Starting phenix.real_space_refine on Sun Jul 28 12:36:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwc_26828/07_2024/7uwc_26828.cif" } resolution = 4.0 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= 0.032 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 28781 2.51 5 N 8562 2.21 5 O 8692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 318": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 311": "NH1" <-> "NH2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ARG 391": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 137": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 318": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 208": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I ARG 208": "NH1" <-> "NH2" Residue "I ARG 214": "NH1" <-> "NH2" Residue "I ARG 221": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 208": "NH1" <-> "NH2" Residue "K ARG 214": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 46123 Number of models: 1 Model: "" Number of chains: 31 Chain: "P" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2099 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 18, 'TRANS': 403} Chain breaks: 1 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1370 Unresolved non-hydrogen angles: 1760 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 27, 'TYR:plan': 13, 'ASN:plan1': 13, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 27, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 700 Chain: "A" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 3935 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 642 Unresolved non-hydrogen angles: 783 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 29, 'PHE:plan': 5, 'GLU:plan': 32, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 436 Chain: "B" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3147 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 24, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 473 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 383 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 14, 'ASP:plan': 23, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 363 Chain: "C" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4146 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 570} Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 29, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 332 Chain: "D" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3213 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 453 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 26, 'GLU:plan': 32, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 355 Chain: "E" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4252 Classifications: {'peptide': 603} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 570} Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 3, 'ASP:plan': 22, 'ARG%COO:plan': 1, 'PHE:plan': 2, 'GLU:plan': 30, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 282 Chain: "F" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3194 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 439 Unresolved non-hydrogen angles: 536 Unresolved non-hydrogen dihedrals: 349 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 346 Chain: "G" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1273 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 236 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 555 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "I" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1357 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 195 Chain: "J" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 517 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 172 Chain: "K" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1364 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 243 Chain: "L" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 582 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 144 Chain: "M" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1096 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 3, 'TRANS': 209} Unresolved non-hydrogen bonds: 602 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 312 Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 544 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "O" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 1571 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 11, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 959 Unresolved non-hydrogen angles: 1233 Unresolved non-hydrogen dihedrals: 790 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 15, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 23, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 558 Chain: "a" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 3590 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 590} Link IDs: {'PTRANS': 22, 'TRANS': 690} Chain breaks: 3 Unresolved non-hydrogen bonds: 2209 Unresolved non-hydrogen angles: 2830 Unresolved non-hydrogen dihedrals: 1853 Unresolved non-hydrogen chiralities: 223 Planarities with less than four sites: {'GLN:plan1': 32, 'ARG:plan': 25, 'TYR:plan': 23, 'ASN:plan1': 25, 'TRP:plan': 8, 'ASP:plan': 26, 'PHE:plan': 55, 'GLU:plan': 41, 'HIS:plan': 15} Unresolved non-hydrogen planarities: 1208 Chain: "b" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'UNK:plan-1': 32} Unresolved non-hydrogen planarities: 32 Chain: "c" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 833 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 5, 'TRANS': 162} Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 163 Chain: "d" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1344 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 5 Unresolved non-hydrogen bonds: 896 Unresolved non-hydrogen angles: 1145 Unresolved non-hydrogen dihedrals: 749 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 16, 'TYR:plan': 19, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 535 Chain: "e" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 358 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "g" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 764 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 5, 'TRANS': 147} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "h" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 763 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 145 Chain: "i" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 780 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "j" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 777 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "k" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 769 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "l" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 752 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 147} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 140 Chain: "m" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 769 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 139 Chain: "n" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 762 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 145 Chain: "o" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 737 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 5, 'TRANS': 146} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 452 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 136 Chain: "r" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 25.42, per 1000 atoms: 0.55 Number of scatterers: 46123 At special positions: 0 Unit cell: (147.147, 182.721, 265.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 8692 8.00 N 8562 7.00 C 28781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.88 Conformation dependent library (CDL) restraints added in 10.6 seconds 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14412 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 38 sheets defined 65.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'P' and resid 1 through 14 removed outlier: 3.673A pdb=" N VAL P 11 " --> pdb=" O THR P 7 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 24 removed outlier: 3.817A pdb=" N TYR P 21 " --> pdb=" O PRO P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 Processing helix chain 'P' and resid 40 through 48 Processing helix chain 'P' and resid 49 through 54 removed outlier: 3.950A pdb=" N ASP P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 68 removed outlier: 4.121A pdb=" N VAL P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 87 removed outlier: 3.721A pdb=" N VAL P 77 " --> pdb=" O THR P 73 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU P 80 " --> pdb=" O TYR P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 101 Processing helix chain 'P' and resid 101 through 112 Proline residue: P 108 - end of helix Processing helix chain 'P' and resid 116 through 127 Processing helix chain 'P' and resid 157 through 163 Processing helix chain 'P' and resid 168 through 173 Processing helix chain 'P' and resid 182 through 196 removed outlier: 3.592A pdb=" N ALA P 186 " --> pdb=" O GLY P 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS P 195 " --> pdb=" O ALA P 191 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU P 196 " --> pdb=" O ALA P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 206 Processing helix chain 'P' and resid 208 through 217 Proline residue: P 214 - end of helix removed outlier: 3.549A pdb=" N SER P 217 " --> pdb=" O THR P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 241 removed outlier: 3.673A pdb=" N LEU P 228 " --> pdb=" O SER P 224 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR P 241 " --> pdb=" O LEU P 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 251 Processing helix chain 'P' and resid 253 through 264 Processing helix chain 'P' and resid 266 through 280 Processing helix chain 'P' and resid 282 through 294 Processing helix chain 'P' and resid 294 through 305 Processing helix chain 'P' and resid 309 through 337 removed outlier: 3.756A pdb=" N LEU P 313 " --> pdb=" O ASP P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 337 through 343 Processing helix chain 'P' and resid 348 through 353 removed outlier: 3.763A pdb=" N LYS P 352 " --> pdb=" O SER P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 365 removed outlier: 4.309A pdb=" N THR P 362 " --> pdb=" O ARG P 358 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN P 363 " --> pdb=" O ASP P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 381 Processing helix chain 'P' and resid 384 through 402 Processing helix chain 'P' and resid 402 through 412 removed outlier: 4.088A pdb=" N ARG P 406 " --> pdb=" O HIS P 402 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL P 407 " --> pdb=" O PRO P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 424 removed outlier: 3.580A pdb=" N MET P 419 " --> pdb=" O LYS P 415 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS P 420 " --> pdb=" O GLU P 416 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN P 423 " --> pdb=" O MET P 419 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 445 removed outlier: 4.015A pdb=" N GLY P 443 " --> pdb=" O ARG P 439 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS P 445 " --> pdb=" O PHE P 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 296 Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 322 through 342 removed outlier: 4.505A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 369 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.808A pdb=" N SER A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 499 removed outlier: 4.100A pdb=" N ILE A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.648A pdb=" N ALA A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 522 Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.664A pdb=" N LYS A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 556 removed outlier: 3.807A pdb=" N PHE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 578 through 588 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 595 through 618 removed outlier: 4.118A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.959A pdb=" N LEU B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.550A pdb=" N ILE B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 215 through 226 removed outlier: 4.174A pdb=" N GLN B 220 " --> pdb=" O MET B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.534A pdb=" N TYR B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 302 through 303 No H-bonds generated for 'chain 'B' and resid 302 through 303' Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 341 through 351 removed outlier: 4.147A pdb=" N TYR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 379 through 384 removed outlier: 4.528A pdb=" N ALA B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 418 removed outlier: 3.677A pdb=" N VAL B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 440 Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 256 through 268 removed outlier: 4.413A pdb=" N SER C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 324 through 344 removed outlier: 4.385A pdb=" N ALA C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 368 removed outlier: 3.896A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.552A pdb=" N TYR C 377 " --> pdb=" O ASP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 379 No H-bonds generated for 'chain 'C' and resid 378 through 379' Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'C' and resid 422 through 430 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 460 through 463 Processing helix chain 'C' and resid 464 through 472 Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.334A pdb=" N GLU C 494 " --> pdb=" O ASP C 490 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 495 " --> pdb=" O ASP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.749A pdb=" N ALA C 503 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 536 through 561 removed outlier: 3.619A pdb=" N GLY C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 565 removed outlier: 3.770A pdb=" N ASP C 565 " --> pdb=" O ALA C 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 565' Processing helix chain 'C' and resid 566 through 577 Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.860A pdb=" N PHE C 582 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 592 through 595 Processing helix chain 'C' and resid 596 through 614 removed outlier: 3.656A pdb=" N ALA C 602 " --> pdb=" O PRO C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 4.120A pdb=" N GLU C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 172 through 184 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 251 through 265 Processing helix chain 'D' and resid 278 through 292 removed outlier: 3.790A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 304 through 314 Processing helix chain 'D' and resid 341 through 351 Processing helix chain 'D' and resid 358 through 364 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 392 through 418 removed outlier: 3.925A pdb=" N VAL D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 439 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 474 through 482 removed outlier: 3.713A pdb=" N GLN D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.822A pdb=" N ALA E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 258 through 269 Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.783A pdb=" N MET E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Proline residue: E 294 - end of helix Processing helix chain 'E' and resid 324 through 343 removed outlier: 4.377A pdb=" N ALA E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 366 removed outlier: 4.845A pdb=" N LEU E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 415 through 419 removed outlier: 3.656A pdb=" N GLY E 418 " --> pdb=" O PRO E 415 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP E 419 " --> pdb=" O PRO E 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 415 through 419' Processing helix chain 'E' and resid 422 through 432 removed outlier: 3.718A pdb=" N ILE E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.542A pdb=" N ALA E 443 " --> pdb=" O ASP E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 463 Processing helix chain 'E' and resid 464 through 472 Processing helix chain 'E' and resid 474 through 500 removed outlier: 3.956A pdb=" N THR E 480 " --> pdb=" O ILE E 476 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 514 through 522 Processing helix chain 'E' and resid 536 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 570 through 578 removed outlier: 3.652A pdb=" N HIS E 576 " --> pdb=" O THR E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 588 Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 592 through 595 Processing helix chain 'E' and resid 596 through 621 Processing helix chain 'F' and resid 98 through 102 Processing helix chain 'F' and resid 148 through 154 removed outlier: 3.588A pdb=" N ASP F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 230 through 233 removed outlier: 4.421A pdb=" N GLU F 233 " --> pdb=" O GLY F 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 246 through 249 Processing helix chain 'F' and resid 250 through 265 removed outlier: 4.113A pdb=" N ARG F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 293 Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.572A pdb=" N GLY F 300 " --> pdb=" O GLY F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 314 Processing helix chain 'F' and resid 341 through 351 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 392 through 417 removed outlier: 4.244A pdb=" N TYR F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA F 405 " --> pdb=" O TYR F 401 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.568A pdb=" N LEU F 422 " --> pdb=" O GLU F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 439 Processing helix chain 'F' and resid 450 through 465 removed outlier: 3.765A pdb=" N LEU F 457 " --> pdb=" O GLN F 453 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 4.176A pdb=" N LEU F 478 " --> pdb=" O PRO F 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR F 481 " --> pdb=" O THR F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 45 removed outlier: 3.784A pdb=" N ARG G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE G 38 " --> pdb=" O GLU G 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 55 removed outlier: 4.002A pdb=" N ARG G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 104 removed outlier: 3.880A pdb=" N GLN G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER G 104 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.543A pdb=" N LYS G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 Processing helix chain 'G' and resid 146 through 157 removed outlier: 4.081A pdb=" N LYS G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 211 through 224 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 15 through 54 removed outlier: 4.028A pdb=" N LYS H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 106 removed outlier: 5.093A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 104 Processing helix chain 'I' and resid 106 through 126 removed outlier: 3.882A pdb=" N LYS I 112 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'I' and resid 148 through 157 Processing helix chain 'I' and resid 174 through 178 removed outlier: 4.079A pdb=" N GLY I 177 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS I 178 " --> pdb=" O GLY I 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 174 through 178' Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 205 through 225 Proline residue: I 218 - end of helix Processing helix chain 'J' and resid 15 through 20 Processing helix chain 'J' and resid 21 through 104 removed outlier: 4.098A pdb=" N ALA J 25 " --> pdb=" O GLN J 21 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA J 27 " --> pdb=" O ILE J 23 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA J 33 " --> pdb=" O ASN J 29 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG J 34 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLN J 99 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 22 Processing helix chain 'K' and resid 24 through 100 removed outlier: 4.495A pdb=" N LYS K 40 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU K 41 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 106 removed outlier: 4.083A pdb=" N ARG K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 126 removed outlier: 4.438A pdb=" N LYS K 112 " --> pdb=" O ASN K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 157 removed outlier: 4.136A pdb=" N GLU K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER K 148 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA K 154 " --> pdb=" O LYS K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 225 Proline residue: K 218 - end of helix Processing helix chain 'L' and resid 10 through 65 removed outlier: 3.915A pdb=" N ALA L 16 " --> pdb=" O GLN L 12 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU L 54 " --> pdb=" O ARG L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 107 removed outlier: 5.511A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP L 96 " --> pdb=" O LYS L 92 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL L 97 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 56 removed outlier: 4.222A pdb=" N GLU M 56 " --> pdb=" O VAL M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 77 removed outlier: 3.968A pdb=" N MET M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 135 Processing helix chain 'M' and resid 137 through 172 removed outlier: 4.217A pdb=" N LYS M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 221 Proline residue: M 179 - end of helix removed outlier: 3.670A pdb=" N ASP M 193 " --> pdb=" O LYS M 189 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU M 194 " --> pdb=" O GLY M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 26 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 52 through 62 Processing helix chain 'N' and resid 80 through 85 Processing helix chain 'N' and resid 86 through 89 removed outlier: 3.634A pdb=" N ASN N 89 " --> pdb=" O ASP N 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 86 through 89' Processing helix chain 'N' and resid 91 through 95 removed outlier: 3.854A pdb=" N ILE N 95 " --> pdb=" O ILE N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 117 Processing helix chain 'O' and resid 11 through 15 removed outlier: 3.776A pdb=" N SER O 15 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 24 removed outlier: 4.176A pdb=" N LEU O 23 " --> pdb=" O TRP O 20 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN O 24 " --> pdb=" O ASN O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 31 Processing helix chain 'O' and resid 48 through 80 removed outlier: 3.973A pdb=" N VAL O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS O 61 " --> pdb=" O ASP O 57 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU O 78 " --> pdb=" O ARG O 74 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU O 80 " --> pdb=" O GLN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 96 removed outlier: 3.724A pdb=" N GLY O 95 " --> pdb=" O SER O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 102 removed outlier: 3.505A pdb=" N LEU O 102 " --> pdb=" O VAL O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 109 Processing helix chain 'O' and resid 117 through 150 removed outlier: 4.105A pdb=" N ILE O 121 " --> pdb=" O PRO O 117 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 156 Processing helix chain 'O' and resid 164 through 169 removed outlier: 3.694A pdb=" N SER O 167 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 241 removed outlier: 3.909A pdb=" N PHE O 236 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 277 removed outlier: 4.182A pdb=" N GLN O 257 " --> pdb=" O SER O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 309 removed outlier: 3.521A pdb=" N PHE O 302 " --> pdb=" O ALA O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 323 through 334 Processing helix chain 'O' and resid 335 through 338 Processing helix chain 'a' and resid 35 through 47 removed outlier: 3.891A pdb=" N LEU a 46 " --> pdb=" O TYR a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 59 removed outlier: 4.044A pdb=" N GLU a 57 " --> pdb=" O LEU a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 89 Processing helix chain 'a' and resid 108 through 161 removed outlier: 3.892A pdb=" N SER a 151 " --> pdb=" O GLY a 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU a 154 " --> pdb=" O PHE a 150 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR a 155 " --> pdb=" O SER a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 211 Processing helix chain 'a' and resid 213 through 218 Processing helix chain 'a' and resid 251 through 267 removed outlier: 3.999A pdb=" N ALA a 255 " --> pdb=" O SER a 251 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS a 258 " --> pdb=" O ARG a 254 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS a 261 " --> pdb=" O ASN a 257 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 336 removed outlier: 3.750A pdb=" N THR a 311 " --> pdb=" O ASN a 307 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP a 314 " --> pdb=" O GLN a 310 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN a 318 " --> pdb=" O ASP a 314 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU a 321 " --> pdb=" O GLU a 317 " (cutoff:3.500A) Processing helix chain 'a' and resid 353 through 357 Processing helix chain 'a' and resid 358 through 370 Processing helix chain 'a' and resid 396 through 406 removed outlier: 4.472A pdb=" N PHE a 400 " --> pdb=" O PHE a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 430 removed outlier: 4.541A pdb=" N VAL a 423 " --> pdb=" O VAL a 419 " (cutoff:3.500A) Proline residue: a 426 - end of helix removed outlier: 3.536A pdb=" N ALA a 430 " --> pdb=" O PRO a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 431 through 434 Processing helix chain 'a' and resid 438 through 452 removed outlier: 3.651A pdb=" N LEU a 449 " --> pdb=" O GLY a 445 " (cutoff:3.500A) Processing helix chain 'a' and resid 452 through 457 Processing helix chain 'a' and resid 462 through 471 removed outlier: 3.812A pdb=" N GLY a 471 " --> pdb=" O MET a 467 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 490 Processing helix chain 'a' and resid 532 through 538 removed outlier: 3.713A pdb=" N HIS a 536 " --> pdb=" O ASP a 532 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY a 537 " --> pdb=" O PRO a 533 " (cutoff:3.500A) Processing helix chain 'a' and resid 540 through 575 removed outlier: 3.633A pdb=" N PHE a 544 " --> pdb=" O SER a 540 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER a 568 " --> pdb=" O GLY a 564 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR a 569 " --> pdb=" O ILE a 565 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE a 570 " --> pdb=" O ILE a 566 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 610 removed outlier: 4.545A pdb=" N ILE a 586 " --> pdb=" O TRP a 582 " (cutoff:3.500A) Proline residue: a 587 - end of helix removed outlier: 3.977A pdb=" N LEU a 592 " --> pdb=" O GLN a 588 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN a 593 " --> pdb=" O ILE a 589 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR a 598 " --> pdb=" O SER a 594 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU a 599 " --> pdb=" O LEU a 595 " (cutoff:3.500A) Processing helix chain 'a' and resid 614 through 625 removed outlier: 3.961A pdb=" N MET a 619 " --> pdb=" O LEU a 615 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE a 620 " --> pdb=" O TYR a 616 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER a 625 " --> pdb=" O TYR a 621 " (cutoff:3.500A) Processing helix chain 'a' and resid 638 through 657 removed outlier: 4.059A pdb=" N LEU a 644 " --> pdb=" O LYS a 640 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL a 654 " --> pdb=" O ALA a 650 " (cutoff:3.500A) Proline residue: a 655 - end of helix Processing helix chain 'a' and resid 659 through 669 Processing helix chain 'a' and resid 711 through 715 Processing helix chain 'a' and resid 716 through 729 removed outlier: 3.624A pdb=" N VAL a 723 " --> pdb=" O VAL a 719 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR a 729 " --> pdb=" O ASN a 725 " (cutoff:3.500A) Processing helix chain 'a' and resid 729 through 756 removed outlier: 4.105A pdb=" N TRP a 733 " --> pdb=" O TYR a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 759 through 777 Processing helix chain 'a' and resid 779 through 797 removed outlier: 3.759A pdb=" N THR a 783 " --> pdb=" O LEU a 779 " (cutoff:3.500A) Processing helix chain 'a' and resid 798 through 802 removed outlier: 3.650A pdb=" N LYS a 801 " --> pdb=" O PHE a 798 " (cutoff:3.500A) Processing helix chain 'b' and resid 274 through 297 removed outlier: 3.642A pdb=" N UNK b 290 " --> pdb=" O UNK b 286 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 304 Processing helix chain 'c' and resid 12 through 19 Processing helix chain 'c' and resid 21 through 59 removed outlier: 3.706A pdb=" N PHE c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE c 34 " --> pdb=" O ILE c 30 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER c 51 " --> pdb=" O ILE c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 90 removed outlier: 3.881A pdb=" N ILE c 68 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER c 69 " --> pdb=" O LYS c 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL c 70 " --> pdb=" O ASN c 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL c 76 " --> pdb=" O PHE c 72 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA c 77 " --> pdb=" O CYS c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 101 through 143 removed outlier: 3.571A pdb=" N LEU c 138 " --> pdb=" O SER c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 158 Processing helix chain 'c' and resid 158 through 173 removed outlier: 3.864A pdb=" N LEU c 162 " --> pdb=" O SER c 158 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA c 173 " --> pdb=" O ILE c 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 Processing helix chain 'd' and resid 13 through 27 Processing helix chain 'd' and resid 70 through 85 removed outlier: 3.504A pdb=" N MET d 85 " --> pdb=" O GLU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 113 removed outlier: 3.984A pdb=" N HIS d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 129 Processing helix chain 'd' and resid 148 through 155 removed outlier: 3.544A pdb=" N LEU d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 168 removed outlier: 3.848A pdb=" N GLU d 166 " --> pdb=" O PRO d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 174 Processing helix chain 'd' and resid 179 through 199 removed outlier: 3.500A pdb=" N LYS d 199 " --> pdb=" O LYS d 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 226 removed outlier: 4.077A pdb=" N ILE d 207 " --> pdb=" O ALA d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 227 through 231 Processing helix chain 'd' and resid 235 through 240 Processing helix chain 'd' and resid 248 through 252 Processing helix chain 'd' and resid 253 through 258 removed outlier: 4.065A pdb=" N VAL d 257 " --> pdb=" O GLU d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 293 through 301 Processing helix chain 'd' and resid 313 through 332 Processing helix chain 'e' and resid 4 through 26 Processing helix chain 'e' and resid 28 through 57 removed outlier: 3.714A pdb=" N GLN e 57 " --> pdb=" O VAL e 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 45 removed outlier: 3.515A pdb=" N SER g 25 " --> pdb=" O ALA g 21 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 51 Processing helix chain 'g' and resid 54 through 60 Processing helix chain 'g' and resid 60 through 78 removed outlier: 4.047A pdb=" N LEU g 64 " --> pdb=" O MET g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 126 removed outlier: 3.815A pdb=" N ALA g 93 " --> pdb=" O PHE g 89 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG g 121 " --> pdb=" O ASP g 117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA g 124 " --> pdb=" O VAL g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 129 through 158 removed outlier: 3.911A pdb=" N LEU g 143 " --> pdb=" O PHE g 139 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA g 144 " --> pdb=" O ALA g 140 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG g 157 " --> pdb=" O ILE g 153 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA g 158 " --> pdb=" O LEU g 154 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 47 removed outlier: 4.094A pdb=" N LEU h 16 " --> pdb=" O PHE h 12 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 54 removed outlier: 4.398A pdb=" N MET h 52 " --> pdb=" O GLU h 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER h 54 " --> pdb=" O VAL h 51 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 78 removed outlier: 3.641A pdb=" N ILE h 75 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY h 78 " --> pdb=" O ILE h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 84 removed outlier: 6.412A pdb=" N LYS h 82 " --> pdb=" O ILE h 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS h 84 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 124 removed outlier: 3.690A pdb=" N ALA h 93 " --> pdb=" O PHE h 89 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N HIS h 94 " --> pdb=" O ASP h 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU h 95 " --> pdb=" O GLY h 91 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA h 124 " --> pdb=" O VAL h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 131 Processing helix chain 'h' and resid 132 through 157 removed outlier: 3.856A pdb=" N ILE h 136 " --> pdb=" O GLY h 132 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU h 143 " --> pdb=" O PHE h 139 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA h 144 " --> pdb=" O ALA h 140 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG h 157 " --> pdb=" O ILE h 153 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 161 removed outlier: 4.333A pdb=" N SER h 161 " --> pdb=" O ALA h 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 158 through 161' Processing helix chain 'i' and resid 9 through 44 removed outlier: 3.726A pdb=" N PHE i 13 " --> pdb=" O THR i 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS i 35 " --> pdb=" O TYR i 31 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 54 removed outlier: 4.210A pdb=" N MET i 52 " --> pdb=" O GLU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 78 removed outlier: 3.735A pdb=" N GLY i 78 " --> pdb=" O ILE i 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 123 removed outlier: 3.629A pdb=" N TYR i 92 " --> pdb=" O LEU i 88 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 128 No H-bonds generated for 'chain 'i' and resid 126 through 128' Processing helix chain 'i' and resid 129 through 157 removed outlier: 4.528A pdb=" N LEU i 143 " --> pdb=" O PHE i 139 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA i 144 " --> pdb=" O ALA i 140 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU i 145 " --> pdb=" O GLU i 141 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER i 156 " --> pdb=" O ILE i 152 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 47 removed outlier: 4.737A pdb=" N LEU j 16 " --> pdb=" O PHE j 12 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU j 22 " --> pdb=" O ALA j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 54 removed outlier: 4.540A pdb=" N MET j 52 " --> pdb=" O PRO j 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS j 53 " --> pdb=" O GLU j 49 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 61 Processing helix chain 'j' and resid 62 through 79 removed outlier: 3.512A pdb=" N ILE j 66 " --> pdb=" O GLY j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 126 removed outlier: 3.661A pdb=" N HIS j 94 " --> pdb=" O ASP j 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG j 121 " --> pdb=" O ASP j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 133 removed outlier: 4.456A pdb=" N VAL j 131 " --> pdb=" O PRO j 127 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY j 132 " --> pdb=" O LYS j 128 " (cutoff:3.500A) Processing helix chain 'j' and resid 133 through 156 removed outlier: 4.165A pdb=" N LEU j 137 " --> pdb=" O MET j 133 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 161 removed outlier: 4.176A pdb=" N SER j 161 " --> pdb=" O ALA j 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 47 removed outlier: 3.608A pdb=" N PHE k 13 " --> pdb=" O THR k 9 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER k 42 " --> pdb=" O VAL k 38 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET k 43 " --> pdb=" O GLY k 39 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL k 45 " --> pdb=" O ALA k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 52 removed outlier: 3.658A pdb=" N MET k 52 " --> pdb=" O PRO k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 78 Processing helix chain 'k' and resid 87 through 126 removed outlier: 3.952A pdb=" N ARG k 121 " --> pdb=" O ASP k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 129 through 158 removed outlier: 3.760A pdb=" N LEU k 143 " --> pdb=" O PHE k 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA k 144 " --> pdb=" O ALA k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 159 through 161 No H-bonds generated for 'chain 'k' and resid 159 through 161' Processing helix chain 'l' and resid 9 through 47 removed outlier: 3.581A pdb=" N PHE l 13 " --> pdb=" O THR l 9 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU l 16 " --> pdb=" O PHE l 12 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS l 35 " --> pdb=" O TYR l 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 54 removed outlier: 4.733A pdb=" N MET l 52 " --> pdb=" O GLU l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 79 removed outlier: 3.874A pdb=" N GLY l 62 " --> pdb=" O VAL l 58 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU l 64 " --> pdb=" O MET l 60 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 126 removed outlier: 3.718A pdb=" N ALA l 93 " --> pdb=" O PHE l 89 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG l 121 " --> pdb=" O ASP l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 129 through 156 removed outlier: 3.875A pdb=" N LEU l 143 " --> pdb=" O PHE l 139 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA l 144 " --> pdb=" O ALA l 140 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 45 removed outlier: 3.898A pdb=" N VAL m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 53 removed outlier: 4.210A pdb=" N MET m 52 " --> pdb=" O PRO m 48 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 79 removed outlier: 3.784A pdb=" N VAL m 59 " --> pdb=" O ILE m 55 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY m 62 " --> pdb=" O VAL m 58 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU m 64 " --> pdb=" O MET m 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY m 65 " --> pdb=" O ALA m 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE m 79 " --> pdb=" O ILE m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 123 removed outlier: 3.606A pdb=" N GLY m 91 " --> pdb=" O TYR m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 124 through 125 No H-bonds generated for 'chain 'm' and resid 124 through 125' Processing helix chain 'm' and resid 126 through 128 No H-bonds generated for 'chain 'm' and resid 126 through 128' Processing helix chain 'm' and resid 129 through 159 removed outlier: 4.194A pdb=" N LEU m 143 " --> pdb=" O PHE m 139 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA m 144 " --> pdb=" O ALA m 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU m 145 " --> pdb=" O GLU m 141 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY m 159 " --> pdb=" O SER m 155 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 47 removed outlier: 3.800A pdb=" N PHE n 13 " --> pdb=" O THR n 9 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU n 16 " --> pdb=" O PHE n 12 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS n 35 " --> pdb=" O TYR n 31 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N MET n 46 " --> pdb=" O SER n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 54 removed outlier: 4.099A pdb=" N MET n 52 " --> pdb=" O GLU n 49 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 78 removed outlier: 4.014A pdb=" N LEU n 64 " --> pdb=" O MET n 60 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE n 66 " --> pdb=" O GLY n 62 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 122 Processing helix chain 'n' and resid 128 through 158 removed outlier: 3.916A pdb=" N ILE n 134 " --> pdb=" O PHE n 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU n 143 " --> pdb=" O PHE n 139 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA n 144 " --> pdb=" O ALA n 140 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 47 removed outlier: 3.940A pdb=" N GLY o 14 " --> pdb=" O ALA o 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA o 18 " --> pdb=" O GLY o 14 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET o 46 " --> pdb=" O SER o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 47 through 78 removed outlier: 3.722A pdb=" N VAL o 51 " --> pdb=" O ARG o 47 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET o 52 " --> pdb=" O PRO o 48 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS o 53 " --> pdb=" O GLU o 49 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL o 56 " --> pdb=" O MET o 52 " (cutoff:3.500A) Proline residue: o 57 - end of helix removed outlier: 3.803A pdb=" N LEU o 64 " --> pdb=" O MET o 60 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY o 65 " --> pdb=" O ALA o 61 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE o 66 " --> pdb=" O GLY o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 126 removed outlier: 3.603A pdb=" N ARG o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) Processing helix chain 'o' and resid 129 through 156 removed outlier: 4.244A pdb=" N LEU o 143 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA o 144 " --> pdb=" O ALA o 140 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU o 145 " --> pdb=" O GLU o 141 " (cutoff:3.500A) Processing helix chain 'r' and resid 333 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 3.720A pdb=" N TYR A 23 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 33 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 27 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.384A pdb=" N VAL A 274 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A 315 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR A 276 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN A 317 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 278 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 221 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.579A pdb=" N ALA A 156 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 139 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 removed outlier: 5.388A pdb=" N VAL A 178 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU A 197 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 195 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 412 through 413 removed outlier: 6.897A pdb=" N VAL A 413 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE A 250 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 20 through 21 current: chain 'B' and resid 31 through 34 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 34 current: chain 'B' and resid 55 through 63 removed outlier: 4.418A pdb=" N VAL B 69 " --> pdb=" O LEU B 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'C' and resid 31 through 35 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 31 through 35 current: chain 'C' and resid 65 through 68 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 65 through 68 current: chain 'D' and resid 31 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 31 through 34 current: chain 'D' and resid 55 through 64 removed outlier: 6.831A pdb=" N VAL D 69 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL D 63 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 67 through 72 current: chain 'E' and resid 31 through 35 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 31 through 35 current: chain 'E' and resid 53 through 61 removed outlier: 6.274A pdb=" N ILE E 57 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN E 68 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG E 59 " --> pdb=" O THR E 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 69 current: chain 'F' and resid 31 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 31 through 34 current: chain 'F' and resid 55 through 64 removed outlier: 6.635A pdb=" N VAL F 69 " --> pdb=" O LEU F 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 72 current: chain 'G' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 199 through 204 current: chain 'I' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 199 through 204 current: chain 'K' and resid 190 through 194 removed outlier: 5.909A pdb=" N ILE K 199 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.290A pdb=" N PHE B 106 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU B 241 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N THR B 236 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 207 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE B 238 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 209 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASN B 240 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 211 " --> pdb=" O ASN B 240 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 206 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE B 274 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 208 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR B 276 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA B 210 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 326 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 318 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB4, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169 removed outlier: 7.593A pdb=" N MET C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 160 " --> pdb=" O MET C 164 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 156 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C 159 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU C 137 " --> pdb=" O PHE C 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.848A pdb=" N ASP C 147 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 179 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 195 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL C 181 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL C 193 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 222 current: chain 'C' and resid 346 through 350 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 346 through 350 current: chain 'C' and resid 404 through 412 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 404 through 412 current: chain 'C' and resid 457 through 458 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 94 through 97 removed outlier: 3.662A pdb=" N THR D 95 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 125 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 105 through 106 removed outlier: 3.636A pdb=" N MET D 212 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 271 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 157 through 158 removed outlier: 4.739A pdb=" N ILE D 157 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 332 through 334 removed outlier: 6.174A pdb=" N LEU D 165 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET D 334 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER D 167 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA D 168 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N GLN D 354 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU D 373 " --> pdb=" O GLN D 354 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR D 356 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.629A pdb=" N TRP E 211 " --> pdb=" O VAL E 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 138 through 140 removed outlier: 3.605A pdb=" N ALA E 156 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.968A pdb=" N LEU E 149 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 179 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU E 195 " --> pdb=" O THR E 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 221 through 222 removed outlier: 3.556A pdb=" N SER E 221 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 247 through 250 Processing sheet with id=AC9, first strand: chain 'E' and resid 312 through 314 removed outlier: 6.788A pdb=" N VAL E 274 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET E 350 " --> pdb=" O VAL E 275 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 297 through 299 Processing sheet with id=AD2, first strand: chain 'E' and resid 434 through 435 Processing sheet with id=AD3, first strand: chain 'F' and resid 94 through 97 removed outlier: 3.521A pdb=" N ALA F 123 " --> pdb=" O VAL F 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 105 through 106 removed outlier: 3.751A pdb=" N VAL F 208 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET F 212 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL F 271 " --> pdb=" O THR F 327 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE F 329 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL F 273 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE F 331 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU F 275 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 165 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR F 356 " --> pdb=" O PRO F 374 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AD6, first strand: chain 'M' and resid 95 through 102 Processing sheet with id=AD7, first strand: chain 'N' and resid 13 through 14 removed outlier: 7.648A pdb=" N ALA N 13 " --> pdb=" O ALA N 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'a' and resid 24 through 32 Processing sheet with id=AD9, first strand: chain 'a' and resid 195 through 196 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 195 through 196 current: chain 'a' and resid 245 through 250 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'a' and resid 232 through 234 removed outlier: 6.520A pdb=" N ASP a 234 " --> pdb=" O GLU a 239 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU a 239 " --> pdb=" O ASP a 234 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 505 through 507 3702 hydrogen bonds defined for protein. 10782 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: 20.89 Time building geometry restraints manager: 21.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8135 1.31 - 1.44: 10957 1.44 - 1.57: 27483 1.57 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 46721 Sorted by residual: bond pdb=" CA GLU P 9 " pdb=" C GLU P 9 " ideal model delta sigma weight residual 1.524 1.431 0.092 1.29e-02 6.01e+03 5.11e+01 bond pdb=" CA ASP P 346 " pdb=" C ASP P 346 " ideal model delta sigma weight residual 1.521 1.443 0.078 1.24e-02 6.50e+03 3.94e+01 bond pdb=" CA TRP P 347 " pdb=" C TRP P 347 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.30e-02 5.92e+03 3.75e+01 bond pdb=" CA LEU P 341 " pdb=" C LEU P 341 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.27e-02 6.20e+03 3.73e+01 bond pdb=" C THR P 8 " pdb=" N GLU P 9 " ideal model delta sigma weight residual 1.335 1.414 -0.080 1.36e-02 5.41e+03 3.42e+01 ... (remaining 46716 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.99: 1162 105.99 - 113.29: 26323 113.29 - 120.59: 19489 120.59 - 127.89: 17264 127.89 - 135.19: 265 Bond angle restraints: 64503 Sorted by residual: angle pdb=" C MET P 1 " pdb=" N ASP P 2 " pdb=" CA ASP P 2 " ideal model delta sigma weight residual 120.29 133.56 -13.27 1.42e+00 4.96e-01 8.73e+01 angle pdb=" C ALA P 4 " pdb=" N GLU P 5 " pdb=" CA GLU P 5 " ideal model delta sigma weight residual 120.28 130.99 -10.71 1.34e+00 5.57e-01 6.38e+01 angle pdb=" C TRP P 18 " pdb=" N GLU P 19 " pdb=" CA GLU P 19 " ideal model delta sigma weight residual 120.38 131.11 -10.73 1.46e+00 4.69e-01 5.40e+01 angle pdb=" C VAL P 340 " pdb=" N LEU P 341 " pdb=" CA LEU P 341 " ideal model delta sigma weight residual 120.44 129.68 -9.24 1.30e+00 5.92e-01 5.05e+01 angle pdb=" O ASP E 620 " pdb=" C ASP E 620 " pdb=" N GLU E 621 " ideal model delta sigma weight residual 122.34 113.62 8.72 1.25e+00 6.40e-01 4.87e+01 ... (remaining 64498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 26340 17.92 - 35.85: 807 35.85 - 53.77: 132 53.77 - 71.70: 25 71.70 - 89.62: 17 Dihedral angle restraints: 27321 sinusoidal: 5001 harmonic: 22320 Sorted by residual: dihedral pdb=" CA CYS C 256 " pdb=" C CYS C 256 " pdb=" N GLY C 257 " pdb=" CA GLY C 257 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ILE K 38 " pdb=" C ILE K 38 " pdb=" N GLU K 39 " pdb=" CA GLU K 39 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C TYR C 339 " pdb=" N TYR C 339 " pdb=" CA TYR C 339 " pdb=" CB TYR C 339 " ideal model delta harmonic sigma weight residual -122.60 -111.91 -10.69 0 2.50e+00 1.60e-01 1.83e+01 ... (remaining 27318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 7108 0.066 - 0.132: 975 0.132 - 0.199: 136 0.199 - 0.265: 26 0.265 - 0.331: 7 Chirality restraints: 8252 Sorted by residual: chirality pdb=" CA SER C 450 " pdb=" N SER C 450 " pdb=" C SER C 450 " pdb=" CB SER C 450 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA TYR D 401 " pdb=" N TYR D 401 " pdb=" C TYR D 401 " pdb=" CB TYR D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA PHE C 448 " pdb=" N PHE C 448 " pdb=" C PHE C 448 " pdb=" CB PHE C 448 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 8249 not shown) Planarity restraints: 8744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 620 " -0.049 2.00e-02 2.50e+03 9.16e-02 8.39e+01 pdb=" C ASP E 620 " 0.159 2.00e-02 2.50e+03 pdb=" O ASP E 620 " -0.058 2.00e-02 2.50e+03 pdb=" N GLU E 621 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 453 " -0.081 2.00e-02 2.50e+03 4.07e-02 4.15e+01 pdb=" CG TRP C 453 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 453 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 453 " 0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP C 453 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP C 453 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 453 " 0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 453 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 453 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 453 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 436 " 0.054 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP C 436 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP C 436 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 436 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 436 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 436 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 436 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 436 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 436 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP C 436 " 0.024 2.00e-02 2.50e+03 ... (remaining 8741 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7089 2.75 - 3.29: 48757 3.29 - 3.83: 79354 3.83 - 4.36: 78143 4.36 - 4.90: 138272 Nonbonded interactions: 351615 Sorted by model distance: nonbonded pdb=" O ILE D 45 " pdb=" OG1 THR D 89 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 45 " pdb=" OG1 THR B 89 " model vdw 2.242 2.440 nonbonded pdb=" NH2 ARG F 104 " pdb=" O PRO F 117 " model vdw 2.248 2.520 nonbonded pdb=" O LEU C 265 " pdb=" OG SER C 269 " model vdw 2.250 2.440 nonbonded pdb=" O GLY D 29 " pdb=" OG1 THR D 76 " model vdw 2.253 2.440 ... (remaining 351610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 78 or (res \ id 79 through 80 and (name N or name CA or name C or name O or name CB )) or res \ id 81 through 92 or (resid 93 and (name N or name CA or name C or name O or name \ CB )) or resid 94 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 120 or (resid 121 and (name N or name \ CA or name C or name O or name CB )) or resid 122 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 146 o \ r (resid 147 through 149 and (name N or name CA or name C or name O or name CB ) \ ) or resid 150 through 162 or (resid 163 through 165 and (name N or name CA or n \ ame C or name O or name CB )) or resid 166 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 193 or (resid \ 194 through 197 and (name N or name CA or name C or name O or name CB )) or res \ id 198 through 208 or (resid 209 through 210 and (name N or name CA or name C or \ name O or name CB )) or resid 211 through 216 or (resid 217 and (name N or name \ CA or name C or name O or name CB )) or resid 218 through 229 or (resid 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 253 o \ r (resid 254 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 55 through 266 or (resid 267 and (name N or name CA or name C or name O or name \ CB )) or resid 268 through 283 or (resid 284 through 285 and (name N or name CA \ or name C or name O or name CB )) or resid 286 through 290 or (resid 291 through \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 throu \ gh 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) or \ resid 297 through 299 or (resid 300 and (name N or name CA or name C or name O \ or name CB )) or resid 301 through 305 or (resid 306 and (name N or name CA or n \ ame C or name O or name CB )) or resid 307 through 313 or (resid 314 and (name N \ or name CA or name C or name O or name CB )) or resid 315 through 320 or (resid \ 321 and (name N or name CA or name C or name O or name CB )) or resid 322 throu \ gh 352 or (resid 353 and (name N or name CA or name C or name O or name CB )) or \ resid 354 or (resid 355 through 356 and (name N or name CA or name C or name O \ or name CB )) or resid 357 through 367 or (resid 368 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 394 or (resid 395 \ through 396 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 97 through 402 or (resid 403 and (name N or name CA or name C or name O or name \ CB )) or resid 404 through 447 or (resid 448 and (name N or name CA or name C or \ name O or name CB )) or resid 449 or (resid 450 and (name N or name CA or name \ C or name O or name CB )) or resid 451 through 489 or (resid 490 through 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 through 497 o \ r (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 99 through 500 or (resid 501 through 506 and (name N or name CA or name C or nam \ e O or name CB )) or resid 507 or (resid 508 through 510 and (name N or name CA \ or name C or name O or name CB )) or resid 511 or (resid 512 through 517 and (na \ me N or name CA or name C or name O or name CB )) or resid 518 through 531 or (r \ esid 532 through 533 and (name N or name CA or name C or name O or name CB )) or \ resid 534 through 546 or (resid 547 and (name N or name CA or name C or name O \ or name CB )) or resid 548 through 552 or (resid 553 through 554 and (name N or \ name CA or name C or name O or name CB )) or resid 555 or (resid 556 through 557 \ and (name N or name CA or name C or name O or name CB )) or resid 558 or (resid \ 569 through 571 and (name N or name CA or name C or name O or name CB )) or res \ id 572 through 576 or (resid 577 through 578 and (name N or name CA or name C or \ name O or name CB )) or resid 579 through 619)) selection = (chain 'C' and (resid 21 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 50 or (resid 51 and ( \ name N or name CA or name C or name O or name CB )) or resid 52 through 59 or (r \ esid 60 through 61 and (name N or name CA or name C or name O or name CB )) or r \ esid 62 through 67 or (resid 68 and (name N or name CA or name C or name O or na \ me CB )) or resid 69 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 92 or (resid 93 and (name N or name CA \ or name C or name O or name CB )) or resid 94 through 99 or (resid 100 and (nam \ e N or name CA or name C or name O or name CB )) or resid 101 through 130 or (re \ sid 131 and (name N or name CA or name C or name O or name CB )) or resid 132 th \ rough 146 or (resid 147 through 149 and (name N or name CA or name C or name O o \ r name CB )) or resid 150 through 174 or (resid 175 and (name N or name CA or na \ me C or name O or name CB )) or resid 176 or (resid 177 and (name N or name CA o \ r name C or name O or name CB )) or resid 178 through 190 or (resid 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 192 through 193 or (re \ sid 194 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 208 or (resid 209 through 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 232 or (resid 233 through 234 and \ (name N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 \ through 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 280 or (resid 281 through 282 and (name N or name CA or name C or name \ O or name CB )) or resid 283 through 319 or (resid 320 through 321 and (name N \ or name CA or name C or name O or name CB )) or resid 322 through 348 or (resid \ 349 through 353 and (name N or name CA or name C or name O or name CB )) or resi \ d 354 through 358 or (resid 359 through 360 and (name N or name CA or name C or \ name O or name CB )) or resid 361 through 366 or (resid 367 through 371 and (nam \ e N or name CA or name C or name O or name CB )) or resid 372 through 419 or (re \ sid 420 and (name N or name CA or name C or name O or name CB )) or resid 421 th \ rough 432 or (resid 433 and (name N or name CA or name C or name O or name CB )) \ or resid 434 through 443 or (resid 444 through 446 and (name N or name CA or na \ me C or name O or name CB )) or resid 447 or (resid 448 and (name N or name CA o \ r name C or name O or name CB )) or resid 449 or (resid 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 459 or (resid 460 and \ (name N or name CA or name C or name O or name CB )) or resid 461 through 467 or \ (resid 468 through 470 and (name N or name CA or name C or name O or name CB )) \ or resid 471 through 476 or (resid 477 and (name N or name CA or name C or name \ O or name CB )) or resid 478 or (resid 479 and (name N or name CA or name C or \ name O or name CB )) or resid 480 through 482 or (resid 483 through 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 or (resid 486 thro \ ugh 495 and (name N or name CA or name C or name O or name CB )) or resid 496 th \ rough 497 or (resid 498 and (name N or name CA or name C or name O or name CB )) \ or resid 499 through 509 or (resid 510 and (name N or name CA or name C or name \ O or name CB )) or resid 511 or (resid 512 through 517 and (name N or name CA o \ r name C or name O or name CB )) or resid 518 or (resid 519 through 521 and (nam \ e N or name CA or name C or name O or name CB )) or resid 522 through 538 or (re \ sid 539 and (name N or name CA or name C or name O or name CB )) or resid 540 th \ rough 542 or (resid 543 through 547 and (name N or name CA or name C or name O o \ r name CB )) or resid 548 through 552 or (resid 553 through 554 and (name N or n \ ame CA or name C or name O or name CB )) or resid 555 through 558 or (resid 569 \ through 571 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 2 through 577 or (resid 578 and (name N or name CA or name C or name O or name C \ B )) or resid 579 or (resid 580 through 592 and (name N or name CA or name C or \ name O or name CB )) or resid 593 through 596 or (resid 597 and (name N or name \ CA or name C or name O or name CB )) or resid 598 through 599 or (resid 600 thro \ ugh 611 and (name N or name CA or name C or name O or name CB )) or resid 612 th \ rough 614 or (resid 615 through 619 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'E' and (resid 21 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 37 or (resid 38 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 39 through 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 50 or (resid 51 and \ (name N or name CA or name C or name O or name CB )) or resid 52 through 53 or ( \ resid 54 and (name N or name CA or name C or name O or name CB )) or resid 55 th \ rough 57 or (resid 58 through 61 and (name N or name CA or name C or name O or n \ ame CB )) or resid 62 or (resid 63 and (name N or name CA or name C or name O or \ name CB )) or resid 64 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 78 or (resid 79 through 80 and (nam \ e N or name CA or name C or name O or name CB )) or resid 81 through 104 or (res \ id 105 through 106 and (name N or name CA or name C or name O or name CB )) or r \ esid 107 through 120 or (resid 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 130 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 or (resid 133 and (name N or name C \ A or name C or name O or name CB )) or resid 134 through 141 or (resid 142 and ( \ name N or name CA or name C or name O or name CB )) or resid 143 through 147 or \ (resid 148 through 149 and (name N or name CA or name C or name O or name CB )) \ or resid 150 through 162 or (resid 163 through 165 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 189 or (resid 190 through 191 a \ nd (name N or name CA or name C or name O or name CB )) or resid 192 through 202 \ or (resid 203 and (name N or name CA or name C or name O or name CB )) or resid \ 204 through 216 or (resid 217 and (name N or name CA or name C or name O or nam \ e CB )) or resid 218 through 221 or (resid 222 and (name N or name CA or name C \ or name O or name CB )) or resid 223 through 225 or (resid 226 and (name N or na \ me CA or name C or name O or name CB )) or resid 227 through 229 or (resid 230 a \ nd (name N or name CA or name C or name O or name CB )) or resid 231 through 232 \ or (resid 233 through 234 and (name N or name CA or name C or name O or name CB \ )) or resid 235 or (resid 236 through 239 and (name N or name CA or name C or n \ ame O or name CB )) or resid 240 through 257 or (resid 258 and (name N or name C \ A or name C or name O or name CB )) or resid 259 through 262 or (resid 263 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) \ or resid 268 through 281 or (resid 282 and (name N or name CA or name C or name \ O or name CB )) or resid 283 or (resid 284 through 285 and (name N or name CA or \ name C or name O or name CB )) or resid 286 through 290 or (resid 291 through 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 294 or (resid 295 through 296 and (name N or name CA or name C or name O or nam \ e CB )) or resid 297 or (resid 298 and (name N or name CA or name C or name O or \ name CB )) or resid 299 or (resid 300 and (name N or name CA or name C or name \ O or name CB )) or resid 301 through 305 or (resid 306 and (name N or name CA or \ name C or name O or name CB )) or resid 307 through 313 or (resid 314 and (name \ N or name CA or name C or name O or name CB )) or resid 315 through 316 or (res \ id 317 and (name N or name CA or name C or name O or name CB )) or resid 318 thr \ ough 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 326 or (resid 327 through 328 and (name N or na \ me CA or name C or name O or name CB )) or resid 329 through 341 or (resid 342 a \ nd (name N or name CA or name C or name O or name CB )) or resid 343 through 348 \ or (resid 349 through 353 and (name N or name CA or name C or name O or name CB \ )) or resid 354 or (resid 355 through 356 and (name N or name CA or name C or n \ ame O or name CB )) or resid 357 through 366 or (resid 367 through 371 and (name \ N or name CA or name C or name O or name CB )) or resid 372 through 373 or (res \ id 374 and (name N or name CA or name C or name O or name CB )) or resid 375 thr \ ough 394 or (resid 395 through 396 and (name N or name CA or name C or name O or \ name CB )) or resid 397 through 401 or (resid 402 through 403 and (name N or na \ me CA or name C or name O or name CB )) or resid 404 through 419 or (resid 420 a \ nd (name N or name CA or name C or name O or name CB )) or resid 421 through 432 \ or (resid 433 and (name N or name CA or name C or name O or name CB )) or resid \ 434 through 459 or (resid 460 and (name N or name CA or name C or name O or nam \ e CB )) or resid 461 through 467 or (resid 468 through 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 or (resid 472 and (name N or na \ me CA or name C or name O or name CB )) or resid 473 or (resid 474 and (name N o \ r name CA or name C or name O or name CB )) or resid 475 through 476 or (resid 4 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 478 or (res \ id 479 and (name N or name CA or name C or name O or name CB )) or resid 480 thr \ ough 482 or (resid 483 through 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 or (resid 486 through 495 and (name N or name CA or nam \ e C or name O or name CB )) or resid 496 through 503 or (resid 504 through 506 a \ nd (name N or name CA or name C or name O or name CB )) or resid 507 through 518 \ or (resid 519 through 521 and (name N or name CA or name C or name O or name CB \ )) or resid 522 through 537 or (resid 538 through 539 and (name N or name CA or \ name C or name O or name CB )) or resid 540 through 542 or (resid 543 through 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 through \ 558 or (resid 569 through 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 576 or (resid 577 through 578 and (name N or name C \ A or name C or name O or name CB )) or (resid 579 through 592 and (name N or nam \ e CA or name C or name O or name CB )) or resid 593 through 599 or (resid 600 th \ rough 611 and (name N or name CA or name C or name O or name CB )) or resid 612 \ through 614 or (resid 615 through 619 and (name N or name CA or name C or name O \ or name CB )))) } ncs_group { reference = (chain 'B' and (resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 99 or (resid 100 thro \ ugh 101 and (name N or name CA or name C or name O or name CB )) or resid 102 th \ rough 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) \ or resid 146 through 151 or (resid 152 and (name N or name CA or name C or name \ O or name CB )) or resid 153 through 173 or (resid 174 through 175 and (name N \ or name CA or name C or name O or name CB )) or resid 176 through 178 or (resid \ 179 and (name N or name CA or name C or name O or name CB )) or resid 180 or (re \ sid 181 through 184 and (name N or name CA or name C or name O or name CB )) or \ resid 185 through 189 or resid 191 or resid 203 through 211 or (resid 212 and (n \ ame N or name CA or name C or name O or name CB )) or resid 213 through 219 or ( \ resid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 \ through 231 or (resid 232 through 233 and (name N or name CA or name C or name O \ or name CB )) or resid 234 through 291 or (resid 292 through 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 304 or (resid 30 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 306 through \ 322 or (resid 323 and (name N or name CA or name C or name O or name CB )) or re \ sid 324 through 337 or (resid 338 and (name N or name CA or name C or name O or \ name CB )) or resid 339 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 359 or (resid 360 and (name N or \ name CA or name C or name O or name CB )) or resid 361 through 362 or (resid 36 \ 3 through 365 and (name N or name CA or name C or name O or name CB )) or resid \ 366 through 372 or (resid 373 and (name N or name CA or name C or name O or name \ CB )) or resid 374 through 387 or (resid 388 and (name N or name CA or name C o \ r name O or name CB )) or resid 389 or (resid 390 through 392 and (name N or nam \ e CA or name C or name O or name CB )) or resid 393 through 403 or (resid 404 th \ rough 406 and (name N or name CA or name C or name O or name CB )) or resid 407 \ through 421 or (resid 422 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 427 through 430 or (resid 431 and (name N or name CA or \ name C or name O or name CB )) or resid 432 through 448 or (resid 449 through 45 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 451 through \ 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) or re \ sid 454 through 461 or (resid 462 through 463 and (name N or name CA or name C o \ r name O or name CB )) or resid 464 or (resid 465 and (name N or name CA or name \ C or name O or name CB )) or resid 466 through 468 or (resid 469 and (name N or \ name CA or name C or name O or name CB )) or resid 470 or (resid 471 through 47 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 473 through \ 479 or (resid 480 through 481 and (name N or name CA or name C or name O or name \ CB )) or resid 482 through 484)) selection = (chain 'D' and (resid 15 through 18 or (resid 19 through 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 37 or (resid 38 and (na \ me N or name CA or name C or name O or name CB )) or resid 39 through 40 or (res \ id 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ esid 43 through 44 and (name N or name CA or name C or name O or name CB )) or r \ esid 45 through 53 or (resid 54 through 55 and (name N or name CA or name C or n \ ame O or name CB )) or resid 56 through 61 or (resid 62 and (name N or name CA o \ r name C or name O or name CB )) or resid 63 through 70 or (resid 71 and (name N \ or name CA or name C or name O or name CB )) or resid 72 through 80 or (resid 8 \ 1 through 82 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 3 through 86 or (resid 87 and (name N or name CA or name C or name O or name CB \ )) or resid 88 through 142 or (resid 143 and (name N or name CA or name C or nam \ e O or name CB )) or resid 144 or (resid 145 and (name N or name CA or name C or \ name O or name CB )) or resid 146 through 153 or (resid 154 through 155 and (na \ me N or name CA or name C or name O or name CB )) or resid 156 through 158 or (r \ esid 159 and (name N or name CA or name C or name O or name CB )) or resid 160 t \ hrough 161 or (resid 162 and (name N or name CA or name C or name O or name CB ) \ ) or resid 163 through 172 or (resid 173 through 175 and (name N or name CA or n \ ame C or name O or name CB )) or resid 176 through 180 or (resid 181 through 184 \ and (name N or name CA or name C or name O or name CB )) or resid 185 through 1 \ 89 or resid 191 or resid 199 or resid 204 through 211 or (resid 212 and (name N \ or name CA or name C or name O or name CB )) or resid 213 through 222 or (resid \ 223 through 229 and (name N or name CA or name C or name O or name CB )) or resi \ d 230 through 260 or (resid 261 and (name N or name CA or name C or name O or na \ me CB )) or resid 262 through 291 or (resid 292 through 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 through 298 or (resid 299 and \ (name N or name CA or name C or name O or name CB )) or resid 300 or (resid 301 \ and (name N or name CA or name C or name O or name CB )) or resid 302 through 30 \ 3 or (resid 304 through 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 or (resid 307 through 308 and (name N or name CA or name C or \ name O or name CB )) or resid 309 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 339 through 358 or (resid 359 thro \ ugh 360 and (name N or name CA or name C or name O or name CB )) or resid 361 th \ rough 372 or (resid 373 and (name N or name CA or name C or name O or name CB )) \ or resid 374 through 377 or (resid 378 and (name N or name CA or name C or name \ O or name CB )) or resid 379 through 403 or (resid 404 through 406 and (name N \ or name CA or name C or name O or name CB )) or resid 407 through 418 or (resid \ 419 through 426 and (name N or name CA or name C or name O or name CB )) or resi \ d 427 through 434 or (resid 435 and (name N or name CA or name C or name O or na \ me CB )) or resid 436 through 448 or (resid 449 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 461 or (resid 462 thro \ ugh 463 and (name N or name CA or name C or name O or name CB )) or resid 464 or \ (resid 465 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 6 or (resid 467 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 470 or (resid 471 through 472 and (name N or name CA or name C or \ name O or name CB )) or resid 473 through 484)) selection = (chain 'F' and (resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 18 or (resid 19 through 20 and (name N or nam \ e CA or name C or name O or name CB )) or resid 21 through 42 or (resid 43 throu \ gh 44 and (name N or name CA or name C or name O or name CB )) or resid 45 throu \ gh 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or r \ esid 50 through 53 or (resid 54 through 55 and (name N or name CA or name C or n \ ame O or name CB )) or resid 56 through 86 or (resid 87 and (name N or name CA o \ r name C or name O or name CB )) or resid 88 through 138 or (resid 139 and (name \ N or name CA or name C or name O or name CB )) or resid 140 through 151 or (res \ id 152 and (name N or name CA or name C or name O or name CB )) or resid 153 or \ (resid 154 through 155 and (name N or name CA or name C or name O or name CB )) \ or resid 156 through 158 or (resid 159 and (name N or name CA or name C or name \ O or name CB )) or resid 160 through 161 or (resid 162 and (name N or name CA or \ name C or name O or name CB )) or resid 163 through 172 or (resid 173 through 1 \ 75 and (name N or name CA or name C or name O or name CB )) or resid 176 through \ 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) or r \ esid 180 through 181 or (resid 182 through 184 and (name N or name CA or name C \ or name O or name CB )) or resid 185 through 189 or resid 201 or resid 203 throu \ gh 225 or (resid 226 through 229 and (name N or name CA or name C or name O or n \ ame CB )) or resid 230 through 231 or (resid 232 through 233 and (name N or name \ CA or name C or name O or name CB )) or resid 234 through 239 or (resid 240 and \ (name N or name CA or name C or name O or name CB )) or resid 241 through 243 o \ r (resid 244 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 45 through 260 or (resid 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 298 or (resid 299 and (name N or name CA or name C or \ name O or name CB )) or resid 300 or (resid 301 and (name N or name CA or name \ C or name O or name CB )) or resid 302 through 303 or (resid 304 through 305 and \ (name N or name CA or name C or name O or name CB )) or resid 306 or (resid 307 \ through 308 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 09 through 322 or (resid 323 and (name N or name CA or name C or name O or name \ CB )) or resid 324 through 333 or (resid 334 and (name N or name CA or name C or \ name O or name CB )) or resid 335 through 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 or (resid 354 and (name N or \ name CA or name C or name O or name CB )) or resid 355 through 358 or (resid 359 \ through 360 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 61 through 370 or (resid 371 and (name N or name CA or name C or name O or name \ CB )) or resid 372 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB )) or resid 379 through 380 or (resid 381 and (name N or name \ CA or name C or name O or name CB )) or resid 382 through 387 or (resid 388 and \ (name N or name CA or name C or name O or name CB )) or resid 389 through 398 o \ r (resid 399 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 00 through 405 or (resid 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 413 or (resid 414 through 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 422 or (resid 423 through \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 throu \ gh 446 or (resid 447 and (name N or name CA or name C or name O or name CB )) or \ resid 448 through 449 or (resid 450 and (name N or name CA or name C or name O \ or name CB )) or resid 451 through 455 or (resid 456 and (name N or name CA or n \ ame C or name O or name CB )) or resid 457 through 468 or (resid 469 and (name N \ or name CA or name C or name O or name CB )) or resid 470 through 480 or (resid \ 481 and (name N or name CA or name C or name O or name CB )) or resid 482 throu \ gh 484)) } ncs_group { reference = (chain 'G' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 or (resid 108 through 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB )) or resid 125 throug \ h 141 or (resid 142 through 158 and (name N or name CA or name C or name O or na \ me CB )) or resid 159 through 164 or resid 178 through 193 or (resid 194 through \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 or (r \ esid 198 and (name N or name CA or name C or name O or name CB )) or resid 199 t \ hrough 201 or (resid 202 through 204 and (name N or name CA or name C or name O \ or name CB )) or resid 205 through 226)) selection = (chain 'I' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 85 or (resid 86 through 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 96 or (resid 97 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 or ( \ resid 104 through 106 and (name N or name CA or name C or name O or name CB )) o \ r resid 107 or (resid 108 through 109 and (name N or name CA or name C or name O \ or name CB )) or resid 110 or (resid 111 through 112 and (name N or name CA or \ name C or name O or name CB )) or resid 113 through 126 or (resid 127 and (name \ N or name CA or name C or name O or name CB )) or resid 128 through 131 or (resi \ d 132 through 133 and (name N or name CA or name C or name O or name CB )) or re \ sid 134 through 136 or (resid 137 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 or (resid 140 through 158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 through 164 or resid 178 \ through 193 or (resid 194 through 196 and (name N or name CA or name C or name \ O or name CB )) or resid 197 or (resid 198 and (name N or name CA or name C or n \ ame O or name CB )) or resid 199 through 202 or (resid 203 through 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 throu \ gh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 thr \ ough 218 or (resid 219 and (name N or name CA or name C or name O or name CB )) \ or resid 220 or (resid 221 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 226)) selection = (chain 'K' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 85 or (resid 86 through 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 92 or (resid 93 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 or ( \ resid 104 through 106 and (name N or name CA or name C or name O or name CB )) o \ r resid 107 through 123 or (resid 124 and (name N or name CA or name C or name O \ or name CB )) or resid 125 through 131 or (resid 132 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 137 or (resid 13 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 139 through \ 140 or (resid 141 through 158 and (name N or name CA or name C or name O or name \ CB )) or resid 159 through 164 or resid 178 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 218 or (resid 219 and (name N or name CA or name C or name \ O or name CB )) or resid 220 or (resid 221 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 through 226)) } ncs_group { reference = (chain 'H' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or (resid 66 through 88 and (name N or name CA or name C or name O \ or name CB )) or (resid 89 through 96 and (name N or name CA or name C or name \ O or name CB )) or resid 97 through 100 or (resid 101 and (name N or name CA or \ name C or name O or name CB )) or resid 102 through 109)) selection = (chain 'J' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 100 or (resid 101 and (name N or name CA or na \ me C or name O or name CB )) or resid 102 or (resid 103 and (name N or name CA o \ r name C or name O or name CB )) or resid 104 through 108 or (resid 109 and (nam \ e N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or (resid 66 through 88 and (name N or name CA or name C or name O \ or name CB )) or (resid 89 through 96 and (name N or name CA or name C or name \ O or name CB )) or resid 97 through 109)) } ncs_group { reference = (chain 'g' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'h' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'i' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 43 and (name N or name CA or name C or name O \ or name CB )) or (resid 44 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name \ O or name CB )) or (resid 91 through 108 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 109 through 115 and (name N or name CA or name C or \ name O or name CB )) or (resid 116 through 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 160)) selection = (chain 'j' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'k' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 101 and (name N or name CA or name C or name \ O or name CB )) or (resid 102 through 131 and (name N or name CA or name C or n \ ame O or name CB )) or resid 132 through 160)) selection = (chain 'l' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'm' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 108 and (name N or name CA or name C or name \ O or name CB )) or (resid 109 through 131 and (name N or name CA or name C or n \ ame O or name CB )) or resid 132 through 160)) selection = (chain 'n' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.980 Check model and map are aligned: 0.360 Set scattering table: 0.490 Process input model: 127.830 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.005 0.092 46721 Z= 0.340 Angle : 0.703 13.271 64503 Z= 0.481 Chirality : 0.049 0.331 8252 Planarity : 0.004 0.094 8744 Dihedral : 10.201 89.621 12909 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 0.50 % Allowed : 0.71 % Favored : 98.78 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.99 % 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: 1.98 (0.10), residues: 7668 helix: 2.97 (0.08), residues: 4398 sheet: -1.81 (0.21), residues: 582 loop : -0.86 (0.13), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP C 453 HIS 0.005 0.001 HIS A 549 PHE 0.043 0.001 PHE C 240 TYR 0.017 0.001 TYR F 139 ARG 0.004 0.000 ARG C 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 5.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8653 (tpp) cc_final: 0.8074 (mpp) REVERT: B 305 MET cc_start: 0.8307 (ttp) cc_final: 0.7900 (tmm) REVERT: B 338 ASP cc_start: 0.8308 (p0) cc_final: 0.8013 (p0) REVERT: E 349 MET cc_start: 0.8295 (ptp) cc_final: 0.8005 (ptp) REVERT: G 92 MET cc_start: 0.7921 (mmp) cc_final: 0.7535 (mmm) REVERT: I 92 MET cc_start: 0.8644 (mmm) cc_final: 0.8402 (mmm) REVERT: I 108 ASN cc_start: 0.8518 (m-40) cc_final: 0.8174 (t0) REVERT: K 91 ASN cc_start: 0.9338 (m-40) cc_final: 0.8968 (m-40) REVERT: K 93 MET cc_start: 0.9463 (tpt) cc_final: 0.9118 (mmm) outliers start: 12 outliers final: 1 residues processed: 301 average time/residue: 0.5022 time to fit residues: 269.9773 Evaluate side-chains 257 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 20.0000 chunk 582 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 601 optimal weight: 40.0000 chunk 232 optimal weight: 0.8980 chunk 366 optimal weight: 0.9980 chunk 448 optimal weight: 0.8980 chunk 697 optimal weight: 6.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 GLN C 447 HIS ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN D 471 HIS G 203 ASN K 26 ASN K 179 HIS e 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46721 Z= 0.225 Angle : 0.515 10.185 64503 Z= 0.276 Chirality : 0.040 0.172 8252 Planarity : 0.004 0.066 8744 Dihedral : 4.051 46.631 8044 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 0.50 % Allowed : 7.17 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.10), residues: 7668 helix: 2.92 (0.08), residues: 4439 sheet: -1.69 (0.21), residues: 631 loop : -0.82 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 453 HIS 0.017 0.001 HIS E 576 PHE 0.015 0.001 PHE E 138 TYR 0.016 0.001 TYR i 87 ARG 0.003 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 4.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8664 (tpp) cc_final: 0.7968 (mpp) REVERT: B 305 MET cc_start: 0.8292 (ttp) cc_final: 0.7936 (tmm) REVERT: B 338 ASP cc_start: 0.8586 (p0) cc_final: 0.8299 (p0) REVERT: B 388 MET cc_start: 0.8903 (pmm) cc_final: 0.8451 (pmm) REVERT: C 42 MET cc_start: 0.7727 (mmm) cc_final: 0.7449 (mmm) REVERT: C 304 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8597 (mmm160) REVERT: F 305 MET cc_start: 0.8108 (ttm) cc_final: 0.7897 (tpp) REVERT: G 92 MET cc_start: 0.7925 (mmp) cc_final: 0.7405 (mmm) REVERT: I 108 ASN cc_start: 0.8684 (m-40) cc_final: 0.8221 (t0) REVERT: K 91 ASN cc_start: 0.9338 (m-40) cc_final: 0.8956 (m-40) REVERT: K 93 MET cc_start: 0.9483 (tpt) cc_final: 0.9283 (mmm) outliers start: 12 outliers final: 10 residues processed: 271 average time/residue: 0.4684 time to fit residues: 230.0944 Evaluate side-chains 264 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 254 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 387 optimal weight: 60.0000 chunk 216 optimal weight: 6.9990 chunk 580 optimal weight: 20.0000 chunk 474 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 698 optimal weight: 5.9990 chunk 754 optimal weight: 10.0000 chunk 622 optimal weight: 7.9990 chunk 692 optimal weight: 20.0000 chunk 238 optimal weight: 0.6980 chunk 560 optimal weight: 9.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS D 87 GLN G 178 HIS ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 46721 Z= 0.314 Angle : 0.555 10.165 64503 Z= 0.300 Chirality : 0.040 0.158 8252 Planarity : 0.004 0.057 8744 Dihedral : 4.168 37.888 8044 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 1.42 % Allowed : 10.73 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 1.87 (0.10), residues: 7668 helix: 2.82 (0.08), residues: 4442 sheet: -1.73 (0.21), residues: 636 loop : -0.86 (0.13), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 542 HIS 0.007 0.001 HIS E 608 PHE 0.021 0.001 PHE B 205 TYR 0.017 0.002 TYR C 531 ARG 0.008 0.001 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8688 (tpp) cc_final: 0.7975 (mpp) REVERT: B 305 MET cc_start: 0.8295 (ttp) cc_final: 0.8062 (tmm) REVERT: B 338 ASP cc_start: 0.8675 (p0) cc_final: 0.8404 (p0) REVERT: B 388 MET cc_start: 0.8849 (pmm) cc_final: 0.8359 (pmm) REVERT: C 304 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8567 (mmm160) REVERT: E 286 MET cc_start: 0.8421 (mmt) cc_final: 0.8201 (mmt) REVERT: F 305 MET cc_start: 0.8215 (ttm) cc_final: 0.7846 (tpp) REVERT: G 92 MET cc_start: 0.7958 (mmp) cc_final: 0.7445 (mmm) REVERT: I 108 ASN cc_start: 0.8871 (m-40) cc_final: 0.8496 (t0) REVERT: K 91 ASN cc_start: 0.9367 (m-40) cc_final: 0.8962 (m-40) outliers start: 34 outliers final: 19 residues processed: 287 average time/residue: 0.4903 time to fit residues: 258.2912 Evaluate side-chains 272 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 362 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 469 optimal weight: 20.0000 chunk 701 optimal weight: 5.9990 chunk 742 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 664 optimal weight: 7.9990 chunk 200 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 46721 Z= 0.344 Angle : 0.571 10.098 64503 Z= 0.310 Chirality : 0.041 0.192 8252 Planarity : 0.004 0.057 8744 Dihedral : 4.304 40.811 8044 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 1.89 % Allowed : 12.53 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 1.66 (0.10), residues: 7668 helix: 2.66 (0.08), residues: 4442 sheet: -1.82 (0.21), residues: 643 loop : -0.95 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP e 47 HIS 0.007 0.001 HIS E 608 PHE 0.023 0.001 PHE B 205 TYR 0.020 0.002 TYR C 531 ARG 0.008 0.001 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 5.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8677 (tpp) cc_final: 0.8133 (mpp) REVERT: B 55 MET cc_start: 0.8629 (mmm) cc_final: 0.8292 (mmm) REVERT: B 86 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8515 (m) REVERT: B 388 MET cc_start: 0.8858 (pmm) cc_final: 0.8364 (pmm) REVERT: C 304 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8555 (mmm160) REVERT: F 305 MET cc_start: 0.8192 (ttm) cc_final: 0.7811 (tpp) REVERT: G 92 MET cc_start: 0.7997 (mmp) cc_final: 0.7452 (mmm) REVERT: I 108 ASN cc_start: 0.8803 (m-40) cc_final: 0.8566 (t0) outliers start: 45 outliers final: 27 residues processed: 295 average time/residue: 0.4868 time to fit residues: 263.4541 Evaluate side-chains 280 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 8.9990 chunk 421 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 552 optimal weight: 30.0000 chunk 306 optimal weight: 0.9990 chunk 633 optimal weight: 10.0000 chunk 513 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 379 optimal weight: 50.0000 chunk 666 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 46721 Z= 0.344 Angle : 0.573 10.136 64503 Z= 0.311 Chirality : 0.041 0.163 8252 Planarity : 0.004 0.055 8744 Dihedral : 4.343 40.908 8044 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 2.85 % Allowed : 14.12 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 1.62 (0.10), residues: 7668 helix: 2.64 (0.08), residues: 4438 sheet: -1.83 (0.21), residues: 632 loop : -0.99 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 357 HIS 0.007 0.001 HIS E 608 PHE 0.023 0.001 PHE B 205 TYR 0.015 0.001 TYR C 583 ARG 0.006 0.000 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 253 time to evaluate : 5.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8669 (tpp) cc_final: 0.8119 (mpp) REVERT: B 86 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 388 MET cc_start: 0.8820 (pmm) cc_final: 0.8318 (pmm) REVERT: C 42 MET cc_start: 0.7706 (mmm) cc_final: 0.7498 (mmm) REVERT: C 213 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9009 (p) REVERT: D 15 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8839 (pt) REVERT: F 305 MET cc_start: 0.8182 (ttm) cc_final: 0.7853 (tpp) REVERT: G 92 MET cc_start: 0.8009 (mmp) cc_final: 0.7356 (mmp) REVERT: I 108 ASN cc_start: 0.8862 (m-40) cc_final: 0.8288 (t0) outliers start: 68 outliers final: 37 residues processed: 314 average time/residue: 0.4766 time to fit residues: 274.0486 Evaluate side-chains 290 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 10.0000 chunk 668 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 743 optimal weight: 5.9990 chunk 616 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 390 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN F 174 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46721 Z= 0.208 Angle : 0.504 10.237 64503 Z= 0.267 Chirality : 0.040 0.280 8252 Planarity : 0.003 0.055 8744 Dihedral : 4.114 37.671 8044 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 1.97 % Allowed : 15.30 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 1.94 (0.10), residues: 7668 helix: 2.90 (0.08), residues: 4453 sheet: -1.68 (0.22), residues: 617 loop : -0.90 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 357 HIS 0.005 0.001 HIS K 178 PHE 0.015 0.001 PHE C 293 TYR 0.012 0.001 TYR D 262 ARG 0.008 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 4.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8616 (tpp) cc_final: 0.8097 (mpp) REVERT: B 55 MET cc_start: 0.8559 (mmm) cc_final: 0.8295 (mmm) REVERT: B 86 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8410 (m) REVERT: C 213 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9057 (p) REVERT: C 304 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8624 (mmm160) REVERT: I 108 ASN cc_start: 0.8841 (m-40) cc_final: 0.8409 (t0) outliers start: 47 outliers final: 26 residues processed: 292 average time/residue: 0.4490 time to fit residues: 239.5500 Evaluate side-chains 278 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 716 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 423 optimal weight: 0.8980 chunk 542 optimal weight: 0.6980 chunk 420 optimal weight: 40.0000 chunk 625 optimal weight: 40.0000 chunk 414 optimal weight: 9.9990 chunk 740 optimal weight: 0.0070 chunk 463 optimal weight: 2.9990 chunk 451 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46721 Z= 0.178 Angle : 0.494 10.819 64503 Z= 0.259 Chirality : 0.040 0.252 8252 Planarity : 0.003 0.054 8744 Dihedral : 3.977 33.920 8044 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 2.01 % Allowed : 15.30 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 2.08 (0.10), residues: 7668 helix: 2.98 (0.08), residues: 4473 sheet: -1.64 (0.22), residues: 612 loop : -0.83 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 47 HIS 0.004 0.001 HIS K 178 PHE 0.013 0.001 PHE C 293 TYR 0.012 0.001 TYR I 153 ARG 0.006 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 5.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8600 (tpp) cc_final: 0.8091 (mpp) REVERT: B 278 MET cc_start: 0.8671 (mmm) cc_final: 0.8100 (mmp) REVERT: B 388 MET cc_start: 0.8558 (pmm) cc_final: 0.7982 (pmm) REVERT: C 213 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9026 (p) REVERT: E 213 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9059 (p) REVERT: E 543 MET cc_start: 0.8007 (mtm) cc_final: 0.7676 (ttm) REVERT: I 108 ASN cc_start: 0.8863 (m-40) cc_final: 0.8611 (t0) REVERT: I 205 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9047 (mt) outliers start: 48 outliers final: 32 residues processed: 292 average time/residue: 0.4571 time to fit residues: 245.1101 Evaluate side-chains 286 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 442 optimal weight: 30.0000 chunk 222 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 470 optimal weight: 50.0000 chunk 504 optimal weight: 50.0000 chunk 365 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 581 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 46721 Z= 0.276 Angle : 0.536 11.441 64503 Z= 0.284 Chirality : 0.040 0.224 8252 Planarity : 0.004 0.053 8744 Dihedral : 4.083 34.298 8044 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 2.51 % Allowed : 14.92 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 1.97 (0.10), residues: 7668 helix: 2.90 (0.08), residues: 4467 sheet: -1.71 (0.21), residues: 627 loop : -0.85 (0.13), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 47 HIS 0.005 0.001 HIS E 608 PHE 0.019 0.001 PHE E 615 TYR 0.020 0.001 TYR C 531 ARG 0.005 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 251 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8622 (tpp) cc_final: 0.8105 (mpp) REVERT: B 55 MET cc_start: 0.8548 (mmm) cc_final: 0.8274 (mmm) REVERT: B 278 MET cc_start: 0.8671 (mmm) cc_final: 0.8338 (mmp) REVERT: B 388 MET cc_start: 0.8612 (pmm) cc_final: 0.8011 (pmm) REVERT: C 213 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9056 (p) REVERT: E 213 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9077 (p) REVERT: E 543 MET cc_start: 0.7992 (mtm) cc_final: 0.7676 (ttm) REVERT: I 108 ASN cc_start: 0.8841 (m-40) cc_final: 0.8393 (t0) REVERT: I 205 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8767 (mt) outliers start: 60 outliers final: 44 residues processed: 303 average time/residue: 0.4737 time to fit residues: 263.7912 Evaluate side-chains 297 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 8.9990 chunk 709 optimal weight: 30.0000 chunk 647 optimal weight: 3.9990 chunk 689 optimal weight: 20.0000 chunk 708 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 541 optimal weight: 0.0470 chunk 211 optimal weight: 0.3980 chunk 623 optimal weight: 40.0000 chunk 652 optimal weight: 5.9990 overall best weight: 2.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 HIS L 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46721 Z= 0.182 Angle : 0.497 12.538 64503 Z= 0.259 Chirality : 0.040 0.297 8252 Planarity : 0.003 0.054 8744 Dihedral : 3.948 30.870 8044 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 2.01 % Allowed : 15.93 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 2.15 (0.10), residues: 7668 helix: 3.04 (0.08), residues: 4473 sheet: -1.59 (0.22), residues: 617 loop : -0.79 (0.13), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 47 HIS 0.004 0.001 HIS K 178 PHE 0.013 0.001 PHE E 615 TYR 0.014 0.001 TYR F 139 ARG 0.005 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 251 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8659 (tpp) cc_final: 0.8182 (mpp) REVERT: B 278 MET cc_start: 0.8625 (mmm) cc_final: 0.8343 (mmp) REVERT: B 388 MET cc_start: 0.8557 (pmm) cc_final: 0.7961 (pmm) REVERT: C 213 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9033 (p) REVERT: C 304 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8538 (mmm160) REVERT: E 213 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9059 (p) REVERT: E 543 MET cc_start: 0.7957 (mtm) cc_final: 0.7635 (ttm) REVERT: I 108 ASN cc_start: 0.8884 (m-40) cc_final: 0.8605 (t0) REVERT: I 205 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9002 (mt) outliers start: 48 outliers final: 38 residues processed: 291 average time/residue: 0.4727 time to fit residues: 254.0810 Evaluate side-chains 292 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 251 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 687 optimal weight: 6.9990 chunk 452 optimal weight: 50.0000 chunk 729 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 507 optimal weight: 0.6980 chunk 765 optimal weight: 1.9990 chunk 704 optimal weight: 0.9990 chunk 609 optimal weight: 0.7980 chunk 63 optimal weight: 40.0000 chunk 470 optimal weight: 50.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS E 270 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46721 Z= 0.187 Angle : 0.500 12.962 64503 Z= 0.259 Chirality : 0.040 0.213 8252 Planarity : 0.003 0.054 8744 Dihedral : 3.852 27.768 8044 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 2.05 % Allowed : 15.80 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 2.22 (0.10), residues: 7668 helix: 3.08 (0.08), residues: 4480 sheet: -1.56 (0.21), residues: 636 loop : -0.74 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP e 47 HIS 0.004 0.001 HIS G 182 PHE 0.012 0.001 PHE E 138 TYR 0.016 0.001 TYR C 531 ARG 0.005 0.000 ARG I 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7925 (mmm) cc_final: 0.7637 (mmm) REVERT: A 309 MET cc_start: 0.8522 (tpp) cc_final: 0.8040 (mpp) REVERT: B 278 MET cc_start: 0.8639 (mmm) cc_final: 0.8349 (mmp) REVERT: B 388 MET cc_start: 0.8542 (pmm) cc_final: 0.7936 (pmm) REVERT: C 213 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9019 (p) REVERT: C 304 ARG cc_start: 0.8837 (mtp85) cc_final: 0.8535 (mmm160) REVERT: E 213 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9010 (p) REVERT: E 543 MET cc_start: 0.7952 (mtm) cc_final: 0.7626 (ttm) REVERT: I 108 ASN cc_start: 0.8794 (m-40) cc_final: 0.8537 (t0) REVERT: I 205 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8952 (mt) outliers start: 49 outliers final: 43 residues processed: 292 average time/residue: 0.4727 time to fit residues: 253.8271 Evaluate side-chains 298 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 5.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 576 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain F residue 43 TYR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain L residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 0.0060 chunk 483 optimal weight: 50.0000 chunk 649 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 561 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 169 optimal weight: 0.0170 chunk 610 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 626 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.065185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.036921 restraints weight = 338110.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037435 restraints weight = 249091.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036929 restraints weight = 202638.304| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 46721 Z= 0.130 Angle : 0.482 13.319 64503 Z= 0.247 Chirality : 0.039 0.211 8252 Planarity : 0.003 0.055 8744 Dihedral : 3.695 24.065 8044 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 1.34 % Allowed : 16.68 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: 2.35 (0.10), residues: 7668 helix: 3.18 (0.08), residues: 4481 sheet: -1.44 (0.22), residues: 631 loop : -0.69 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP e 47 HIS 0.004 0.001 HIS A 549 PHE 0.012 0.001 PHE E 138 TYR 0.017 0.001 TYR F 139 ARG 0.005 0.000 ARG I 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7234.42 seconds wall clock time: 130 minutes 2.70 seconds (7802.70 seconds total)