Starting phenix.real_space_refine on Mon Mar 25 04:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwd_26829/03_2024/7uwd_26829.pdb" } resolution = 4.1 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= 0.028 sd= 0.116 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 28805 2.51 5 N 8570 2.21 5 O 8699 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46162 Number of models: 1 Model: "" Number of chains: 31 Chain: "P" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2137 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1796 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 28, 'TYR:plan': 13, 'ASN:plan1': 13, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 27, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 717 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: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 545 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 36 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: 26.77, per 1000 atoms: 0.58 Number of scatterers: 46162 At special positions: 0 Unit cell: (147.147, 184.338, 266.805, 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 8699 8.00 N 8570 7.00 C 28805 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: 19.86 Conformation dependent library (CDL) restraints added in 10.4 seconds 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14430 Finding SS restraints... Secondary structure from input PDB file: 317 helices and 38 sheets defined 65.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'P' and resid 1 through 14 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 25 removed outlier: 3.769A pdb=" N TYR P 21 " --> pdb=" O PRO P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 4.080A pdb=" N LEU P 32 " --> pdb=" O SER P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 48 removed outlier: 3.998A pdb=" N ARG P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 68 removed outlier: 3.670A pdb=" N PHE P 61 " --> pdb=" O TYR P 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 87 removed outlier: 3.603A pdb=" N VAL P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR P 86 " --> pdb=" O ASP P 82 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 101 removed outlier: 3.650A pdb=" N HIS P 96 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP P 97 " --> pdb=" O ARG P 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 112 removed outlier: 4.109A pdb=" N THR P 105 " --> pdb=" O ALA P 101 " (cutoff:3.500A) Proline residue: P 108 - end of helix Processing helix chain 'P' and resid 116 through 124 Processing helix chain 'P' and resid 125 through 135 removed outlier: 3.890A pdb=" N SER P 130 " --> pdb=" O LYS P 126 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE P 131 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 174 Processing helix chain 'P' and resid 181 through 195 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 Processing helix chain 'P' and resid 221 through 241 removed outlier: 3.516A pdb=" N ILE P 225 " --> pdb=" O THR P 221 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 251 Processing helix chain 'P' and resid 253 through 263 Processing helix chain 'P' and resid 266 through 281 removed outlier: 3.682A pdb=" N ILE P 276 " --> pdb=" O VAL P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 292 Processing helix chain 'P' and resid 294 through 305 removed outlier: 3.505A pdb=" N VAL P 298 " --> pdb=" O GLY P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 331 Processing helix chain 'P' and resid 333 through 341 removed outlier: 3.501A pdb=" N LYS P 337 " --> pdb=" O PHE P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 365 removed outlier: 4.111A pdb=" N TRP P 357 " --> pdb=" O ASP P 353 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR P 362 " --> pdb=" O ARG P 358 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN P 363 " --> pdb=" O ASP P 359 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU P 365 " --> pdb=" O ILE P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 381 Processing helix chain 'P' and resid 384 through 402 removed outlier: 3.769A pdb=" N LEU P 388 " --> pdb=" O ASP P 384 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA P 389 " --> pdb=" O PRO P 385 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL P 390 " --> pdb=" O ARG P 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE P 398 " --> pdb=" O ASP P 394 " (cutoff:3.500A) Processing helix chain 'P' and resid 402 through 412 Processing helix chain 'P' and resid 412 through 423 removed outlier: 3.811A pdb=" N GLU P 416 " --> pdb=" O LEU P 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 445 removed outlier: 3.595A pdb=" N LEU P 440 " --> pdb=" O CYS P 436 " (cutoff:3.500A) removed outlier: 4.014A 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: 4.506A 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: 3.784A 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: 3.805A 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 590 Processing helix chain 'A' and resid 596 through 618 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.958A 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: 4.173A 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: 3.535A pdb=" N TYR B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.525A 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: 4.148A pdb=" N TYR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.957A 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: 4.527A 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: 4.386A pdb=" N ALA C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 368 removed outlier: 3.895A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.553A 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: 4.333A pdb=" N GLU C 494 " --> pdb=" O ASP C 490 " (cutoff:3.500A) removed outlier: 4.298A 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: 3.620A pdb=" N GLY C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 565 removed outlier: 3.771A 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: 3.657A 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: 3.789A 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: 3.712A 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: 3.820A 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: 4.844A pdb=" N LEU E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.655A 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: 3.717A 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: 4.227A 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: 3.651A 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: 4.422A 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: 4.114A 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: 3.571A 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: 4.245A 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: 3.535A 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: 3.766A 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: 4.175A 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: 3.914A pdb=" N ILE G 38 " --> pdb=" O GLU G 34 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 55 removed outlier: 4.003A 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: 3.757A pdb=" N SER G 104 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.544A 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: 4.083A 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: 3.660A 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: 5.416A 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: 3.883A 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: 4.078A pdb=" N GLY I 177 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 4.528A 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: 4.480A 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: 4.077A pdb=" N SER J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN J 99 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 21 Processing helix chain 'K' and resid 23 through 100 removed outlier: 3.919A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU K 47 " --> pdb=" O LEU K 43 " (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: 4.437A 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: 4.116A 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 107 removed outlier: 3.914A pdb=" N ALA L 16 " --> pdb=" O GLN L 12 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG L 44 " --> pdb=" O GLU L 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 45 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L 68 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 5.513A 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: 3.852A 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: 3.967A 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: 3.669A 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: 3.852A 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: 3.775A 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: 3.729A pdb=" N ILE O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.504A 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: 4.106A 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: 3.695A 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: 4.181A 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: 3.892A pdb=" N LEU a 46 " --> pdb=" O TYR a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 59 removed outlier: 4.045A 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: 3.893A pdb=" N SER a 151 " --> pdb=" O GLY a 147 " (cutoff:3.500A) removed outlier: 4.431A 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: 3.751A pdb=" N THR a 311 " --> pdb=" O ASN a 307 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP a 314 " --> pdb=" O GLN a 310 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN a 318 " --> pdb=" O ASP a 314 " (cutoff:3.500A) removed outlier: 3.935A 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: 4.540A pdb=" N VAL a 423 " --> pdb=" O VAL a 419 " (cutoff:3.500A) Proline residue: a 426 - end of helix removed outlier: 3.535A 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: 3.650A 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: 3.634A 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: 4.167A pdb=" N TYR a 569 " --> pdb=" O ILE a 565 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.976A pdb=" N LEU a 592 " --> pdb=" O GLN a 588 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN a 593 " --> pdb=" O ILE a 589 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR a 598 " --> pdb=" O SER a 594 " (cutoff:3.500A) removed outlier: 4.497A 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: 4.051A pdb=" N ILE a 620 " --> pdb=" O TYR a 616 " (cutoff:3.500A) removed outlier: 3.675A 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: 3.548A 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: 3.707A pdb=" N PHE c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE c 34 " --> pdb=" O ILE c 30 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.739A 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: 3.570A 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: 3.863A pdb=" N LEU c 162 " --> pdb=" O SER c 158 " (cutoff:3.500A) removed outlier: 3.632A 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: 3.503A pdb=" N MET d 85 " --> pdb=" O GLU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 113 removed outlier: 3.985A pdb=" N HIS d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.260A 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: 3.501A pdb=" N LYS d 199 " --> pdb=" O LYS d 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 226 removed outlier: 4.078A 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: 4.064A 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: 3.713A pdb=" N GLN e 57 " --> pdb=" O VAL e 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 45 removed outlier: 3.514A pdb=" N SER g 25 " --> pdb=" O ALA g 21 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.800A pdb=" N ALA g 144 " --> pdb=" O ALA g 140 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG g 157 " --> pdb=" O ILE g 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA g 158 " --> pdb=" O LEU g 154 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 47 removed outlier: 4.096A 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: 4.122A 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: 3.640A pdb=" N ILE h 75 " --> pdb=" O ILE h 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY h 78 " --> pdb=" O ILE h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 84 removed outlier: 6.413A pdb=" N LYS h 82 " --> pdb=" O ILE h 79 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.727A 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: 4.334A 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: 3.725A 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: 3.734A pdb=" N GLY i 78 " --> pdb=" O ILE i 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 123 removed outlier: 3.630A 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: 4.529A pdb=" N LEU i 143 " --> pdb=" O PHE i 139 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA i 144 " --> pdb=" O ALA i 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU i 145 " --> pdb=" O GLU i 141 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER i 156 " --> pdb=" O ILE i 152 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 47 removed outlier: 4.738A pdb=" N LEU j 16 " --> pdb=" O PHE j 12 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU j 22 " --> pdb=" O ALA j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 54 removed outlier: 4.539A pdb=" N MET j 52 " --> pdb=" O PRO j 48 " (cutoff:3.500A) removed outlier: 4.536A 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: 3.513A 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: 4.455A 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: 4.166A 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: 4.343A pdb=" N SER k 42 " --> pdb=" O VAL k 38 " (cutoff:3.500A) removed outlier: 3.999A 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: 3.656A 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: 3.953A pdb=" N ARG k 121 " --> pdb=" O ASP k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 129 through 158 removed outlier: 3.761A 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: 4.732A pdb=" N MET l 52 " --> pdb=" O GLU l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 79 removed outlier: 3.873A pdb=" N GLY l 62 " --> pdb=" O VAL l 58 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.717A pdb=" N ALA l 93 " --> pdb=" O PHE l 89 " (cutoff:3.500A) removed outlier: 3.879A 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: 3.899A pdb=" N VAL m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 53 removed outlier: 4.209A pdb=" N MET m 52 " --> pdb=" O PRO m 48 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 79 removed outlier: 3.783A 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: 3.941A pdb=" N LEU m 64 " --> pdb=" O MET m 60 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.605A 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: 4.195A 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: 3.512A pdb=" N LEU m 145 " --> pdb=" O GLU m 141 " (cutoff:3.500A) removed outlier: 3.993A 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: 4.119A 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: 3.636A 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: 4.038A pdb=" N GLY n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.917A pdb=" N ILE n 134 " --> pdb=" O PHE n 130 " (cutoff:3.500A) removed outlier: 3.852A 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: 4.003A 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: 5.077A 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: 4.133A pdb=" N GLY o 65 " --> pdb=" O ALA o 61 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.536A pdb=" N ALA o 144 " --> pdb=" O ALA o 140 " (cutoff:3.500A) removed outlier: 3.663A 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: 6.580A pdb=" N ILE A 33 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 27 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.851A 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: 6.385A pdb=" N VAL A 274 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 315 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.549A 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: 3.544A 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: 6.830A pdb=" N VAL D 69 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL D 63 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.260A 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: 6.757A pdb=" N GLN E 68 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 3.809A 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: 6.634A 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: 7.796A pdb=" N LEU B 241 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR B 236 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE B 207 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.385A 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: 7.782A 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: 7.988A 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: 8.180A pdb=" N THR B 276 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.525A 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: 4.218A 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: 7.592A 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: 3.583A 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: 3.849A pdb=" N ASP C 147 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 179 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU C 195 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.945A 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: 3.635A 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: 6.433A 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: 4.740A 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: 6.176A 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: 6.961A pdb=" N SER D 167 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA D 168 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 9.555A 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: 4.538A 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: 3.967A pdb=" N LEU E 149 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 179 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 6.694A 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: 6.787A 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: 3.520A 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: 3.580A pdb=" N MET F 212 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.339A 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: 6.690A pdb=" N VAL F 273 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE F 331 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU F 275 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU F 165 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 5.691A 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: 7.649A 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: 6.521A pdb=" N ASP a 234 " --> pdb=" O GLU a 239 " (cutoff:3.500A) removed outlier: 6.438A 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 3696 hydrogen bonds defined for protein. 10764 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: 19.56 Time building geometry restraints manager: 21.22 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: 8147 1.31 - 1.44: 10992 1.44 - 1.56: 27470 1.56 - 1.69: 5 1.69 - 1.82: 146 Bond restraints: 46760 Sorted by residual: bond pdb=" CA ILE P 64 " pdb=" C ILE P 64 " ideal model delta sigma weight residual 1.523 1.426 0.097 1.27e-02 6.20e+03 5.87e+01 bond pdb=" CA ARG P 91 " pdb=" C ARG P 91 " ideal model delta sigma weight residual 1.523 1.427 0.097 1.34e-02 5.57e+03 5.19e+01 bond pdb=" CA GLU P 9 " pdb=" C GLU P 9 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.29e-02 6.01e+03 5.05e+01 bond pdb=" N PHE P 286 " pdb=" CA PHE P 286 " ideal model delta sigma weight residual 1.459 1.374 0.085 1.21e-02 6.83e+03 4.99e+01 bond pdb=" CA LEU P 78 " pdb=" C LEU P 78 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.30e-02 5.92e+03 4.52e+01 ... (remaining 46755 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.97: 1169 105.97 - 113.29: 26284 113.29 - 120.60: 19760 120.60 - 127.91: 17066 127.91 - 135.23: 279 Bond angle restraints: 64558 Sorted by residual: angle pdb=" C LYS P 98 " pdb=" N SER P 99 " pdb=" CA SER P 99 " ideal model delta sigma weight residual 120.44 132.70 -12.26 1.30e+00 5.92e-01 8.89e+01 angle pdb=" C MET P 290 " pdb=" N ILE P 291 " pdb=" CA ILE P 291 " ideal model delta sigma weight residual 120.72 131.03 -10.31 1.22e+00 6.72e-01 7.14e+01 angle pdb=" C TRP P 18 " pdb=" N GLU P 19 " pdb=" CA GLU P 19 " ideal model delta sigma weight residual 120.38 131.08 -10.70 1.37e+00 5.33e-01 6.10e+01 angle pdb=" C ARG P 93 " pdb=" N LEU P 94 " pdb=" CA LEU P 94 " ideal model delta sigma weight residual 120.54 130.98 -10.44 1.35e+00 5.49e-01 5.97e+01 angle pdb=" CA GLN P 400 " pdb=" C GLN P 400 " pdb=" O GLN P 400 " ideal model delta sigma weight residual 120.42 128.33 -7.91 1.06e+00 8.90e-01 5.57e+01 ... (remaining 64553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 26338 17.91 - 35.83: 817 35.83 - 53.74: 143 53.74 - 71.65: 31 71.65 - 89.57: 17 Dihedral angle restraints: 27346 sinusoidal: 5000 harmonic: 22346 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 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+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 -111.92 -10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" CA GLY P 54 " pdb=" C GLY P 54 " pdb=" N PRO P 55 " pdb=" CA PRO P 55 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 27343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 7082 0.068 - 0.135: 970 0.135 - 0.203: 175 0.203 - 0.270: 23 0.270 - 0.338: 10 Chirality restraints: 8260 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 2.17 0.34 2.00e-01 2.50e+01 2.85e+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 2.57e+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 2.53e+00 ... (remaining 8257 not shown) Planarity restraints: 8752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 620 " -0.049 2.00e-02 2.50e+03 9.17e-02 8.42e+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 4.06e-02 4.11e+01 pdb=" CG TRP C 453 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 453 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 453 " 0.042 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 " 0.013 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=" CA LYS P 70 " -0.020 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LYS P 70 " 0.074 2.00e-02 2.50e+03 pdb=" O LYS P 70 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU P 71 " -0.026 2.00e-02 2.50e+03 ... (remaining 8749 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7266 2.75 - 3.29: 48793 3.29 - 3.83: 79273 3.83 - 4.36: 78250 4.36 - 4.90: 138160 Nonbonded interactions: 351742 Sorted by model distance: nonbonded pdb=" O ILE D 45 " pdb=" OG1 THR D 89 " model vdw 2.218 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 2.249 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 2.254 2.440 ... (remaining 351737 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: 2.140 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: 8.520 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 126.140 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 46760 Z= 0.401 Angle : 0.782 12.259 64558 Z= 0.551 Chirality : 0.052 0.338 8260 Planarity : 0.005 0.095 8752 Dihedral : 10.378 89.566 12916 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 1.17 % Allowed : 0.71 % Favored : 98.11 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.98 % 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: 1.93 (0.10), residues: 7676 helix: 2.93 (0.08), residues: 4395 sheet: -1.81 (0.21), residues: 582 loop : -0.89 (0.13), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP C 453 HIS 0.004 0.001 HIS A 549 PHE 0.043 0.001 PHE C 240 TYR 0.017 0.001 TYR F 139 ARG 0.005 0.000 ARG C 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8875 (m) REVERT: C 309 MET cc_start: 0.8116 (mmm) cc_final: 0.7677 (mmm) REVERT: D 373 LEU cc_start: 0.9034 (tp) cc_final: 0.8752 (tt) REVERT: E 298 MET cc_start: 0.8675 (ppp) cc_final: 0.8414 (ppp) REVERT: E 349 MET cc_start: 0.8639 (ptp) cc_final: 0.8131 (ptp) REVERT: G 139 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8631 (t70) REVERT: I 178 HIS cc_start: 0.8274 (m90) cc_final: 0.7934 (p-80) REVERT: K 93 MET cc_start: 0.9203 (tpt) cc_final: 0.8907 (tpt) outliers start: 28 outliers final: 4 residues processed: 317 average time/residue: 0.4901 time to fit residues: 273.5385 Evaluate side-chains 264 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 4.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 393 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 602 optimal weight: 40.0000 chunk 233 optimal weight: 1.9990 chunk 366 optimal weight: 0.9990 chunk 448 optimal weight: 20.0000 chunk 698 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 GLN C 447 HIS ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 362 GLN G 139 HIS K 179 HIS L 104 HIS e 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 46760 Z= 0.305 Angle : 0.551 10.233 64558 Z= 0.301 Chirality : 0.041 0.176 8260 Planarity : 0.004 0.070 8752 Dihedral : 4.158 31.151 8051 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.59 % Favored : 94.29 % Rotamer: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 1.89 (0.10), residues: 7676 helix: 2.86 (0.08), residues: 4435 sheet: -1.85 (0.20), residues: 654 loop : -0.83 (0.13), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 453 HIS 0.018 0.001 HIS A 576 PHE 0.022 0.001 PHE A 293 TYR 0.018 0.002 TYR D 42 ARG 0.007 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8285 (tmm) cc_final: 0.8080 (tmm) REVERT: C 309 MET cc_start: 0.8208 (mmm) cc_final: 0.7889 (mmm) REVERT: G 91 ASN cc_start: 0.9001 (m110) cc_final: 0.8798 (m110) REVERT: K 93 MET cc_start: 0.9201 (tpt) cc_final: 0.8913 (tpt) outliers start: 4 outliers final: 2 residues processed: 280 average time/residue: 0.4843 time to fit residues: 244.8579 Evaluate side-chains 263 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 4.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 50.0000 chunk 216 optimal weight: 0.6980 chunk 581 optimal weight: 20.0000 chunk 475 optimal weight: 0.0970 chunk 192 optimal weight: 2.9990 chunk 699 optimal weight: 0.8980 chunk 755 optimal weight: 5.9990 chunk 623 optimal weight: 9.9990 chunk 693 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 561 optimal weight: 8.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 GLN C 444 GLN D 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46760 Z= 0.181 Angle : 0.481 10.414 64558 Z= 0.256 Chirality : 0.040 0.160 8260 Planarity : 0.004 0.056 8752 Dihedral : 3.944 32.974 8051 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.11 (0.10), residues: 7676 helix: 3.01 (0.08), residues: 4450 sheet: -1.65 (0.21), residues: 633 loop : -0.74 (0.13), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 357 HIS 0.010 0.001 HIS L 104 PHE 0.031 0.001 PHE F 226 TYR 0.014 0.001 TYR E 551 ARG 0.003 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 298 MET cc_start: 0.8601 (ppp) cc_final: 0.8033 (ppp) REVERT: G 91 ASN cc_start: 0.8960 (m110) cc_final: 0.8744 (m110) REVERT: I 87 ASP cc_start: 0.7952 (m-30) cc_final: 0.7744 (m-30) REVERT: K 93 MET cc_start: 0.9246 (tpt) cc_final: 0.8956 (tpt) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.5072 time to fit residues: 250.0368 Evaluate side-chains 264 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 7.9990 chunk 525 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 469 optimal weight: 40.0000 chunk 702 optimal weight: 1.9990 chunk 743 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 chunk 665 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN B 453 GLN D 87 GLN D 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46760 Z= 0.247 Angle : 0.505 10.319 64558 Z= 0.270 Chirality : 0.040 0.165 8260 Planarity : 0.004 0.053 8752 Dihedral : 3.943 31.648 8051 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.10 (0.10), residues: 7676 helix: 3.00 (0.08), residues: 4450 sheet: -1.64 (0.21), residues: 638 loop : -0.76 (0.13), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.008 0.001 HIS A 576 PHE 0.017 0.001 PHE E 205 TYR 0.043 0.001 TYR D 401 ARG 0.008 0.000 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 5.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8449 (tmm) cc_final: 0.8190 (tmm) REVERT: C 42 MET cc_start: 0.8092 (tpp) cc_final: 0.7876 (mmm) REVERT: E 298 MET cc_start: 0.8465 (ppp) cc_final: 0.7873 (ppp) REVERT: E 321 MET cc_start: 0.8862 (mtp) cc_final: 0.8270 (mtp) REVERT: G 49 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8103 (mtmm) REVERT: G 91 ASN cc_start: 0.8989 (m110) cc_final: 0.8762 (m110) REVERT: H 86 LEU cc_start: 0.9404 (mp) cc_final: 0.9165 (mm) REVERT: I 87 ASP cc_start: 0.7936 (m-30) cc_final: 0.7712 (m-30) REVERT: K 93 MET cc_start: 0.9253 (tpt) cc_final: 0.8991 (tpt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4891 time to fit residues: 241.9732 Evaluate side-chains 260 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 8.9990 chunk 421 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 553 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 634 optimal weight: 9.9990 chunk 513 optimal weight: 2.9990 chunk 0 optimal weight: 90.0000 chunk 379 optimal weight: 3.9990 chunk 667 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN D 328 GLN E 549 HIS G 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 46760 Z= 0.392 Angle : 0.604 10.152 64558 Z= 0.328 Chirality : 0.042 0.177 8260 Planarity : 0.004 0.064 8752 Dihedral : 4.351 31.334 8051 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 1.75 (0.10), residues: 7676 helix: 2.73 (0.08), residues: 4449 sheet: -1.82 (0.21), residues: 615 loop : -0.92 (0.13), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 542 HIS 0.006 0.001 HIS E 166 PHE 0.033 0.002 PHE E 205 TYR 0.022 0.002 TYR D 42 ARG 0.006 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 5.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8324 (tmm) cc_final: 0.8115 (tmm) REVERT: D 19 MET cc_start: 0.8813 (mmm) cc_final: 0.8354 (mmm) REVERT: E 37 MET cc_start: 0.8944 (mmp) cc_final: 0.8679 (mmp) REVERT: E 298 MET cc_start: 0.8087 (ppp) cc_final: 0.7786 (ppp) REVERT: H 86 LEU cc_start: 0.9469 (mp) cc_final: 0.9235 (mm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.5663 time to fit residues: 278.2517 Evaluate side-chains 254 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 3.9990 chunk 669 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 436 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 744 optimal weight: 0.0020 chunk 617 optimal weight: 20.0000 chunk 344 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 390 optimal weight: 40.0000 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN D 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 46760 Z= 0.152 Angle : 0.482 10.322 64558 Z= 0.253 Chirality : 0.040 0.156 8260 Planarity : 0.003 0.054 8752 Dihedral : 3.982 29.369 8051 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 7676 helix: 2.99 (0.08), residues: 4479 sheet: -1.52 (0.21), residues: 653 loop : -0.69 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 47 HIS 0.006 0.001 HIS A 576 PHE 0.027 0.001 PHE E 293 TYR 0.019 0.001 TYR F 139 ARG 0.006 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 4.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 MET cc_start: 0.8421 (tmm) cc_final: 0.8188 (ptm) REVERT: E 42 MET cc_start: 0.7651 (tpp) cc_final: 0.6981 (tmm) REVERT: E 298 MET cc_start: 0.8328 (ppp) cc_final: 0.7846 (ppp) REVERT: F 305 MET cc_start: 0.8695 (ttt) cc_final: 0.8353 (tpp) REVERT: G 49 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8090 (mtmm) REVERT: G 91 ASN cc_start: 0.8978 (m110) cc_final: 0.8769 (m110) REVERT: I 87 ASP cc_start: 0.7892 (m-30) cc_final: 0.7589 (m-30) REVERT: K 93 MET cc_start: 0.9264 (tpt) cc_final: 0.9015 (tpt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4830 time to fit residues: 241.3594 Evaluate side-chains 258 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 4.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 423 optimal weight: 0.9990 chunk 543 optimal weight: 0.5980 chunk 420 optimal weight: 30.0000 chunk 626 optimal weight: 40.0000 chunk 415 optimal weight: 8.9990 chunk 741 optimal weight: 6.9990 chunk 463 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46760 Z= 0.245 Angle : 0.504 10.156 64558 Z= 0.268 Chirality : 0.040 0.159 8260 Planarity : 0.004 0.052 8752 Dihedral : 3.954 29.180 8051 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.14 (0.10), residues: 7676 helix: 3.01 (0.08), residues: 4475 sheet: -1.63 (0.21), residues: 641 loop : -0.72 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.004 0.001 HIS A 576 PHE 0.021 0.001 PHE E 293 TYR 0.019 0.001 TYR I 70 ARG 0.004 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 5.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8466 (tmm) cc_final: 0.8251 (tmm) REVERT: D 62 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8564 (tm-30) REVERT: E 37 MET cc_start: 0.9111 (mmp) cc_final: 0.8859 (mmp) REVERT: E 298 MET cc_start: 0.8125 (ppp) cc_final: 0.7861 (ppp) REVERT: F 305 MET cc_start: 0.8726 (ttt) cc_final: 0.8388 (tpp) REVERT: G 61 GLN cc_start: 0.8463 (pp30) cc_final: 0.8193 (pp30) REVERT: G 91 ASN cc_start: 0.9003 (m110) cc_final: 0.8800 (m110) REVERT: I 87 ASP cc_start: 0.7950 (m-30) cc_final: 0.7676 (m-30) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.4869 time to fit residues: 240.0249 Evaluate side-chains 258 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 0.8980 chunk 295 optimal weight: 0.7980 chunk 442 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 471 optimal weight: 50.0000 chunk 504 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 582 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN D 328 GLN F 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46760 Z= 0.172 Angle : 0.476 10.314 64558 Z= 0.250 Chirality : 0.039 0.149 8260 Planarity : 0.003 0.052 8752 Dihedral : 3.843 28.277 8051 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.26 (0.10), residues: 7676 helix: 3.08 (0.08), residues: 4484 sheet: -1.53 (0.20), residues: 667 loop : -0.63 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 47 HIS 0.004 0.001 HIS A 576 PHE 0.044 0.001 PHE A 293 TYR 0.015 0.001 TYR F 139 ARG 0.006 0.000 ARG G 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 305 MET cc_start: 0.8471 (tmm) cc_final: 0.8255 (tmm) REVERT: E 37 MET cc_start: 0.9138 (mmp) cc_final: 0.8911 (mmp) REVERT: E 42 MET cc_start: 0.7811 (tpp) cc_final: 0.7113 (tmm) REVERT: E 298 MET cc_start: 0.8091 (ppp) cc_final: 0.7813 (ppp) REVERT: F 305 MET cc_start: 0.8705 (ttt) cc_final: 0.8375 (tpp) REVERT: I 87 ASP cc_start: 0.7757 (m-30) cc_final: 0.7478 (m-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.4942 time to fit residues: 243.5036 Evaluate side-chains 259 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 5.9990 chunk 710 optimal weight: 5.9990 chunk 647 optimal weight: 5.9990 chunk 690 optimal weight: 20.0000 chunk 709 optimal weight: 5.9990 chunk 415 optimal weight: 20.0000 chunk 300 optimal weight: 0.9990 chunk 542 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 624 optimal weight: 40.0000 chunk 653 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN F 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 46760 Z= 0.266 Angle : 0.516 10.167 64558 Z= 0.275 Chirality : 0.040 0.162 8260 Planarity : 0.004 0.075 8752 Dihedral : 3.928 28.387 8051 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.18 (0.10), residues: 7676 helix: 3.03 (0.08), residues: 4480 sheet: -1.61 (0.21), residues: 641 loop : -0.69 (0.13), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 47 HIS 0.004 0.001 HIS E 166 PHE 0.030 0.001 PHE A 293 TYR 0.017 0.001 TYR D 43 ARG 0.007 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 MET cc_start: 0.7871 (tpp) cc_final: 0.7158 (tmm) REVERT: E 298 MET cc_start: 0.8092 (ppp) cc_final: 0.7834 (ppp) REVERT: F 305 MET cc_start: 0.8740 (ttt) cc_final: 0.8407 (tpp) REVERT: G 49 LYS cc_start: 0.8253 (mtmm) cc_final: 0.8038 (mtmm) REVERT: G 61 GLN cc_start: 0.8455 (pp30) cc_final: 0.8194 (pp30) REVERT: G 91 ASN cc_start: 0.8987 (m110) cc_final: 0.8783 (m110) REVERT: I 87 ASP cc_start: 0.7818 (m-30) cc_final: 0.7570 (m-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.5389 time to fit residues: 262.9332 Evaluate side-chains 253 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 30.0000 chunk 453 optimal weight: 50.0000 chunk 730 optimal weight: 8.9990 chunk 445 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 507 optimal weight: 50.0000 chunk 766 optimal weight: 4.9990 chunk 705 optimal weight: 0.9990 chunk 610 optimal weight: 0.0170 chunk 63 optimal weight: 6.9990 chunk 471 optimal weight: 40.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46760 Z= 0.231 Angle : 0.504 10.212 64558 Z= 0.267 Chirality : 0.040 0.210 8260 Planarity : 0.004 0.063 8752 Dihedral : 3.909 27.704 8051 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.21 (0.10), residues: 7676 helix: 3.05 (0.08), residues: 4497 sheet: -1.55 (0.21), residues: 633 loop : -0.71 (0.13), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 542 HIS 0.004 0.001 HIS A 576 PHE 0.029 0.001 PHE A 293 TYR 0.017 0.001 TYR D 43 ARG 0.005 0.000 ARG G 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 MET cc_start: 0.7861 (tpp) cc_final: 0.7145 (tmm) REVERT: E 321 MET cc_start: 0.8979 (mtp) cc_final: 0.8431 (mtp) REVERT: E 349 MET cc_start: 0.8601 (ptp) cc_final: 0.8109 (ptp) REVERT: F 305 MET cc_start: 0.8735 (ttt) cc_final: 0.8402 (tpp) REVERT: G 61 GLN cc_start: 0.8452 (pp30) cc_final: 0.8197 (pp30) REVERT: I 87 ASP cc_start: 0.7791 (m-30) cc_final: 0.7532 (m-30) REVERT: K 72 MET cc_start: 0.8392 (mmm) cc_final: 0.7823 (mmm) REVERT: K 91 ASN cc_start: 0.9394 (m-40) cc_final: 0.8898 (m110) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.4866 time to fit residues: 238.5423 Evaluate side-chains 254 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 10.0000 chunk 484 optimal weight: 50.0000 chunk 649 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 562 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 611 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 627 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.066088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035720 restraints weight = 340388.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035726 restraints weight = 303857.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035713 restraints weight = 229209.319| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46760 Z= 0.218 Angle : 0.497 10.244 64558 Z= 0.263 Chirality : 0.040 0.177 8260 Planarity : 0.003 0.053 8752 Dihedral : 3.862 27.078 8051 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % 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: 2.25 (0.10), residues: 7676 helix: 3.07 (0.08), residues: 4502 sheet: -1.49 (0.21), residues: 645 loop : -0.69 (0.13), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 47 HIS 0.004 0.001 HIS A 549 PHE 0.030 0.001 PHE A 293 TYR 0.015 0.001 TYR D 43 ARG 0.004 0.000 ARG C 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7203.67 seconds wall clock time: 131 minutes 8.23 seconds (7868.23 seconds total)