb=" O TYR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 193 through 199 removed outlier: 4.149A pdb=" N LYS F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 193 through 199' Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.543A pdb=" N MET F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 250 removed outlier: 5.384A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 308 through 310 No H-bonds generated for 'chain 'F' and resid 308 through 310' Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 405 through 426 removed outlier: 3.517A pdb=" N ASN F 414 " --> pdb=" O TRP F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 475 through 497 removed outlier: 3.619A pdb=" N HIS F 485 " --> pdb=" O ALA F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 540 removed outlier: 3.517A pdb=" N ASP F 512 " --> pdb=" O ASN F 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 517 " --> pdb=" O GLU F 513 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS F 518 " --> pdb=" O TYR F 514 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP F 519 " --> pdb=" O ASP F 515 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 520 " --> pdb=" O PHE F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 594 Processing helix chain 'F' and resid 606 through 615 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.959A pdb=" N LYS G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 101 removed outlier: 3.503A pdb=" N TYR G 100 " --> pdb=" O ASN G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 113 removed outlier: 4.094A pdb=" N ASN G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'G' and resid 120 through 137 removed outlier: 3.930A pdb=" N ALA G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 157 removed outlier: 4.031A pdb=" N LEU G 150 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 removed outlier: 3.503A pdb=" N ALA G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.670A pdb=" N VAL G 204 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 205' Processing helix chain 'G' and resid 216 through 222 removed outlier: 4.032A pdb=" N TYR G 220 " --> pdb=" O TRP G 216 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU G 222 " --> pdb=" O HIS G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.839A pdb=" N TYR G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 256 removed outlier: 3.531A pdb=" N ALA G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 251 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 255 " --> pdb=" O ARG G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 257 through 270 removed outlier: 3.618A pdb=" N VAL H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 310 removed outlier: 3.525A pdb=" N ALA H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS H 292 " --> pdb=" O ARG H 288 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU H 293 " --> pdb=" O ALA H 289 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 294 " --> pdb=" O ARG H 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS H 295 " --> pdb=" O ARG H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 315 Processing helix chain 'H' and resid 327 through 339 removed outlier: 3.694A pdb=" N LYS H 333 " --> pdb=" O GLU H 329 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS H 334 " --> pdb=" O ALA H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 354 through 361 Processing helix chain 'H' and resid 362 through 365 Processing helix chain 'H' and resid 371 through 377 removed outlier: 3.522A pdb=" N ARG H 376 " --> pdb=" O PRO H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 384 removed outlier: 3.947A pdb=" N GLN H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 396 removed outlier: 3.607A pdb=" N ASN H 396 " --> pdb=" O PRO H 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 393 through 396' Processing helix chain 'H' and resid 418 through 426 Processing helix chain 'H' and resid 431 through 446 Processing helix chain 'I' and resid 148 through 154 removed outlier: 3.847A pdb=" N GLN I 152 " --> pdb=" O TRP I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.954A pdb=" N VAL I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA I 170 " --> pdb=" O PRO I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 202 Processing helix chain 'I' and resid 244 through 249 removed outlier: 3.967A pdb=" N LEU I 249 " --> pdb=" O SER I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.509A pdb=" N LEU I 254 " --> pdb=" O ASN I 250 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU I 256 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 268 Processing helix chain 'I' and resid 269 through 286 removed outlier: 3.505A pdb=" N THR I 275 " --> pdb=" O SER I 271 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 278 " --> pdb=" O SER I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 302 removed outlier: 3.941A pdb=" N ARG I 302 " --> pdb=" O PRO I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 311 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 325 through 332 Processing helix chain 'I' and resid 333 through 342 Processing helix chain 'I' and resid 351 through 357 removed outlier: 4.318A pdb=" N GLN I 357 " --> pdb=" O GLN I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 405 through 409 removed outlier: 3.659A pdb=" N ILE I 408 " --> pdb=" O ASP I 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR I 409 " --> pdb=" O VAL I 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 405 through 409' Processing helix chain 'I' and resid 417 through 433 Processing helix chain 'I' and resid 439 through 457 removed outlier: 4.362A pdb=" N PHE I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 481 Processing helix chain 'i' and resid 269 through 274 Processing helix chain 'i' and resid 302 through 309 Processing helix chain 'i' and resid 326 through 338 removed outlier: 3.504A pdb=" N VAL i 330 " --> pdb=" O CYS i 326 " (cutoff:3.500A) Processing helix chain 'i' and resid 350 through 363 Processing helix chain 'i' and resid 405 through 409 Processing helix chain 'i' and resid 410 through 417 Processing helix chain 'i' and resid 425 through 428 Processing helix chain 'i' and resid 429 through 448 removed outlier: 3.804A pdb=" N LEU i 434 " --> pdb=" O PRO i 430 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY i 448 " --> pdb=" O LYS i 444 " (cutoff:3.500A) Processing helix chain 'i' and resid 458 through 462 removed outlier: 3.553A pdb=" N TRP i 461 " --> pdb=" O PHE i 458 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU i 462 " --> pdb=" O PRO i 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 458 through 462' Processing helix chain 'i' and resid 463 through 477 removed outlier: 5.044A pdb=" N GLN i 473 " --> pdb=" O THR i 469 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA i 474 " --> pdb=" O PHE i 470 " (cutoff:3.500A) Processing helix chain 'i' and resid 485 through 493 Processing helix chain 'i' and resid 514 through 519 removed outlier: 3.759A pdb=" N ILE i 518 " --> pdb=" O PRO i 514 " (cutoff:3.500A) Processing helix chain 'i' and resid 520 through 522 No H-bonds generated for 'chain 'i' and resid 520 through 522' Processing helix chain 'i' and resid 564 through 582 removed outlier: 3.815A pdb=" N GLY i 568 " --> pdb=" O MET i 564 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN i 582 " --> pdb=" O MET i 578 " (cutoff:3.500A) Processing helix chain 'i' and resid 583 through 586 removed outlier: 3.700A pdb=" N MET i 586 " --> pdb=" O PRO i 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 583 through 586' Processing helix chain 'i' and resid 588 through 615 Processing helix chain 'i' and resid 634 through 639 Processing helix chain 'J' and resid 100 through 109 removed outlier: 4.011A pdb=" N GLY J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 178 removed outlier: 4.030A pdb=" N ILE J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 199 removed outlier: 3.565A pdb=" N ASP J 198 " --> pdb=" O LEU J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 208 removed outlier: 3.995A pdb=" N LEU J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 211 No H-bonds generated for 'chain 'J' and resid 209 through 211' Processing helix chain 'J' and resid 219 through 223 Processing helix chain 'J' and resid 224 through 231 removed outlier: 3.532A pdb=" N LEU J 231 " --> pdb=" O ASP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 255 Processing helix chain 'J' and resid 260 through 267 removed outlier: 3.893A pdb=" N LEU J 266 " --> pdb=" O LYS J 262 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA J 267 " --> pdb=" O ILE J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 284 removed outlier: 4.180A pdb=" N PHE J 273 " --> pdb=" O ASP J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 361 removed outlier: 3.631A pdb=" N PHE J 356 " --> pdb=" O LYS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 389 Processing helix chain 'J' and resid 413 through 423 removed outlier: 3.540A pdb=" N ARG J 421 " --> pdb=" O ILE J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 456 removed outlier: 3.667A pdb=" N LYS J 440 " --> pdb=" O SER J 436 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA J 441 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE J 456 " --> pdb=" O MET J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 470 removed outlier: 3.684A pdb=" N MET J 470 " --> pdb=" O ILE J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 506 removed outlier: 3.982A pdb=" N LEU J 506 " --> pdb=" O GLN J 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 231 through 233 No H-bonds generated for 'chain 'K' and resid 231 through 233' Processing helix chain 'K' and resid 283 through 286 Processing helix chain 'K' and resid 298 through 320 removed outlier: 3.541A pdb=" N ILE K 303 " --> pdb=" O PRO K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 327 Processing helix chain 'L' and resid 66 through 76 Processing helix chain 'L' and resid 76 through 90 Processing helix chain 'L' and resid 98 through 108 removed outlier: 3.572A pdb=" N ASN L 108 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 132 removed outlier: 3.685A pdb=" N MET L 132 " --> pdb=" O PHE L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 151 removed outlier: 3.561A pdb=" N GLN L 146 " --> pdb=" O GLY L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 164 removed outlier: 3.567A pdb=" N ALA L 164 " --> pdb=" O LYS L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 removed outlier: 3.637A pdb=" N THR L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 Processing helix chain 'L' and resid 226 through 231 removed outlier: 4.216A pdb=" N TYR L 230 " --> pdb=" O TRP L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 248 removed outlier: 3.609A pdb=" N SER L 243 " --> pdb=" O PRO L 239 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE L 244 " --> pdb=" O ASP L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 282 Processing helix chain 'M' and resid 76 through 86 Processing helix chain 'M' and resid 101 through 118 removed outlier: 3.985A pdb=" N ILE M 105 " --> pdb=" O CYS M 101 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET M 107 " --> pdb=" O PRO M 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN M 109 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.601A pdb=" N ALA M 136 " --> pdb=" O GLU M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 176 Processing helix chain 'm' and resid 76 through 86 Processing helix chain 'm' and resid 101 through 119 removed outlier: 3.784A pdb=" N ILE m 105 " --> pdb=" O CYS m 101 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU m 106 " --> pdb=" O GLY m 102 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN m 109 " --> pdb=" O ILE m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 139 Processing helix chain 'm' and resid 166 through 177 Processing helix chain 'N' and resid 239 through 246 Processing helix chain 'N' and resid 286 through 298 Processing helix chain 'N' and resid 309 through 313 removed outlier: 3.590A pdb=" N GLU N 312 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 333 removed outlier: 4.412A pdb=" N ALA N 333 " --> pdb=" O LEU N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 345 Proline residue: N 340 - end of helix removed outlier: 3.716A pdb=" N THR N 345 " --> pdb=" O SER N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 370 removed outlier: 3.768A pdb=" N THR N 358 " --> pdb=" O GLY N 354 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR N 360 " --> pdb=" O THR N 356 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU N 361 " --> pdb=" O THR N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 411 removed outlier: 3.570A pdb=" N ASN N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 428 Processing helix chain 'N' and resid 447 through 452 Processing helix chain 'N' and resid 455 through 468 removed outlier: 3.723A pdb=" N MET N 468 " --> pdb=" O LEU N 464 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 491 removed outlier: 3.601A pdb=" N ALA N 486 " --> pdb=" O ASP N 482 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN N 491 " --> pdb=" O PHE N 487 " (cutoff:3.500A) Processing helix chain 'N' and resid 542 through 559 removed outlier: 3.713A pdb=" N ALA N 553 " --> pdb=" O LEU N 549 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 554 " --> pdb=" O ALA N 550 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL N 558 " --> pdb=" O VAL N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 564 removed outlier: 3.689A pdb=" N ASP N 564 " --> pdb=" O PRO N 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 561 through 564' Processing helix chain 'N' and resid 565 through 573 Processing helix chain 'N' and resid 597 through 612 Processing helix chain 'N' and resid 629 through 642 removed outlier: 3.950A pdb=" N ILE N 633 " --> pdb=" O GLY N 629 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS N 641 " --> pdb=" O ILE N 637 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 666 Processing helix chain 'N' and resid 667 through 669 No H-bonds generated for 'chain 'N' and resid 667 through 669' Processing helix chain 'N' and resid 671 through 680 Processing helix chain 'N' and resid 698 through 709 removed outlier: 3.852A pdb=" N ALA N 702 " --> pdb=" O ILE N 698 " (cutoff:3.500A) Processing helix chain 'N' and resid 738 through 756 removed outlier: 4.150A pdb=" N CYS N 742 " --> pdb=" O ASP N 738 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP N 750 " --> pdb=" O LEU N 746 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU N 751 " --> pdb=" O GLN N 747 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.654A pdb=" N GLY O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 removed outlier: 3.935A pdb=" N THR O 73 " --> pdb=" O GLY O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing helix chain 'O' and resid 85 through 104 removed outlier: 3.646A pdb=" N PHE O 89 " --> pdb=" O ASN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 108 removed outlier: 3.573A pdb=" N TYR O 108 " --> pdb=" O ARG O 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 105 through 108' Processing helix chain 'O' and resid 112 through 125 Processing helix chain 'O' and resid 130 through 134 Processing helix chain 'P' and resid 43 through 49 removed outlier: 3.644A pdb=" N LEU P 47 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 63 Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 24 removed outlier: 5.869A pdb=" N CYS A 17 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 33 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 19 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 194 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 196 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 181 " --> pdb=" O TRP A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.650A pdb=" N SER A 107 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 64 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU A 152 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 62 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN A 154 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR A 60 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'a' and resid 16 through 24 removed outlier: 5.992A pdb=" N CYS a 17 " --> pdb=" O ILE a 33 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE a 33 " --> pdb=" O CYS a 17 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU a 19 " --> pdb=" O ARG a 31 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU a 27 " --> pdb=" O ASP a 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN a 181 " --> pdb=" O TRP a 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 121 through 122 removed outlier: 6.340A pdb=" N GLY a 148 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL a 65 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN a 150 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 96 through 97 Processing sheet with id=AA8, first strand: chain 'a' and resid 114 through 117 Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 105 removed outlier: 4.126A pdb=" N GLN B 95 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 86 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN B 103 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER B 78 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 83 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR B 56 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N GLY B 85 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N VAL B 54 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N ILE B 87 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N LEU B 52 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE H 430 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 59 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 3.549A pdb=" N GLN B 125 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 124 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 137 removed outlier: 3.850A pdb=" N TYR B 146 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 162 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 160 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 443 through 444 removed outlier: 3.723A pdb=" N ARG B 443 " --> pdb=" O GLU B 451 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 466 through 469 current: chain 'B' and resid 496 through 501 Processing sheet with id=AB5, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB6, first strand: chain 'B' and resid 579 through 580 removed outlier: 6.571A pdb=" N ALA B 579 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 602 through 607 removed outlier: 6.728A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR B 590 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 596 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 612 through 613 Processing sheet with id=AB9, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AC1, first strand: chain 'B' and resid 653 through 654 removed outlier: 7.410A pdb=" N VAL B 671 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 833 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 673 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 672 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 658 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 941 " --> pdb=" O TYR B 659 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 685 through 694 removed outlier: 5.601A pdb=" N LYS B 793 " --> pdb=" O PRO B 801 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 787 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 809 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 785 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 737 through 739 removed outlier: 6.608A pdb=" N LEU B 775 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 959 through 961 removed outlier: 3.523A pdb=" N SER C 386 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 983 through 985 removed outlier: 3.568A pdb=" N GLN B 983 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1065 through 1068 removed outlier: 4.680A pdb=" N HIS B1055 " --> pdb=" O LYS B1068 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS C 14 " --> pdb=" O VAL B1058 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.557A pdb=" N LYS C 33 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 112 through 121 removed outlier: 3.560A pdb=" N GLY C 112 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 116 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 274 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N CYS C 118 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N VAL C 272 " --> pdb=" O CYS C 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 588 through 589 removed outlier: 3.559A pdb=" N GLU C 629 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 263 " --> pdb=" O ILE K 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 154 through 155 removed outlier: 3.706A pdb=" N GLN c 159 " --> pdb=" O ASP c 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 215 through 217 Processing sheet with id=AD3, first strand: chain 'c' and resid 226 through 228 Processing sheet with id=AD4, first strand: chain 'c' and resid 253 through 255 removed outlier: 6.701A pdb=" N ILE c 253 " --> pdb=" O ILE c 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 351 through 353 removed outlier: 3.633A pdb=" N ALA c 421 " --> pdb=" O VAL c 352 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 395 through 399 removed outlier: 4.053A pdb=" N LYS c 359 " --> pdb=" O GLU c 390 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 435 through 441 removed outlier: 4.004A pdb=" N VAL c1130 " --> pdb=" O ILE c 440 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU c1129 " --> pdb=" O HIS c1116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 472 through 477 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 472 through 477 current: chain 'c' and resid 1034 through 1035 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 1034 through 1035 current: chain 'c' and resid 1089 through 1095 removed outlier: 6.418A pdb=" N VAL c1100 " --> pdb=" O ILE c1092 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 1099 through 1109 current: chain 'F' and resid 292 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 303 through 306 current: chain 'F' and resid 342 through 346 Processing sheet with id=AD9, first strand: chain 'c' and resid 480 through 482 Processing sheet with id=AE1, first strand: chain 'c' and resid 497 through 498 removed outlier: 6.671A pdb=" N GLN c 497 " --> pdb=" O HIS F 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 570 through 571 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 574 through 578 current: chain 'c' and resid 851 through 859 removed outlier: 3.579A pdb=" N PHE c 867 " --> pdb=" O VAL c 856 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 596 through 597 removed outlier: 5.694A pdb=" N ILE c 610 " --> pdb=" O LEU c 837 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU c 837 " --> pdb=" O ILE c 610 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN c 838 " --> pdb=" O GLN c 805 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 662 through 664 Processing sheet with id=AE5, first strand: chain 'c' and resid 669 through 674 removed outlier: 3.691A pdb=" N SER c 685 " --> pdb=" O VAL c 705 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 722 through 724 removed outlier: 3.510A pdb=" N ASP c 722 " --> pdb=" O VAL c 775 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 1044 through 1045 Processing sheet with id=AE8, first strand: chain 'c' and resid 1248 through 1250 Processing sheet with id=AE9, first strand: chain 'E' and resid 700 through 701 removed outlier: 6.738A pdb=" N TRP E 706 " --> pdb=" O SER E 744 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL E 746 " --> pdb=" O TRP E 706 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 708 " --> pdb=" O VAL E 746 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 387 through 388 removed outlier: 6.215A pdb=" N ARG F 387 " --> pdb=" O VAL F 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 191 through 197 removed outlier: 7.078A pdb=" N GLY G 178 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP G 214 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 180 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY G 212 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G 182 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AF4, first strand: chain 'I' and resid 209 through 212 removed outlier: 6.599A pdb=" N LYS I 210 " --> pdb=" O PHE I 182 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY I 184 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP I 212 " --> pdb=" O GLY I 184 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL I 186 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU I 118 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N HIS I 261 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE I 120 " --> pdb=" O HIS I 261 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASN I 263 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE I 122 " --> pdb=" O ASN I 263 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE I 260 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASP I 293 " --> pdb=" O PHE I 260 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE I 262 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE I 321 " --> pdb=" O PHE I 381 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR I 383 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL I 323 " --> pdb=" O THR I 383 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 230 through 236 removed outlier: 6.799A pdb=" N HIS I 221 " --> pdb=" O LYS I 235 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR M 146 " --> pdb=" O PHE M 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE M 93 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL M 127 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP M 95 " --> pdb=" O VAL M 127 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS M 73 " --> pdb=" O LYS M 126 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP M 128 " --> pdb=" O LYS M 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'i' and resid 370 through 372 removed outlier: 6.258A pdb=" N ARG i 371 " --> pdb=" O PHE i 343 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY i 345 " --> pdb=" O ARG i 371 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN i 423 " --> pdb=" O PHE i 283 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE i 420 " --> pdb=" O PHE i 451 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP i 453 " --> pdb=" O PHE i 420 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE i 422 " --> pdb=" O ASP i 453 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'i' and resid 295 through 296 removed outlier: 3.607A pdb=" N ARG i 295 " --> pdb=" O ARG i 321 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 391 through 393 removed outlier: 5.422A pdb=" N LEU i 391 " --> pdb=" O GLY i 386 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY i 386 " --> pdb=" O LEU i 391 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR m 146 " --> pdb=" O PHE m 96 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU m 92 " --> pdb=" O ILE m 150 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE m 93 " --> pdb=" O VAL m 125 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL m 127 " --> pdb=" O ILE m 93 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP m 95 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS m 73 " --> pdb=" O LYS m 126 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ASP m 128 " --> pdb=" O LYS m 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AG1, first strand: chain 'J' and resid 112 through 113 removed outlier: 6.247A pdb=" N VAL J 141 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE J 331 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 151 through 154 Processing sheet with id=AG3, first strand: chain 'J' and resid 309 through 310 removed outlier: 5.362A pdb=" N ASN J 309 " --> pdb=" O VAL J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'J' and resid 380 through 381 removed outlier: 6.092A pdb=" N ILE J 380 " --> pdb=" O TRP J 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'J' and resid 391 through 393 Processing sheet with id=AG6, first strand: chain 'K' and resid 138 through 142 removed outlier: 3.522A pdb=" N ARG K 151 " --> pdb=" O GLU K 165 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU K 165 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG K 191 " --> pdb=" O HIS K 229 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N SER K 222 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N VAL K 249 " --> pdb=" O SER K 222 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL K 224 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ILE K 247 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU K 226 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU K 245 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS K 228 " --> pdb=" O ASP K 243 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER K 256 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG K 180 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ARG K 259 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 201 through 203 Processing sheet with id=AG8, first strand: chain 'L' and resid 201 through 207 removed outlier: 7.108A pdb=" N GLY L 173 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP L 224 " --> pdb=" O GLY L 173 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA L 175 " --> pdb=" O THR L 222 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR L 222 " --> pdb=" O ALA L 175 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU L 177 " --> pdb=" O LEU L 220 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 347 through 349 Processing sheet with id=AH1, first strand: chain 'N' and resid 589 through 592 removed outlier: 6.368A pdb=" N GLY N 589 " --> pdb=" O VAL N 716 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL N 718 " --> pdb=" O GLY N 589 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE N 591 " --> pdb=" O VAL N 718 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE N 617 " --> pdb=" O VAL N 717 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL N 616 " --> pdb=" O VAL N 644 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE N 646 " --> pdb=" O VAL N 616 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR N 618 " --> pdb=" O ILE N 646 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR N 648 " --> pdb=" O THR N 618 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE N 620 " --> pdb=" O THR N 648 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP N 650 " --> pdb=" O PHE N 620 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS N 622 " --> pdb=" O ASP N 650 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR N 645 " --> pdb=" O PHE N 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'N' and resid 727 through 729 removed outlier: 4.012A pdb=" N LYS N 732 " --> pdb=" O GLU N 729 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 51 through 54 removed outlier: 3.877A pdb=" N ARG P 51 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN P 87 " --> pdb=" O TYR P 117 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP P 86 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER P 70 " --> pdb=" O TYR P 135 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 77 through 82 2804 hydrogen bonds defined for protein. 7977 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: 30.21 Time building geometry restraints manager: 13.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 10448 1.28 - 1.42: 16030 1.42 - 1.55: 35435 1.55 - 1.68: 75 1.68 - 1.82: 408 Bond restraints: 62396 Sorted by residual: bond pdb=" CA GLU F 545 " pdb=" C GLU F 545 " ideal model delta sigma weight residual 1.526 1.411 0.115 1.14e-02 7.69e+03 1.02e+02 bond pdb=" CA ASN C 563 " pdb=" C ASN C 563 " ideal model delta sigma weight residual 1.527 1.443 0.084 1.02e-02 9.61e+03 6.86e+01 bond pdb=" CA THR G 57 " pdb=" C THR G 57 " ideal model delta sigma weight residual 1.528 1.436 0.092 1.18e-02 7.18e+03 6.11e+01 bond pdb=" CA ILE F 533 " pdb=" C ILE F 533 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.22e-02 6.72e+03 5.75e+01 bond pdb=" CA SER I 246 " pdb=" C SER I 246 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.27e-02 6.20e+03 4.89e+01 ... (remaining 62391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 81284 3.85 - 7.69: 3154 7.69 - 11.54: 478 11.54 - 15.38: 71 15.38 - 19.23: 6 Bond angle restraints: 84993 Sorted by residual: angle pdb=" N VAL C 102 " pdb=" CA VAL C 102 " pdb=" C VAL C 102 " ideal model delta sigma weight residual 110.42 126.00 -15.58 9.60e-01 1.09e+00 2.63e+02 angle pdb=" N ASP B1011 " pdb=" CA ASP B1011 " pdb=" C ASP B1011 " ideal model delta sigma weight residual 111.90 130.00 -18.10 1.32e+00 5.74e-01 1.88e+02 angle pdb=" N VAL C 393 " pdb=" CA VAL C 393 " pdb=" C VAL C 393 " ideal model delta sigma weight residual 110.62 124.27 -13.65 1.02e+00 9.61e-01 1.79e+02 angle pdb=" N ALA C 530 " pdb=" CA ALA C 530 " pdb=" C ALA C 530 " ideal model delta sigma weight residual 111.07 124.18 -13.11 1.07e+00 8.73e-01 1.50e+02 angle pdb=" N GLN I 346 " pdb=" CA GLN I 346 " pdb=" C GLN I 346 " ideal model delta sigma weight residual 111.14 124.00 -12.86 1.08e+00 8.57e-01 1.42e+02 ... (remaining 84988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 34028 17.70 - 35.40: 2406 35.40 - 53.09: 648 53.09 - 70.79: 126 70.79 - 88.49: 23 Dihedral angle restraints: 37231 sinusoidal: 13036 harmonic: 24195 Sorted by residual: dihedral pdb=" C PHE J 162 " pdb=" N PHE J 162 " pdb=" CA PHE J 162 " pdb=" CB PHE J 162 " ideal model delta harmonic sigma weight residual -122.60 -149.10 26.50 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N PHE J 162 " pdb=" C PHE J 162 " pdb=" CA PHE J 162 " pdb=" CB PHE J 162 " ideal model delta harmonic sigma weight residual 122.80 148.70 -25.90 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" CB CYS m 101 " pdb=" SG CYS m 101 " pdb=" SG CYS m 104 " pdb=" CB CYS m 104 " ideal model delta sinusoidal sigma weight residual 93.00 -179.95 -87.05 1 1.00e+01 1.00e-02 9.11e+01 ... (remaining 37228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 8460 0.240 - 0.481: 1027 0.481 - 0.721: 86 0.721 - 0.961: 5 0.961 - 1.202: 2 Chirality restraints: 9580 Sorted by residual: chirality pdb=" CA PHE J 162 " pdb=" N PHE J 162 " pdb=" C PHE J 162 " pdb=" CB PHE J 162 " both_signs ideal model delta sigma weight residual False 2.51 1.31 1.20 2.00e-01 2.50e+01 3.61e+01 chirality pdb=" CA LEU M 144 " pdb=" N LEU M 144 " pdb=" C LEU M 144 " pdb=" CB LEU M 144 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA GLU c 417 " pdb=" N GLU c 417 " pdb=" C GLU c 417 " pdb=" CB GLU c 417 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 9577 not shown) Planarity restraints: 11159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 438 " 0.027 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ARG C 438 " -0.096 2.00e-02 2.50e+03 pdb=" O ARG C 438 " 0.036 2.00e-02 2.50e+03 pdb=" N GLU C 439 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.027 2.00e-02 2.50e+03 5.41e-02 2.93e+01 pdb=" C GLY A 156 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR A 157 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 117 " -0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C LEU D 117 " 0.089 2.00e-02 2.50e+03 pdb=" O LEU D 117 " -0.034 2.00e-02 2.50e+03 pdb=" N ASN D 118 " -0.030 2.00e-02 2.50e+03 ... (remaining 11156 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 6 2.14 - 2.83: 20626 2.83 - 3.52: 80987 3.52 - 4.21: 136477 4.21 - 4.90: 231651 Nonbonded interactions: 469747 Sorted by model distance: nonbonded pdb=" OD2 ASP L 224 " pdb="FE FE L2001 " model vdw 1.455 2.260 nonbonded pdb=" OD2 ASP G 214 " pdb="FE FE G2001 " model vdw 1.465 2.260 nonbonded pdb=" OE1 GLU B 535 " pdb="ZN ZN B1101 " model vdw 1.979 2.230 nonbonded pdb=" OD2 ASP C 496 " pdb="MG MG C3001 " model vdw 2.000 2.170 nonbonded pdb=" OD1 ASP C 500 " pdb="MG MG C3001 " model vdw 2.125 2.170 ... (remaining 469742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 25 or (resid 26 and (name N or na \ me CA or name C or name O or name CB )) or resid 27 through 34 or resid 36 throu \ gh 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or r \ esid 39 through 67 or (resid 68 through 78 and (name N or name CA or name C or n \ ame O or name CB )) or resid 79 through 82 or (resid 83 and (name N or name CA o \ r name C or name O or name CB )) or resid 84 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 or (resid 111 and ( \ name N or name CA or name C or name O or name CB )) or resid 112 through 130 or \ (resid 131 and (name N or name CA or name C or name O or name CB )) or resid 132 \ through 146 or (resid 147 and (name N or name CA or name C or name O or name CB \ )) or resid 148 through 192 or (resid 193 through 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 233 or (resid 234 through 2 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 236 through \ 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) or r \ esid 270 through 278 or (resid 279 and (name N or name CA or name C or name O or \ name CB )) or resid 280 through 297 or (resid 298 and (name N or name CA or nam \ e C or name O or name CB )) or resid 299 through 300 or (resid 301 and (name N o \ r name CA or name C or name O or name CB )) or resid 302 or (resid 303 through 3 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 305 through \ 308 or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 or (resid 312 through 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 317 or (resid 318 and (name N or na \ me CA or name C or name O or name CB )) or resid 319 through 327)) selection = (chain 'a' and (resid 11 through 23 or (resid 24 through 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 69 or (resid 70 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 81 or (resid 82 through 83 and (name N or name CA or name C or name O or name C \ B )) or resid 84 or (resid 85 through 86 and (name N or name CA or name C or nam \ e O or name CB )) or resid 87 through 137 or (resid 138 through 141 and (name N \ or name CA or name C or name O or name CB )) or resid 142 through 156 or (resid \ 157 and (name N or name CA or name C or name O or name CB )) or resid 158 or (re \ sid 159 through 167 and (name N or name CA or name C or name O or name CB )) or \ resid 168 through 190 or (resid 191 and (name N or name CA or name C or name O o \ r name CB )) or (resid 192 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 197 or (resid 198 and (name N or name CA or \ name C or name O or name CB )) or resid 199 through 208 or (resid 209 and (name \ N or name CA or name C or name O or name CB )) or resid 210 through 214 or (res \ id 215 and (name N or name CA or name C or name O or name CB )) or resid 216 thr \ ough 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) \ or resid 226 through 231 or (resid 232 and (name N or name CA or name C or name \ O or name CB )) or resid 233 through 234 or (resid 235 and (name N or name CA or \ name C or name O or name CB )) or resid 263 or resid 267 through 306 or (resid \ 307 and (name N or name CA or name C or name O or name CB )) or resid 308 throug \ h 327)) } ncs_group { reference = (chain 'M' and ((resid 69 through 70 and (name N or name CA or name C or name O \ or name CB )) or resid 71 or (resid 72 through 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 87 or (resid 88 through 90 and (n \ ame N or name CA or name C or name O or name CB )) or resid 91 through 117 or (r \ esid 118 through 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 132 or (resid 133 and (name N or name CA or name C or name O \ or name CB )) or resid 134 through 152 or (resid 153 and (name N or name CA or n \ ame C or name O or name CB )) or resid 154 or (resid 155 and (name N or name CA \ or name C or name O or name CB )) or resid 156 through 177)) selection = (chain 'm' and (resid 69 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 177)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.070 Extract box with map and model: 2.010 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 123.410 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.015 0.115 62396 Z= 1.023 Angle : 1.727 19.227 84993 Z= 1.204 Chirality : 0.153 1.202 9580 Planarity : 0.008 0.103 11159 Dihedral : 13.639 88.488 21611 Min Nonbonded Distance : 1.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.39 % Allowed : 11.07 % Favored : 83.55 % Cbeta Deviations : 1.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8284 helix: 1.68 (0.08), residues: 3364 sheet: 0.44 (0.17), residues: 950 loop : -0.78 (0.09), residues: 3970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 177 HIS 0.016 0.003 HIS I 374 PHE 0.050 0.003 PHE C 638 TYR 0.033 0.003 TYR c1008 ARG 0.011 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16568 Ramachandran restraints generated. 8284 Oldfield, 0 Emsley, 8284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16568 Ramachandran restraints generated. 8284 Oldfield, 0 Emsley, 8284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 996 time to evaluate : 5.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8146 (m) REVERT: a 278 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: B 323 ASP cc_start: 0.8746 (t0) cc_final: 0.8403 (t0) REVERT: B 327 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8932 (mp) REVERT: B 718 ARG cc_start: 0.8457 (ptm160) cc_final: 0.8064 (ttp-110) REVERT: B 737 ILE cc_start: 0.9518 (mt) cc_final: 0.9270 (tp) REVERT: B 812 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: B 1045 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 225 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8893 (tm-30) REVERT: C 257 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9279 (mp) REVERT: C 340 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8478 (OUTLIER) REVERT: C 379 LEU cc_start: 0.8560 (mt) cc_final: 0.7657 (mt) REVERT: C 496 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7700 (p0) REVERT: C 614 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.7444 (t60) REVERT: C 674 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7618 (tm-30) REVERT: c 71 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8923 (mt) REVERT: c 1307 ASP cc_start: 0.8525 (t0) cc_final: 0.8265 (t0) REVERT: D 447 ARG cc_start: 0.7221 (mtt-85) cc_final: 0.6737 (mmp-170) REVERT: D 735 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7824 (tp) REVERT: D 816 MET cc_start: 0.7693 (tpp) cc_final: 0.7211 (mmm) REVERT: E 510 TRP cc_start: 0.6823 (t-100) cc_final: 0.6615 (t-100) REVERT: E 516 VAL cc_start: 0.6675 (p) cc_final: 0.6444 (m) REVERT: E 555 PRO cc_start: 0.0018 (Cg_exo) cc_final: -0.0664 (Cg_endo) REVERT: E 626 MET cc_start: 0.3059 (mmt) cc_final: 0.1972 (pp-130) REVERT: E 642 ASN cc_start: 0.7915 (t0) cc_final: 0.7556 (p0) REVERT: E 675 TRP cc_start: 0.6762 (t-100) cc_final: 0.6514 (t-100) REVERT: F 182 TRP cc_start: 0.8157 (t-100) cc_final: 0.7848 (t-100) REVERT: F 211 MET cc_start: 0.8292 (mtp) cc_final: 0.7865 (mpp) REVERT: F 529 MET cc_start: 0.9501 (ttm) cc_final: 0.9157 (mmm) REVERT: G 57 THR cc_start: 0.9490 (p) cc_final: 0.9273 (p) REVERT: G 103 THR cc_start: 0.9113 (m) cc_final: 0.8780 (p) REVERT: G 150 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8980 (tm) REVERT: G 227 ASP cc_start: 0.8461 (m-30) cc_final: 0.7635 (t0) REVERT: G 231 TYR cc_start: 0.8398 (t80) cc_final: 0.7856 (t80) REVERT: I 467 PHE cc_start: 0.9634 (OUTLIER) cc_final: 0.9178 (m-80) REVERT: I 486 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8598 (p90) REVERT: i 383 MET cc_start: 0.8848 (mtm) cc_final: 0.8524 (mtp) REVERT: J 90 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8203 (p) REVERT: K 199 CYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7545 (p) REVERT: L 236 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7570 (t0) REVERT: L 253 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8808 (pm20) REVERT: M 153 ASP cc_start: 0.8731 (t70) cc_final: 0.7923 (t0) REVERT: m 107 MET cc_start: 0.9119 (tpp) cc_final: 0.8897 (tpp) REVERT: m 110 GLU cc_start: 0.8760 (pt0) cc_final: 0.8446 (pt0) REVERT: m 169 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8574 (ttp) REVERT: N 584 GLU cc_start: 0.4708 (pm20) cc_final: 0.4116 (pp20) REVERT: N 626 SER cc_start: 0.0704 (p) cc_final: -0.0470 (m) REVERT: N 630 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7631 (ttpt) REVERT: N 634 MET cc_start: 0.6143 (mtp) cc_final: 0.5673 (mtp) REVERT: N 673 GLN cc_start: 0.7254 (mt0) cc_final: 0.6747 (tm-30) REVERT: N 678 HIS cc_start: 0.7863 (m170) cc_final: 0.7415 (m-70) REVERT: N 683 TYR cc_start: 0.7044 (t80) cc_final: 0.6835 (t80) REVERT: N 684 TYR cc_start: 0.3874 (m-80) cc_final: 0.3466 (m-80) REVERT: N 744 GLU cc_start: 0.5590 (tp30) cc_final: 0.5188 (tt0) REVERT: N 762 PHE cc_start: 0.6288 (t80) cc_final: 0.6068 (t80) REVERT: O 55 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8987 (mp) REVERT: O 104 ASN cc_start: 0.8465 (t0) cc_final: 0.7973 (t0) REVERT: P 44 LEU cc_start: 0.9168 (mt) cc_final: 0.8774 (tm) REVERT: P 87 GLN cc_start: 0.8672 (tt0) cc_final: 0.8213 (tt0) REVERT: P 124 ASP cc_start: 0.8420 (m-30) cc_final: 0.7786 (t0) REVERT: P 129 ASP cc_start: 0.7123 (m-30) cc_final: 0.6737 (m-30) outliers start: 292 outliers final: 40 residues processed: 1230 average time/residue: 1.4290 time to fit residues: 2241.3599 Evaluate side-chains 552 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 493 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 278 GLU Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 614 TRP Chi-restraints excluded: chain c residue 71 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 605 PHE Chi-restraints excluded: chain c residue 978 SER Chi-restraints excluded: chain c residue 1125 GLU Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1233 LEU Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain c residue 1293 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 735 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 367 ARG Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 322 TRP Chi-restraints excluded: chain I residue 152 GLN Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 486 TRP Chi-restraints excluded: chain i residue 423 ASN Chi-restraints excluded: chain i residue 546 ASN Chi-restraints excluded: chain i residue 629 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain K residue 199 CYS Chi-restraints excluded: chain K residue 312 ARG Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 236 ASN Chi-restraints excluded: chain L residue 253 GLU Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 698 optimal weight: 1.9990 chunk 626 optimal weight: 0.9980 chunk 347 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 422 optimal weight: 6.9990 chunk 334 optimal weight: 0.9980 chunk 648 optimal weight: 0.5980 chunk 250 optimal weight: 6.9990 chunk 394 optimal weight: 20.0000 chunk 482 optimal weight: 1.9990 chunk 751 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 81 GLN A 187 HIS A 196 GLN A 276 GLN A 285 ASN a 41 GLN a 119 GLN a 187 HIS a 196 GLN a 221 ASN a 263 ASN a 285 ASN B 58 GLN B 128 GLN B 267 ASN B 278 ASN B 307 ASN B 334 ASN B 372 HIS B 386 GLN B 495 GLN B 522 GLN B 600 ASN B 621 HIS B 622 GLN B 636 GLN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN B 865 GLN B 910 GLN B 934 ASN B 938 GLN B 953 GLN B 971 GLN B1000 HIS B1017 GLN B1064 GLN C 135 ASN C 300 ASN C 453 GLN C 471 GLN C 474 GLN C 513 GLN C 523 HIS C 591 ASN C 605 ASN C 666 HIS c 10 HIS c 37 HIS c 49 GLN c 73 GLN c 77 GLN c 90 ASN c 92 HIS c 145 GLN c 449 HIS c 497 GLN c 924 GLN c1007 ASN c1031 ASN c1051 ASN c1076 ASN c1116 HIS c1196 GLN c1206 GLN c1212 GLN D 175 GLN D 188 ASN D 194 ASN D 218 GLN D 227 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 420 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 882 GLN E 476 ASN E 579 GLN ** E 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 HIS F 81 ASN F 128 ASN F 148 GLN ** F 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN F 288 HIS F 301 HIS F 324 HIS F 402 ASN F 417 GLN F 518 HIS ** F 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 ASN G 81 HIS G 92 GLN G 116 ASN H 216 HIS H 247 GLN H 271 GLN H 332 GLN H 399 GLN H 426 HIS I 139 GLN I 152 GLN I 193 GLN I 346 GLN I 374 HIS I 440 GLN i 287 GLN i 288 HIS i 361 ASN i 363 ASN ** i 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 584 HIS i 607 GLN J 243 GLN J 244 GLN J 256 HIS J 281 GLN J 288 GLN J 313 GLN J 367 ASN J 496 GLN K 313 GLN L 84 ASN L 169 GLN L 188 ASN M 121 ASN N 596 HIS N 651 ASN N 673 GLN O 61 GLN O 82 ASN O 85 ASN O 104 ASN O 120 ASN Total number of N/Q/H flips: 131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62396 Z= 0.228 Angle : 0.643 9.409 84993 Z= 0.358 Chirality : 0.045 0.233 9580 Planarity : 0.006 0.075 11159 Dihedral : 7.081 80.465 9331 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.61 % Allowed : 17.39 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8284 helix: 1.53 (0.09), residues: 3452 sheet: 0.43 (0.16), residues: 1020 loop : -0.76 (0.09), residues: 3812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 177 HIS 0.010 0.001 HIS K 139 PHE 0.024 0.002 PHE c 991 TYR 0.029 0.001 TYR N 594 ARG 0.008 0.001 ARG D 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16568 Ramachandran restraints generated. 8284 Oldfield, 0 Emsley, 8284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16568 Ramachandran restraints generated. 8284 Oldfield, 0 Emsley, 8284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 527 time to evaluate : 5.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 86 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 36 TYR cc_start: 0.8343 (m-80) cc_final: 0.8143 (m-80) REVERT: B 195 LEU cc_start: 0.8591 (mm) cc_final: 0.8390 (mm) REVERT: B 715 HIS cc_start: 0.7834 (t-90) cc_final: 0.7253 (t70) REVERT: B 812 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7714 (mtt180) REVERT: B 1045 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 129 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6898 (tt) REVERT: C 225 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8937 (tm-30) REVERT: C 257 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9197 (tp) REVERT: C 298 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7922 (t0) REVERT: C 340 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (t0) REVERT: C 467 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6083 (mtp180) REVERT: C 674 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7502 (tm-30) REVERT: c 83 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8084 (mm-30) REVERT: c 1028 MET cc_start: 0.8491 (ttp) cc_final: 0.8134 (ttm) REVERT: c 1049 ASN cc_start: 0.8944 (m-40) cc_final: 0.8734 (m-40) REVERT: c 1236 GLU cc_start: 0.8526 (mp0) cc_final: 0.8322 (mp0) REVERT: D 447 ARG cc_start: 0.6785 (mtt-85) cc_final: 0.6483 (mmp-170) REVERT: D 816 MET cc_start: 0.7625 (tpp) cc_final: 0.7334 (mmt) REVERT: E 502 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6813 (mm) REVERT: E 548 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.2601 (ptm) REVERT: E 642 ASN cc_start: 0.7967 (t0) cc_final: 0.7695 (p0) REVERT: E 675 TRP cc_start: 0.6756 (t-100) cc_final: 0.6468 (t-100) REVERT: E 729 MET cc_start: 0.8840 (tmt) cc_final: 0.8473 (pp-130) REVERT: F 211 MET cc_start: 0.8118 (mtp) cc_final: 0.7818 (mtp) REVERT: F 529 MET cc_start: 0.9447 (ttm) cc_final: 0.8887 (tmm) REVERT: F 530 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8379 (mm) REVERT: G 98 ILE cc_start: 0.9230 (mt) cc_final: 0.9012 (mp) REVERT: G 103 THR cc_start: 0.9043 (m) cc_final: 0.8715 (p) REVERT: G 151 GLN cc_start: 0.9461 (mt0) cc_final: 0.9099 (mp10) REVERT: G 188 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: G 242 TRP cc_start: 0.8224 (m100) cc_final: 0.7926 (m100) REVERT: I 237 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8366 (mtpt) REVERT: I 486 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8602 (p90) REVERT: i 378 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.6546 (m) REVERT: i 472 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7249 (tm-30) REVERT: i 612 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8037 (mmt90) REVERT: J 277 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8670 (ttm) REVERT: J 348 MET cc_start: 0.7591 (ptp) cc_final: 0.7349 (ptp) REVERT: J 452 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8502 (mtt) REVERT: L 58 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.1802 (ppp) REVERT: L 236 ASN cc_start: 0.7967 (t0) cc_final: 0.7460 (t0) REVERT: m 80 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.9017 (tp) REVERT: N 366 TYR cc_start: 0.3043 (m-10) cc_final: 0.1881 (t80) REVERT: N 584 GLU cc_start: 0.4825 (pm20) cc_final: 0.4209 (pp20) REVERT: N 626 SER cc_start: -0.0060 (p) cc_final: -0.0918 (m) REVERT: N 673 GLN cc_start: 0.7041 (mt0) cc_final: 0.6465 (tm130) REVERT: N 678 HIS cc_start: 0.7703 (m170) cc_final: 0.7248 (m170) REVERT: N 744 GLU cc_start: 0.5738 (tp30) cc_final: 0.5269 (tt0) REVERT: N 762 PHE cc_start: 0.6430 (t80) cc_final: 0.6219 (t80) REVERT: O 104 ASN cc_start: 0.8010 (t0) cc_final: 0.7801 (t0) REVERT: O 150 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8460 (pp) REVERT: P 48 TYR cc_start: 0.8740 (m-80) cc_final: 0.8524 (m-80) REVERT: P 124 ASP cc_start: 0.8529 (m-30) cc_final: 0.8213 (t0) REVERT: P 126 TYR cc_start: 0.8285 (m-80) cc_final: 0.6620 (m-10) REVERT: P 131 TYR cc_start: 0.7754 (t80) cc_final: 0.7401 (t80) REVERT: P 133 GLU cc_start: 0.8606 (tt0) cc_final: 0.8384 (pt0) outliers start: 196 outliers final: 48 residues processed: 687 average time/residue: 1.2989 time to fit residues: 1169.6964 Evaluate side-chains 512 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 443 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 812 ARG Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 293 SER Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 1170 GLU Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1243 PHE Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 832 TYR Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 380 ASP Chi-restraints excluded: chain I residue 237 LYS Chi-restraints excluded: chain I residue 418 SER Chi-restraints excluded: chain I residue 486 TRP Chi-restraints excluded: chain i residue 378 THR Chi-restraints excluded: chain i residue 612 ARG Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 277 MET Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 437 LEU Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 182 ASN Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 233 ASP Chi-restraints excluded: chain m residue 80 ILE Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain N residue 716 VAL Chi-restraints excluded: chain N residue 737 ASP Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain P residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1769 > 50: distance: 4 - 9: 29.003 distance: 9 - 10: 38.523 distance: 9 - 145: 28.688 distance: 10 - 11: 43.106 distance: 10 - 13: 21.687 distance: 11 - 12: 56.923 distance: 11 - 18: 46.603 distance: 12 - 142: 32.475 distance: 13 - 14: 29.509 distance: 14 - 15: 28.532 distance: 15 - 16: 8.563 distance: 16 - 17: 25.870 distance: 18 - 19: 23.668 distance: 19 - 20: 32.584 distance: 19 - 22: 19.989 distance: 20 - 21: 26.000 distance: 20 - 29: 24.346 distance: 22 - 23: 25.218 distance: 23 - 24: 6.084 distance: 23 - 25: 24.810 distance: 24 - 26: 19.971 distance: 25 - 27: 16.474 distance: 26 - 28: 49.675 distance: 27 - 28: 39.335 distance: 29 - 30: 28.380 distance: 30 - 31: 26.171 distance: 30 - 33: 21.784 distance: 31 - 32: 37.403 distance: 31 - 37: 37.329 distance: 33 - 34: 27.105 distance: 34 - 35: 14.255 distance: 34 - 36: 12.412 distance: 37 - 38: 31.923 distance: 38 - 39: 25.061 distance: 38 - 41: 20.553 distance: 39 - 40: 36.515 distance: 39 - 46: 23.857 distance: 41 - 42: 21.730 distance: 42 - 43: 15.416 distance: 43 - 44: 29.324 distance: 43 - 45: 19.488 distance: 46 - 47: 21.640 distance: 47 - 48: 31.676 distance: 47 - 50: 36.308 distance: 48 - 49: 30.003 distance: 48 - 54: 30.821 distance: 50 - 51: 17.359 distance: 51 - 52: 15.056 distance: 51 - 53: 39.865 distance: 54 - 55: 27.937 distance: 55 - 56: 32.696 distance: 55 - 58: 33.934 distance: 56 - 57: 29.745 distance: 56 - 62: 4.851 distance: 58 - 59: 29.759 distance: 59 - 60: 17.018 distance: 59 - 61: 28.057 distance: 62 - 63: 49.550 distance: 63 - 64: 29.753 distance: 63 - 66: 57.860 distance: 64 - 65: 61.964 distance: 64 - 69: 46.859 distance: 66 - 67: 62.455 distance: 66 - 68: 70.177 distance: 69 - 70: 38.217 distance: 69 - 125: 31.987 distance: 70 - 71: 33.620 distance: 70 - 73: 41.809 distance: 71 - 72: 51.413 distance: 71 - 79: 17.220 distance: 72 - 122: 34.417 distance: 73 - 74: 51.904 distance: 74 - 75: 41.842 distance: 74 - 76: 44.655 distance: 75 - 77: 45.025 distance: 76 - 78: 36.496 distance: 77 - 78: 38.929 distance: 79 - 80: 29.654 distance: 79 - 85: 37.112 distance: 80 - 81: 23.207 distance: 80 - 83: 28.180 distance: 81 - 82: 34.235 distance: 81 - 86: 16.448 distance: 83 - 84: 21.365 distance: 84 - 85: 27.347 distance: 86 - 87: 22.860 distance: 86 - 109: 12.235 distance: 87 - 88: 34.360 distance: 87 - 90: 32.418 distance: 88 - 89: 9.706 distance: 88 - 93: 23.775 distance: 89 - 106: 30.981 distance: 90 - 91: 34.375 distance: 90 - 92: 25.079