Starting phenix.real_space_refine on Mon Mar 25 03:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uw9_26825/03_2024/7uw9_26825.pdb" } resolution = 4.2 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= 0.034 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 28808 2.51 5 N 8565 2.21 5 O 8695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "F PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 196": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46156 Number of models: 1 Model: "" Number of chains: 31 Chain: "P" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2099 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PTRANS': 18, 'TRANS': 403} Chain breaks: 1 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1370 Unresolved non-hydrogen angles: 1760 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 27, 'TYR:plan': 13, 'ASN:plan1': 13, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 27, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 700 Chain: "E" 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: "F" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3167 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 24, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 450 Unresolved non-hydrogen angles: 548 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 23, 'TYR:plan': 2, 'ASN:plan1': 14, 'HIS:plan': 1, 'GLU:plan': 31, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 343 Chain: "A" 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: "B" 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: "C" 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: "D" 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: "M" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1109 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 3, 'TRANS': 209} Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 735 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 300 Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 544 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "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: "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 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: "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: "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 Time building chain proxies: 24.15, per 1000 atoms: 0.52 Number of scatterers: 46156 At special positions: 0 Unit cell: (150.381, 184.338, 268.422, 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 8695 8.00 N 8565 7.00 C 28808 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: 20.18 Conformation dependent library (CDL) restraints added in 10.1 seconds 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14412 Finding SS restraints... Secondary structure from input PDB file: 292 helices and 41 sheets defined 66.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'P' and resid 1 through 14 removed outlier: 4.219A pdb=" N ARG P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 24 Processing helix chain 'P' and resid 28 through 40 Processing helix chain 'P' and resid 40 through 47 Processing helix chain 'P' and resid 49 through 54 Processing helix chain 'P' and resid 54 through 68 removed outlier: 3.967A pdb=" N ILE P 68 " --> pdb=" O ILE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 87 Processing helix chain 'P' and resid 91 through 101 removed outlier: 3.932A pdb=" N PHE P 95 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS P 96 " --> pdb=" O ALA P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 112 removed outlier: 3.787A pdb=" N THR P 105 " --> pdb=" O ALA P 101 " (cutoff:3.500A) Proline residue: P 108 - end of helix removed outlier: 3.845A pdb=" N ARG P 111 " --> pdb=" O GLU P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 129 removed outlier: 4.175A pdb=" N CYS P 125 " --> pdb=" O GLN P 121 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS P 126 " --> pdb=" O GLU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 162 Processing helix chain 'P' and resid 168 through 173 Processing helix chain 'P' and resid 182 through 196 removed outlier: 4.279A pdb=" N ALA P 186 " --> pdb=" O GLY P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 206 Processing helix chain 'P' and resid 208 through 213 Processing helix chain 'P' and resid 223 through 241 Processing helix chain 'P' and resid 241 through 250 Processing helix chain 'P' and resid 253 through 264 Processing helix chain 'P' and resid 266 through 280 Processing helix chain 'P' and resid 284 through 305 Proline residue: P 296 - end of helix Processing helix chain 'P' and resid 309 through 337 removed outlier: 3.622A pdb=" N LEU P 313 " --> pdb=" O ASP P 309 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 332 " --> pdb=" O LYS P 328 " (cutoff:3.500A) Processing helix chain 'P' and resid 337 through 343 Processing helix chain 'P' and resid 348 through 353 Processing helix chain 'P' and resid 353 through 366 Processing helix chain 'P' and resid 369 through 381 Processing helix chain 'P' and resid 384 through 402 Processing helix chain 'P' and resid 402 through 412 removed outlier: 3.897A pdb=" N ARG P 406 " --> pdb=" O HIS P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 424 removed outlier: 3.728A pdb=" N ARG P 417 " --> pdb=" O LYS P 413 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN P 423 " --> pdb=" O MET P 419 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 445 removed outlier: 3.752A pdb=" N GLY P 443 " --> pdb=" O ARG P 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 296 Proline residue: E 294 - end of helix Processing helix chain 'E' and resid 322 through 343 removed outlier: 4.244A pdb=" N ILE E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 369 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 415 through 419 removed outlier: 4.239A pdb=" N ASP E 419 " --> pdb=" O PRO E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.675A pdb=" N ALA E 443 " --> pdb=" O ASP E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 464 through 472 Processing helix chain 'E' and resid 474 through 499 removed outlier: 3.903A pdb=" N GLU E 494 " --> pdb=" O ASP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 522 Processing helix chain 'E' and resid 536 through 558 Processing helix chain 'E' and resid 570 through 578 Processing helix chain 'E' and resid 578 through 591 removed outlier: 4.091A pdb=" N LYS E 589 " --> pdb=" O LEU E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 595 Processing helix chain 'E' and resid 596 through 619 Processing helix chain 'F' and resid 98 through 102 Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 172 through 184 Processing helix chain 'F' and resid 187 through 192 Processing helix chain 'F' and resid 215 through 228 Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'F' and resid 245 through 265 Proline residue: F 253 - end of helix Processing helix chain 'F' and resid 277 through 292 removed outlier: 3.994A pdb=" N TYR F 281 " --> pdb=" O ASP F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 315 removed outlier: 3.978A pdb=" N ARG F 315 " --> pdb=" O GLN F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 338 Processing helix chain 'F' and resid 341 through 351 Processing helix chain 'F' and resid 358 through 364 removed outlier: 3.513A pdb=" N GLN F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 391 through 418 removed outlier: 4.712A pdb=" N ASP F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 440 Processing helix chain 'F' and resid 450 through 463 Processing helix chain 'F' and resid 477 through 482 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.648A pdb=" N SER A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.580A pdb=" N MET A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.527A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 369 removed outlier: 3.960A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.638A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 460 through 463 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.303A pdb=" N GLU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.805A 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 534 removed outlier: 4.608A pdb=" N PHE A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 561 removed outlier: 3.586A pdb=" N GLY A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.805A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 596 through 614 Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.996A pdb=" N ARG B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 277 through 293 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.619A pdb=" N GLY B 300 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 392 through 418 Processing helix chain 'B' and resid 423 through 440 Processing helix chain 'B' and resid 451 through 465 removed outlier: 4.067A pdb=" N PHE B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 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 257 through 269 removed outlier: 4.290A pdb=" N ILE C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.748A pdb=" N MET C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.876A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 311' Processing helix chain 'C' and resid 324 through 343 removed outlier: 4.503A pdb=" N ALA C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 368 removed outlier: 3.817A pdb=" N TRP C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 391 Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.187A pdb=" N ASP C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 432 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.543A pdb=" N ALA C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 472 Processing helix chain 'C' and resid 473 through 500 removed outlier: 4.395A pdb=" N ASN C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 514 through 522 Processing helix chain 'C' and resid 529 through 534 removed outlier: 4.571A pdb=" N PHE C 534 " --> pdb=" O PRO C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 560 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 570 through 578 Processing helix chain 'C' and resid 578 through 588 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 removed outlier: 3.704A pdb=" N GLU C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 592 through 595' Processing helix chain 'C' and resid 596 through 621 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.693A pdb=" N ASP D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 230 through 233 removed outlier: 3.820A pdb=" N GLU D 233 " --> pdb=" O GLY D 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 247 through 265 removed outlier: 3.564A pdb=" N ILE D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Proline residue: D 253 - end of helix removed outlier: 4.242A pdb=" N LEU D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 293 Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.680A pdb=" N GLY D 300 " --> pdb=" O GLY D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 314 removed outlier: 3.996A pdb=" N ILE D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) 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: 4.119A pdb=" N TYR D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 removed outlier: 3.524A pdb=" N LEU D 422 " --> pdb=" O GLU D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 425 through 439 Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.684A pdb=" N LEU D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 481 removed outlier: 3.897A pdb=" N LEU D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR D 481 " --> pdb=" O THR D 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 76 removed outlier: 4.825A pdb=" N GLY M 59 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 221 removed outlier: 3.513A pdb=" N ARG M 136 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU M 144 " --> pdb=" O VAL M 140 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU M 174 " --> pdb=" O VAL M 170 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN M 175 " --> pdb=" O ASN M 171 " (cutoff:3.500A) Proline residue: M 179 - end of helix removed outlier: 4.438A pdb=" N GLU M 194 " --> pdb=" O GLY M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 27 removed outlier: 4.007A pdb=" N GLY N 26 " --> pdb=" O ASP N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.859A pdb=" N LEU N 37 " --> pdb=" O GLY N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 62 Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 80 through 89 removed outlier: 3.903A pdb=" N PHE N 83 " --> pdb=" O MET N 80 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP N 86 " --> pdb=" O PHE N 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 89 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 118 Processing helix chain 'b' and resid 275 through 297 removed outlier: 4.078A pdb=" N UNK b 290 " --> pdb=" O UNK b 286 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N UNK b 291 " --> pdb=" O UNK b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 304 removed outlier: 3.983A pdb=" N UNK b 303 " --> pdb=" O UNK b 299 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 19 removed outlier: 4.019A pdb=" N VAL c 18 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS c 19 " --> pdb=" O ARG c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 56 removed outlier: 3.606A pdb=" N PHE c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA c 33 " --> pdb=" O GLY c 29 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE c 34 " --> pdb=" O ILE c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 91 Processing helix chain 'c' and resid 101 through 143 removed outlier: 3.535A pdb=" N ALA c 121 " --> pdb=" O ILE c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 147 through 172 Processing helix chain 'd' and resid 7 through 12 Processing helix chain 'd' and resid 13 through 27 removed outlier: 3.513A pdb=" N LEU d 27 " --> pdb=" O TYR d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 86 Processing helix chain 'd' and resid 93 through 114 Processing helix chain 'd' and resid 121 through 129 Processing helix chain 'd' and resid 148 through 156 removed outlier: 3.698A pdb=" N VAL d 156 " --> pdb=" O ARG d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 168 removed outlier: 3.610A pdb=" N PHE d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 176 removed outlier: 3.636A pdb=" N MET d 176 " --> pdb=" O LEU d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 198 Processing helix chain 'd' and resid 202 through 227 Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 252 through 257 Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.670A pdb=" N GLY d 266 " --> pdb=" O ASP d 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL d 267 " --> pdb=" O GLN d 263 " (cutoff:3.500A) Processing helix chain 'd' and resid 293 through 305 Processing helix chain 'd' and resid 313 through 332 Processing helix chain 'g' and resid 9 through 45 removed outlier: 3.608A pdb=" N VAL g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 removed outlier: 3.812A pdb=" N LYS g 53 " --> pdb=" O GLU g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 79 removed outlier: 3.565A pdb=" N ILE g 79 " --> pdb=" O ILE g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 126 removed outlier: 3.776A pdb=" N ALA g 118 " --> pdb=" O ILE g 114 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG g 121 " --> pdb=" O ASP g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 160 removed outlier: 3.549A pdb=" N GLY g 159 " --> pdb=" O SER g 155 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN g 160 " --> pdb=" O SER g 156 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 47 Processing helix chain 'h' and resid 47 through 54 removed outlier: 3.563A pdb=" N VAL h 51 " --> pdb=" O ARG h 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET h 52 " --> pdb=" O PRO h 48 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS h 53 " --> pdb=" O GLU h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 79 Processing helix chain 'h' and resid 87 through 126 removed outlier: 4.202A pdb=" N GLY h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG h 121 " --> pdb=" O ASP h 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA h 124 " --> pdb=" O VAL h 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN h 125 " --> pdb=" O ARG h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 157 removed outlier: 4.454A pdb=" N GLY h 132 " --> pdb=" O LYS h 128 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 44 removed outlier: 4.000A pdb=" N PHE i 13 " --> pdb=" O THR i 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU i 22 " --> pdb=" O ALA i 18 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 49 No H-bonds generated for 'chain 'i' and resid 47 through 49' Processing helix chain 'i' and resid 50 through 79 removed outlier: 3.733A pdb=" N VAL i 56 " --> pdb=" O MET i 52 " (cutoff:3.500A) Proline residue: i 57 - end of helix Processing helix chain 'i' and resid 88 through 124 removed outlier: 3.896A pdb=" N TYR i 92 " --> pdb=" O LEU i 88 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA i 124 " --> pdb=" O VAL i 120 " (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: 3.901A pdb=" N LEU i 143 " --> pdb=" O PHE i 139 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA i 144 " --> pdb=" O ALA i 140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG i 157 " --> pdb=" O ILE i 153 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 163 Processing helix chain 'j' and resid 9 through 47 removed outlier: 3.546A pdb=" N LEU j 16 " --> pdb=" O PHE j 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU j 22 " --> pdb=" O ALA j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 54 Processing helix chain 'j' and resid 54 through 79 removed outlier: 4.515A pdb=" N VAL j 58 " --> pdb=" O SER j 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE j 79 " --> pdb=" O ILE j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 126 removed outlier: 3.544A pdb=" N GLY j 91 " --> pdb=" O TYR j 87 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS j 94 " --> pdb=" O ASP j 90 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA j 124 " --> pdb=" O VAL j 120 " (cutoff:3.500A) Processing helix chain 'j' and resid 126 through 157 removed outlier: 3.813A pdb=" N LEU j 135 " --> pdb=" O VAL j 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE j 136 " --> pdb=" O GLY j 132 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 161 Processing helix chain 'k' and resid 9 through 47 Processing helix chain 'k' and resid 47 through 52 removed outlier: 3.981A pdb=" N MET k 52 " --> pdb=" O PRO k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 79 removed outlier: 3.937A pdb=" N ILE k 79 " --> pdb=" O ILE k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 126 removed outlier: 3.872A pdb=" N GLY k 91 " --> pdb=" O TYR k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 160 removed outlier: 3.986A pdb=" N VAL k 131 " --> pdb=" O PRO k 127 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA k 142 " --> pdb=" O ILE k 138 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU k 143 " --> pdb=" O PHE k 139 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA k 144 " --> pdb=" O ALA k 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 47 removed outlier: 3.629A pdb=" N PHE l 13 " --> pdb=" O THR l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 55 removed outlier: 3.537A pdb=" N MET l 52 " --> pdb=" O PRO l 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS l 53 " --> pdb=" O GLU l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 79 removed outlier: 3.551A pdb=" N VAL l 59 " --> pdb=" O ILE l 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU l 64 " --> pdb=" O MET l 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 126 removed outlier: 4.046A pdb=" N GLY l 91 " --> pdb=" O TYR l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 157 Processing helix chain 'm' and resid 9 through 47 removed outlier: 3.576A pdb=" N SER m 42 " --> pdb=" O VAL m 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET m 46 " --> pdb=" O SER m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 55 Processing helix chain 'm' and resid 55 through 77 Processing helix chain 'm' and resid 87 through 125 Processing helix chain 'm' and resid 126 through 160 removed outlier: 3.701A pdb=" N PHE m 130 " --> pdb=" O GLN m 126 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU m 143 " --> pdb=" O PHE m 139 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA m 144 " --> pdb=" O ALA m 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU m 145 " --> pdb=" O GLU m 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 47 removed outlier: 3.723A pdb=" N GLY n 39 " --> pdb=" O LYS n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 76 removed outlier: 3.662A pdb=" N MET n 52 " --> pdb=" O PRO n 48 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL n 56 " --> pdb=" O MET n 52 " (cutoff:3.500A) Proline residue: n 57 - end of helix removed outlier: 3.850A pdb=" N ALA n 72 " --> pdb=" O GLY n 68 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL n 73 " --> pdb=" O LEU n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 123 removed outlier: 3.935A pdb=" N GLY n 91 " --> pdb=" O TYR n 87 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA n 118 " --> pdb=" O ILE n 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 158 removed outlier: 3.828A pdb=" N PHE n 130 " --> pdb=" O GLN n 126 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL n 131 " --> pdb=" O PRO n 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA n 140 " --> pdb=" O ILE n 136 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU n 143 " --> pdb=" O PHE n 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 159 through 161 No H-bonds generated for 'chain 'n' and resid 159 through 161' Processing helix chain 'o' and resid 10 through 47 removed outlier: 4.076A pdb=" N LEU o 22 " --> pdb=" O ALA o 18 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR o 31 " --> pdb=" O MET o 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY o 32 " --> pdb=" O GLY o 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER o 42 " --> pdb=" O VAL o 38 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET o 46 " --> pdb=" O SER o 42 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG o 47 " --> pdb=" O MET o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 47 through 78 Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 87 through 125 Processing helix chain 'o' and resid 129 through 157 Processing helix chain 'r' and resid 333 through 353 removed outlier: 3.662A pdb=" N UNK r 339 " --> pdb=" O UNK r 335 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N UNK r 350 " --> pdb=" O UNK r 346 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK r 351 " --> pdb=" O UNK r 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 45 removed outlier: 3.689A pdb=" N VAL G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 55 removed outlier: 3.843A pdb=" N LYS G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 105 removed outlier: 3.788A pdb=" N ILE G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 126 removed outlier: 4.188A pdb=" N LYS G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 204 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 107 removed outlier: 3.617A pdb=" N LYS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 106 removed outlier: 3.715A pdb=" N ASP I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 126 removed outlier: 3.510A pdb=" N TYR I 110 " --> pdb=" O ASP I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'I' and resid 147 through 157 Processing helix chain 'I' and resid 174 through 178 removed outlier: 4.354A pdb=" N GLY I 177 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 4.389A 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 205 through 225 Proline residue: I 218 - end of helix Processing helix chain 'J' and resid 15 through 89 removed outlier: 3.550A pdb=" N ALA J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS J 22 " --> pdb=" O GLN J 18 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 105 removed outlier: 3.793A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 104 removed outlier: 3.600A pdb=" N ALA K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 126 Processing helix chain 'K' and resid 138 through 157 removed outlier: 4.256A pdb=" N GLU K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER K 148 " --> pdb=" O SER K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 226 Proline residue: K 218 - end of helix removed outlier: 3.603A pdb=" N SER K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 107 removed outlier: 3.611A pdb=" N GLU L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASP L 96 " --> pdb=" O LYS L 92 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR L 107 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 48 through 81 removed outlier: 4.950A pdb=" N VAL O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS O 61 " --> pdb=" O ASP O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.723A pdb=" N GLY O 85 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE O 86 " --> pdb=" O VAL O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 87 through 92 Processing helix chain 'O' and resid 93 through 96 Processing helix chain 'O' and resid 97 through 104 removed outlier: 3.759A pdb=" N THR O 103 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 109 removed outlier: 3.687A pdb=" N GLU O 109 " --> pdb=" O VAL O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 153 removed outlier: 3.563A pdb=" N ASP O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP O 134 " --> pdb=" O ALA O 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP O 135 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE O 153 " --> pdb=" O GLN O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 169 removed outlier: 3.760A pdb=" N SER O 167 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 241 Processing helix chain 'O' and resid 253 through 309 removed outlier: 4.232A pdb=" N LEU O 278 " --> pdb=" O LEU O 274 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU O 279 " --> pdb=" O ARG O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 323 through 334 Processing helix chain 'O' and resid 335 through 338 removed outlier: 4.014A pdb=" N CYS O 338 " --> pdb=" O GLU O 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 335 through 338' Processing helix chain 'a' and resid 32 through 44 removed outlier: 3.768A pdb=" N LEU a 38 " --> pdb=" O GLU a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 59 Processing helix chain 'a' and resid 65 through 90 Processing helix chain 'a' and resid 108 through 149 Processing helix chain 'a' and resid 149 through 161 Processing helix chain 'a' and resid 205 through 212 Processing helix chain 'a' and resid 213 through 218 removed outlier: 3.587A pdb=" N ARG a 218 " --> pdb=" O PHE a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 267 removed outlier: 3.538A pdb=" N GLY a 267 " --> pdb=" O CYS a 263 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 336 removed outlier: 4.251A pdb=" N THR a 311 " --> pdb=" O ASN a 307 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU a 321 " --> pdb=" O GLU a 317 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 357 removed outlier: 3.754A pdb=" N LYS a 357 " --> pdb=" O PHE a 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 354 through 357' Processing helix chain 'a' and resid 358 through 371 removed outlier: 3.785A pdb=" N ALA a 362 " --> pdb=" O GLN a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 407 removed outlier: 4.320A pdb=" N PHE a 400 " --> pdb=" O PHE a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 433 removed outlier: 3.930A pdb=" N VAL a 423 " --> pdb=" O VAL a 419 " (cutoff:3.500A) Proline residue: a 426 - end of helix Processing helix chain 'a' and resid 435 through 452 Processing helix chain 'a' and resid 452 through 459 Processing helix chain 'a' and resid 463 through 471 removed outlier: 3.648A pdb=" N MET a 467 " --> pdb=" O ASP a 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 490 removed outlier: 3.577A pdb=" N TYR a 484 " --> pdb=" O LEU a 480 " (cutoff:3.500A) Processing helix chain 'a' and resid 532 through 537 Processing helix chain 'a' and resid 541 through 576 Processing helix chain 'a' and resid 579 through 610 removed outlier: 4.041A pdb=" N ILE a 586 " --> pdb=" O TRP a 582 " (cutoff:3.500A) Proline residue: a 587 - end of helix removed outlier: 4.288A pdb=" N ILE a 590 " --> pdb=" O ILE a 586 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE a 591 " --> pdb=" O PRO a 587 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU a 592 " --> pdb=" O GLN a 588 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN a 593 " --> pdb=" O ILE a 589 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU a 599 " --> pdb=" O LEU a 595 " (cutoff:3.500A) Processing helix chain 'a' and resid 614 through 616 No H-bonds generated for 'chain 'a' and resid 614 through 616' Processing helix chain 'a' and resid 617 through 624 Processing helix chain 'a' and resid 638 through 657 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 756 Processing helix chain 'a' and resid 759 through 779 removed outlier: 3.624A pdb=" N LEU a 763 " --> pdb=" O ASN a 759 " (cutoff:3.500A) Processing helix chain 'a' and resid 780 through 802 Processing helix chain 'e' and resid 4 through 26 Processing helix chain 'e' and resid 28 through 58 Processing sheet with id=AA1, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.534A pdb=" N ALA E 34 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=AA3, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.083A pdb=" N PHE E 102 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR E 318 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 273 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER E 221 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AA5, first strand: chain 'E' and resid 148 through 149 removed outlier: 7.126A pdb=" N GLU E 195 " --> pdb=" O THR E 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 228 through 229 removed outlier: 4.838A pdb=" N SER E 242 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 412 through 413 removed outlier: 6.607A pdb=" N VAL E 413 " --> pdb=" O CYS E 248 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE E 250 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.578A pdb=" N GLU E 306 " --> pdb=" O MET E 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 372 through 374 removed outlier: 6.681A pdb=" N TYR E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 21 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 63 removed outlier: 4.674A 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 'A' and resid 31 through 35 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 31 through 35 current: chain 'A' and resid 53 through 60 removed outlier: 3.552A pdb=" N GLU A 56 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 66 " --> pdb=" O ILE A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 65 through 68 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 64 removed outlier: 6.842A pdb=" N VAL B 69 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL B 63 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 67 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 53 through 61 removed outlier: 6.644A pdb=" N ILE C 57 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN C 68 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C 59 " --> pdb=" O THR C 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 64 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: 6.978A pdb=" N VAL D 69 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL D 63 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.072A 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 'I' and resid 189 through 194 removed outlier: 5.415A pdb=" N ILE I 199 " --> pdb=" O SER I 194 " (cutoff:3.500A) 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: 3.682A pdb=" N VAL K 190 " --> pdb=" O ASN K 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 94 through 97 Processing sheet with id=AB3, first strand: chain 'F' and resid 105 through 106 removed outlier: 6.061A pdb=" N PHE F 106 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU F 241 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA F 206 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE F 274 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL F 208 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 276 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA F 210 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL F 271 " --> pdb=" O THR F 327 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE F 329 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 273 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 331 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU F 275 " --> pdb=" O ILE F 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 137 through 138 removed outlier: 4.372A pdb=" N ARG F 318 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB6, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AB7, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.695A pdb=" N TRP A 211 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 101 through 102 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 101 through 102 current: chain 'A' and resid 312 through 315 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 312 through 315 current: chain 'A' and resid 404 through 412 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AC1, first strand: chain 'A' and resid 148 through 149 removed outlier: 6.780A pdb=" N GLU A 195 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 181 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 193 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 194 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 158 through 161 removed outlier: 7.187A pdb=" N MET A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AC4, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AC5, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.433A pdb=" N PHE B 106 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU B 241 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 212 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AC7, first strand: chain 'B' and resid 332 through 333 removed outlier: 6.129A pdb=" N LEU B 165 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N GLN B 354 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU B 373 " --> pdb=" O GLN B 354 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 356 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.673A pdb=" N VAL C 91 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP C 211 " --> pdb=" O VAL C 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AD1, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.748A pdb=" N THR C 179 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU C 195 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 181 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 193 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 194 " --> pdb=" O PHE C 205 " (cutoff:3.500A) Processing sheet with id=AD2, 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 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 312 through 314 current: chain 'C' and resid 406 through 412 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 406 through 412 current: chain 'C' and resid 457 through 458 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 228 through 229 removed outlier: 4.737A pdb=" N SER C 242 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 372 through 374 Processing sheet with id=AD5, first strand: chain 'D' and resid 86 through 88 removed outlier: 4.072A pdb=" N MET D 19 " --> pdb=" O PHE D 88 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.637A pdb=" N LEU D 125 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 105 through 106 removed outlier: 5.779A pdb=" N PHE D 106 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU D 241 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 208 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR D 276 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ALA D 210 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 271 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE D 329 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 273 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 137 through 138 removed outlier: 3.996A pdb=" N ARG D 318 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE1, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AE2, first strand: chain 'M' and resid 96 through 102 removed outlier: 3.858A pdb=" N GLU M 111 " --> pdb=" O ARG M 96 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG M 98 " --> pdb=" O LYS M 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 190 through 191 Processing sheet with id=AE4, first strand: chain 'a' and resid 337 through 339 removed outlier: 3.801A pdb=" N SER a 337 " --> pdb=" O VAL a 346 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER a 351 " --> pdb=" O GLN a 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN a 25 " --> pdb=" O SER a 351 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE a 30 " --> pdb=" O ILE a 377 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE a 377 " --> pdb=" O ILE a 30 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 195 through 197 removed outlier: 3.539A pdb=" N TYR a 250 " --> pdb=" O GLY a 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE a 197 " --> pdb=" O VAL a 248 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL a 248 " --> pdb=" O ILE a 197 " (cutoff:3.500A) 3899 hydrogen bonds defined for protein. 11475 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: 19.95 Time building geometry restraints manager: 21.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8144 1.32 - 1.44: 10979 1.44 - 1.57: 27489 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 46758 Sorted by residual: bond pdb=" CA SER D 280 " pdb=" CB SER D 280 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.56e-02 4.11e+03 1.40e+01 bond pdb=" CA SER D 279 " pdb=" CB SER D 279 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.07e+01 bond pdb=" C PRO D 253 " pdb=" O PRO D 253 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 1.02e+01 bond pdb=" N VAL C 219 " pdb=" CA VAL C 219 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.14e-02 7.69e+03 9.95e+00 bond pdb=" N SER B 448 " pdb=" CA SER B 448 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.93e+00 ... (remaining 46753 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.77: 1097 105.77 - 112.90: 26102 112.90 - 120.02: 13504 120.02 - 127.15: 23481 127.15 - 134.27: 368 Bond angle restraints: 64552 Sorted by residual: angle pdb=" N ARG D 254 " pdb=" CA ARG D 254 " pdb=" C ARG D 254 " ideal model delta sigma weight residual 112.13 102.23 9.90 1.37e+00 5.33e-01 5.22e+01 angle pdb=" N MET D 278 " pdb=" CA MET D 278 " pdb=" C MET D 278 " ideal model delta sigma weight residual 111.71 103.51 8.20 1.15e+00 7.56e-01 5.09e+01 angle pdb=" N LEU D 309 " pdb=" CA LEU D 309 " pdb=" C LEU D 309 " ideal model delta sigma weight residual 112.45 102.97 9.48 1.39e+00 5.18e-01 4.65e+01 angle pdb=" N VAL I 142 " pdb=" CA VAL I 142 " pdb=" C VAL I 142 " ideal model delta sigma weight residual 110.62 103.76 6.86 1.02e+00 9.61e-01 4.53e+01 angle pdb=" N SER I 148 " pdb=" CA SER I 148 " pdb=" C SER I 148 " ideal model delta sigma weight residual 111.36 104.71 6.65 1.09e+00 8.42e-01 3.72e+01 ... (remaining 64547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 26202 16.79 - 33.58: 892 33.58 - 50.37: 193 50.37 - 67.16: 37 67.16 - 83.95: 13 Dihedral angle restraints: 27337 sinusoidal: 5014 harmonic: 22323 Sorted by residual: dihedral pdb=" CA ILE D 350 " pdb=" C ILE D 350 " pdb=" N THR D 351 " pdb=" CA THR D 351 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TYR a 803 " pdb=" C TYR a 803 " pdb=" N GLU a 804 " pdb=" CA GLU a 804 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C GLU D 320 " pdb=" N GLU D 320 " pdb=" CA GLU D 320 " pdb=" CB GLU D 320 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 27334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 7060 0.060 - 0.121: 1101 0.121 - 0.181: 73 0.181 - 0.241: 13 0.241 - 0.302: 5 Chirality restraints: 8252 Sorted by residual: chirality pdb=" CA VAL A 410 " pdb=" N VAL A 410 " pdb=" C VAL A 410 " pdb=" CB VAL A 410 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA VAL I 142 " pdb=" N VAL I 142 " pdb=" C VAL I 142 " pdb=" CB VAL I 142 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS I 115 " pdb=" N LYS I 115 " pdb=" C LYS I 115 " pdb=" CB LYS I 115 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 8249 not shown) Planarity restraints: 8749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 620 " 0.038 2.00e-02 2.50e+03 7.40e-02 5.48e+01 pdb=" C ASP C 620 " -0.128 2.00e-02 2.50e+03 pdb=" O ASP C 620 " 0.048 2.00e-02 2.50e+03 pdb=" N GLU C 621 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 135 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C SER D 135 " 0.079 2.00e-02 2.50e+03 pdb=" O SER D 135 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU D 136 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 248 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU D 248 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU D 248 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG D 249 " -0.019 2.00e-02 2.50e+03 ... (remaining 8746 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5860 2.75 - 3.28: 50453 3.28 - 3.82: 82455 3.82 - 4.36: 81156 4.36 - 4.90: 141094 Nonbonded interactions: 361018 Sorted by model distance: nonbonded pdb=" O LEU F 373 " pdb=" OH TYR F 401 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR A 318 " pdb=" OD1 ASN A 320 " model vdw 2.212 2.440 nonbonded pdb=" O ALA A 427 " pdb=" OG SER A 430 " model vdw 2.213 2.440 nonbonded pdb=" ND2 ASN C 320 " pdb=" O GLU D 314 " model vdw 2.221 2.520 nonbonded pdb=" OG1 THR A 354 " pdb=" O ALA A 412 " model vdw 2.230 2.440 ... (remaining 361013 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 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 '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 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 )))) selection = (chain 'E' 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)) } ncs_group { reference = (chain 'B' 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 throu \ gh 53 or (resid 54 through 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 61 or (resid 62 and (name N or name CA or name C or n \ ame O or name CB )) or resid 63 through 70 or (resid 71 and (name N or name CA o \ r name C or name O or name CB )) or resid 72 through 80 or (resid 81 through 82 \ and (name N or name CA or name C or name O or name CB )) or resid 83 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 8 through 142 or (resid 143 and (name N or name CA or name C or name O or name C \ B )) or resid 144 or (resid 145 and (name N or name CA or name C or name O or na \ me CB )) or resid 146 through 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 16 \ 3 through 172 or (resid 173 through 175 and (name N or name CA or name 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 189 or resid 2 \ 04 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 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 260 or (resid 261 and (na \ me N or name CA or name C or name O or name CB )) or resid 262 through 291 or (r \ esid 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 nam \ e 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 309 throu \ gh 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 through 360 and (name N or name CA or name \ C or name O or name CB )) or resid 361 through 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 4 \ 03 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 resid 427 through 434 or (resid 435 and (na \ me N or name CA or name C or name O or name CB )) or resid 436 through 448 or (r \ esid 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 through 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 n \ ame C or name O or name CB )) or resid 466 or (resid 467 through 469 and (name N \ or name CA or name C or name O or name CB )) 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 throu \ gh 484)) selection = (chain 'D' 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 48 or (resid 49 and ( \ name N or name CA or name C or name O or name CB )) or resid 50 through 53 or (r \ esid 54 through 55 and (name N or name CA or name C or name O or name CB )) or r \ esid 56 through 86 or (resid 87 and (name N or name CA or name C or name O or na \ me 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 (resid 152 and (name N or na \ me CA or name C or name O or name CB )) or resid 153 or (resid 154 through 155 a \ nd (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 nam \ e CB )) or resid 163 through 172 or (resid 173 through 175 and (name N or name C \ A 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 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 204 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 24 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B )) or resid 245 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 n \ ame 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 30 \ 6 or (resid 307 through 308 and (name N or name CA or name C or name O or name C \ B )) or resid 309 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 35 \ 8 or (resid 359 through 360 and (name N or name CA or name C or name O or name C \ B )) or resid 361 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 38 \ 9 through 398 or (resid 399 and (name N or name CA or name C or name O or name C \ B )) or resid 400 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 (nam \ e N or name CA or name C or name O or name CB )) or resid 416 through 422 or (re \ sid 423 through 426 and (name N or name CA or name C or name O or name CB )) or \ resid 427 through 446 or (resid 447 and (name N or name CA or name C or name O o \ r name CB )) or resid 448 through 449 or (resid 450 and (name N or name CA or na \ me C or name O or name CB )) or resid 451 through 455 or (resid 456 and (name N \ or name CA or name 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 throug \ h 480 or (resid 481 and (name N or name CA or name C or name O or name CB )) or \ resid 482 through 484)) selection = (chain 'F' 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 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) \ or resid 140 through 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 o \ r 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 throug \ h 178 or (resid 179 and (name N or name CA or name C or name O or name CB )) or \ resid 180 or (resid 181 through 184 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 189 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 219 o \ r (resid 220 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 21 through 231 or (resid 232 through 233 and (name N or name CA or name C or nam \ e 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 \ 305 and (name N or name CA or name C or name O or name CB )) or resid 306 throu \ gh 322 or (resid 323 and (name N or name CA or name C or name O or name CB )) or \ resid 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 n \ ame 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 \ 363 through 365 and (name N or name CA or name C or name O or name CB )) or res \ id 366 through 372 or (resid 373 and (name N or name CA or name C or name O or n \ ame CB )) or resid 374 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 or (resid 390 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 403 or (resid 404 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 07 through 421 or (resid 422 through 426 and (name N or name CA or name C or nam \ e 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 \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) or \ resid 454 through 461 or (resid 462 through 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 n \ ame 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 \ 472 and (name N or name CA or name C or name O or name CB )) or resid 473 throu \ gh 479 or (resid 480 through 481 and (name N or name CA or name C or name O or n \ ame CB )) or resid 482 through 484)) } ncs_group { reference = (chain 'G' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 or (resid 108 through 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 123 or (resid \ 124 and (name N or name CA or name C or name O or name CB )) or resid 125 throug \ h 141 or (resid 142 through 158 and (name N or name CA or name C or name O or na \ me CB )) or resid 159 through 164 or resid 178 through 193 or (resid 194 through \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 or (r \ esid 198 and (name N or name CA or name C or name O or name CB )) or resid 199 t \ hrough 201 or (resid 202 through 204 and (name N or name CA or name C or name O \ or name CB )) or resid 205 through 226)) selection = (chain 'I' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 85 or (resid 86 through 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 96 or (resid 97 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 or ( \ resid 104 through 106 and (name N or name CA or name C or name O or name CB )) o \ r resid 107 or (resid 108 through 109 and (name N or name CA or name C or name O \ or name CB )) or resid 110 or (resid 111 through 112 and (name N or name CA or \ name C or name O or name CB )) or resid 113 through 126 or (resid 127 and (name \ N or name CA or name C or name O or name CB )) or resid 128 through 131 or (resi \ d 132 through 133 and (name N or name CA or name C or name O or name CB )) or re \ sid 134 through 136 or (resid 137 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 or (resid 140 through 158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 through 164 or resid 178 \ through 193 or (resid 194 through 196 and (name N or name CA or name C or name \ O or name CB )) or resid 197 or (resid 198 and (name N or name CA or name C or n \ ame O or name CB )) or resid 199 through 202 or (resid 203 through 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 or (resid 206 throu \ gh 207 and (name N or name CA or name C or name O or name CB )) or resid 208 thr \ ough 218 or (resid 219 and (name N or name CA or name C or name O or name CB )) \ or resid 220 or (resid 221 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 226)) selection = (chain 'K' and ((resid 13 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 85 or (resid 86 through 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 92 or (resid 93 throug \ h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 or ( \ resid 104 through 106 and (name N or name CA or name C or name O or name CB )) o \ r resid 107 through 123 or (resid 124 and (name N or name CA or name C or name O \ or name CB )) or resid 125 through 131 or (resid 132 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 137 or (resid 13 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 139 through \ 140 or (resid 141 through 158 and (name N or name CA or name C or name O or name \ CB )) or resid 159 through 164 or resid 178 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 218 or (resid 219 and (name N or name CA or name C or name \ O or name CB )) or resid 220 or (resid 221 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 through 226)) } ncs_group { reference = (chain 'H' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or (resid 66 through 88 and (name N or name CA or name C or name O \ or name CB )) or (resid 89 through 96 and (name N or name CA or name C or name \ O or name CB )) or resid 97 through 100 or (resid 101 and (name N or name CA or \ name C or name O or name CB )) or resid 102 through 109)) selection = (chain 'J' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 100 or (resid 101 and (name N or name CA or na \ me C or name O or name CB )) or resid 102 or (resid 103 and (name N or name CA o \ r name C or name O or name CB )) or resid 104 through 108 or (resid 109 and (nam \ e N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 14 through 65 and (name N or name CA or name C or name O \ or name CB )) or (resid 66 through 88 and (name N or name CA or name C or name O \ or name CB )) or (resid 89 through 96 and (name N or name CA or name C or name \ O or name CB )) or resid 97 through 109)) } ncs_group { reference = (chain 'g' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'h' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'i' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 43 and (name N or name CA or name C or name O \ or name CB )) or (resid 44 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name \ O or name CB )) or (resid 91 through 108 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 109 through 115 and (name N or name CA or name C or \ name O or name CB )) or (resid 116 through 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 160)) selection = (chain 'j' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'k' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 101 and (name N or name CA or name C or name \ O or name CB )) or (resid 102 through 131 and (name N or name CA or name C or n \ ame O or name CB )) or resid 132 through 160)) selection = (chain 'l' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = (chain 'm' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 108 and (name N or name CA or name C or name \ O or name CB )) or (resid 109 through 131 and (name N or name CA or name C or n \ ame O or name CB )) or resid 132 through 160)) selection = (chain 'n' and ((resid 9 through 13 and (name N or name CA or name C or name O o \ r name CB )) or (resid 14 through 61 and (name N or name CA or name C or name O \ or name CB )) or (resid 62 through 90 and (name N or name CA or name C or name O \ or name CB )) or (resid 91 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 through 160)) selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.350 Check model and map are aligned: 0.530 Set scattering table: 0.360 Process input model: 125.020 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.003 0.058 46758 Z= 0.218 Angle : 0.618 10.098 64552 Z= 0.388 Chirality : 0.042 0.302 8252 Planarity : 0.004 0.074 8749 Dihedral : 10.303 83.949 12925 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 1.21 % Allowed : 0.96 % Favored : 97.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.10), residues: 7668 helix: 2.92 (0.08), residues: 4612 sheet: -1.07 (0.21), residues: 609 loop : -0.95 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 795 HIS 0.006 0.001 HIS C 166 PHE 0.019 0.001 PHE C 293 TYR 0.023 0.001 TYR M 209 ARG 0.005 0.000 ARG E 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8054 (tmm) cc_final: 0.7775 (tmm) REVERT: E 558 VAL cc_start: -0.0291 (OUTLIER) cc_final: -0.0545 (t) REVERT: F 305 MET cc_start: 0.8138 (ptm) cc_final: 0.7931 (ptm) REVERT: A 543 MET cc_start: 0.8711 (mtm) cc_final: 0.8435 (ptm) REVERT: B 212 MET cc_start: 0.8628 (mpp) cc_final: 0.8031 (mpp) REVERT: C 215 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9078 (p) REVERT: C 309 MET cc_start: 0.8491 (tpt) cc_final: 0.8074 (tpp) REVERT: C 543 MET cc_start: 0.8983 (mtm) cc_final: 0.8771 (mtm) REVERT: D 249 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8697 (tpp80) REVERT: D 334 MET cc_start: 0.8698 (mpp) cc_final: 0.8298 (mmm) REVERT: K 72 MET cc_start: 0.8175 (mmp) cc_final: 0.7848 (mmp) REVERT: e 47 TRP cc_start: 0.8263 (t60) cc_final: 0.7994 (t60) outliers start: 29 outliers final: 9 residues processed: 294 average time/residue: 0.4833 time to fit residues: 252.8836 Evaluate side-chains 268 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 256 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 6.9990 chunk 582 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 392 optimal weight: 50.0000 chunk 310 optimal weight: 10.0000 chunk 601 optimal weight: 50.0000 chunk 232 optimal weight: 0.0010 chunk 366 optimal weight: 6.9990 chunk 448 optimal weight: 9.9990 chunk 697 optimal weight: 40.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN B 71 GLN C 186 GLN D 362 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 46758 Z= 0.316 Angle : 0.547 10.053 64552 Z= 0.303 Chirality : 0.040 0.159 8252 Planarity : 0.004 0.052 8749 Dihedral : 4.280 52.273 8047 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.10), residues: 7668 helix: 2.90 (0.07), residues: 4656 sheet: -1.27 (0.22), residues: 583 loop : -1.01 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 542 HIS 0.004 0.001 HIS E 576 PHE 0.017 0.001 PHE A 205 TYR 0.022 0.002 TYR M 209 ARG 0.005 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 5.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8007 (tmm) cc_final: 0.7746 (tmm) REVERT: B 212 MET cc_start: 0.8587 (mpp) cc_final: 0.8059 (mpp) REVERT: C 309 MET cc_start: 0.8532 (tpt) cc_final: 0.8039 (tpp) REVERT: C 543 MET cc_start: 0.9119 (mtm) cc_final: 0.8891 (mtm) REVERT: C 573 LEU cc_start: 0.9485 (tp) cc_final: 0.9272 (tp) REVERT: D 308 ASP cc_start: 0.7365 (t0) cc_final: 0.7061 (t0) REVERT: D 334 MET cc_start: 0.8801 (mpp) cc_final: 0.7987 (mpp) REVERT: e 47 TRP cc_start: 0.8334 (t60) cc_final: 0.8085 (t60) outliers start: 2 outliers final: 0 residues processed: 269 average time/residue: 0.4747 time to fit residues: 232.9508 Evaluate side-chains 253 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 4.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 387 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 580 optimal weight: 8.9990 chunk 474 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 698 optimal weight: 30.0000 chunk 754 optimal weight: 2.9990 chunk 622 optimal weight: 50.0000 chunk 692 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 560 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 555 ASN ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN e 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46758 Z= 0.184 Angle : 0.473 10.445 64552 Z= 0.258 Chirality : 0.039 0.181 8252 Planarity : 0.004 0.067 8749 Dihedral : 4.094 54.789 8047 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.10), residues: 7668 helix: 3.04 (0.07), residues: 4677 sheet: -1.22 (0.22), residues: 583 loop : -0.93 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 50 HIS 0.008 0.001 HIS e 35 PHE 0.030 0.001 PHE A 293 TYR 0.020 0.001 TYR M 209 ARG 0.004 0.000 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 4.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 291 MET cc_start: 0.7719 (ptm) cc_final: 0.7364 (ptp) REVERT: E 343 MET cc_start: 0.7948 (tmm) cc_final: 0.7621 (tmm) REVERT: A 293 PHE cc_start: 0.7385 (m-80) cc_final: 0.7108 (m-80) REVERT: C 309 MET cc_start: 0.8454 (tpt) cc_final: 0.7993 (tpp) REVERT: C 543 MET cc_start: 0.8970 (mtm) cc_final: 0.8742 (mtm) REVERT: C 573 LEU cc_start: 0.9468 (tp) cc_final: 0.9247 (tp) REVERT: D 308 ASP cc_start: 0.7406 (t0) cc_final: 0.7186 (t0) REVERT: D 334 MET cc_start: 0.8743 (mpp) cc_final: 0.6876 (mpp) REVERT: e 47 TRP cc_start: 0.8303 (t60) cc_final: 0.8052 (t60) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4880 time to fit residues: 235.9304 Evaluate side-chains 254 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 50.0000 chunk 525 optimal weight: 3.9990 chunk 362 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 469 optimal weight: 10.0000 chunk 701 optimal weight: 40.0000 chunk 742 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 664 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN D 362 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN H 85 HIS ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 46758 Z= 0.489 Angle : 0.671 17.801 64552 Z= 0.372 Chirality : 0.043 0.201 8252 Planarity : 0.005 0.098 8749 Dihedral : 4.671 57.015 8047 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 7668 helix: 2.55 (0.07), residues: 4661 sheet: -1.60 (0.22), residues: 563 loop : -1.25 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 542 HIS 0.008 0.002 HIS M 30 PHE 0.024 0.002 PHE B 83 TYR 0.030 0.002 TYR F 43 ARG 0.012 0.001 ARG F 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8006 (tmm) cc_final: 0.7443 (tmm) REVERT: B 212 MET cc_start: 0.8752 (mpp) cc_final: 0.7664 (mpp) REVERT: C 309 MET cc_start: 0.8681 (tpt) cc_final: 0.7987 (tpt) REVERT: C 543 MET cc_start: 0.9162 (mtm) cc_final: 0.8919 (mtm) REVERT: C 573 LEU cc_start: 0.9560 (tp) cc_final: 0.9326 (tp) REVERT: D 305 MET cc_start: 0.8716 (ttp) cc_final: 0.8510 (ttp) REVERT: D 308 ASP cc_start: 0.7790 (t0) cc_final: 0.7478 (t0) REVERT: D 334 MET cc_start: 0.8862 (mpp) cc_final: 0.7261 (mpp) REVERT: e 47 TRP cc_start: 0.8318 (t60) cc_final: 0.8087 (t60) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.4722 time to fit residues: 229.7598 Evaluate side-chains 255 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 5.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 1.9990 chunk 421 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 552 optimal weight: 30.0000 chunk 306 optimal weight: 20.0000 chunk 633 optimal weight: 50.0000 chunk 513 optimal weight: 10.0000 chunk 0 optimal weight: 90.0000 chunk 379 optimal weight: 20.0000 chunk 666 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN D 399 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 46758 Z= 0.468 Angle : 0.651 16.226 64552 Z= 0.363 Chirality : 0.043 0.261 8252 Planarity : 0.005 0.066 8749 Dihedral : 4.808 61.473 8047 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.10), residues: 7668 helix: 2.40 (0.07), residues: 4651 sheet: -1.79 (0.22), residues: 536 loop : -1.42 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 459 HIS 0.020 0.002 HIS G 178 PHE 0.021 0.002 PHE B 83 TYR 0.045 0.002 TYR F 43 ARG 0.012 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 5.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 286 MET cc_start: 0.9026 (mmt) cc_final: 0.8758 (mmp) REVERT: E 343 MET cc_start: 0.8112 (tmm) cc_final: 0.7534 (tmm) REVERT: A 286 MET cc_start: 0.9108 (mmm) cc_final: 0.8902 (mmt) REVERT: B 212 MET cc_start: 0.8678 (mpp) cc_final: 0.8302 (mpp) REVERT: C 309 MET cc_start: 0.8691 (tpt) cc_final: 0.8079 (tpt) REVERT: C 543 MET cc_start: 0.9173 (mtm) cc_final: 0.8874 (mtm) REVERT: C 573 LEU cc_start: 0.9532 (tp) cc_final: 0.9310 (tp) REVERT: D 305 MET cc_start: 0.8870 (ttp) cc_final: 0.8544 (ttp) REVERT: D 308 ASP cc_start: 0.7802 (t0) cc_final: 0.7575 (t0) REVERT: D 334 MET cc_start: 0.8846 (mpp) cc_final: 0.7214 (mpp) REVERT: G 92 MET cc_start: 0.8964 (mmp) cc_final: 0.8750 (mmp) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.4830 time to fit residues: 234.6610 Evaluate side-chains 254 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 6.9990 chunk 668 optimal weight: 50.0000 chunk 146 optimal weight: 4.9990 chunk 435 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 743 optimal weight: 0.0470 chunk 616 optimal weight: 30.0000 chunk 344 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 245 optimal weight: 7.9990 chunk 390 optimal weight: 50.0000 overall best weight: 1.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 555 ASN ** E 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN C 549 HIS D 87 GLN D 243 ASN D 362 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 46758 Z= 0.169 Angle : 0.491 10.489 64552 Z= 0.265 Chirality : 0.040 0.181 8252 Planarity : 0.004 0.054 8749 Dihedral : 4.308 61.579 8047 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.10), residues: 7668 helix: 2.96 (0.07), residues: 4682 sheet: -1.53 (0.21), residues: 574 loop : -1.14 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 459 HIS 0.012 0.001 HIS E 576 PHE 0.026 0.001 PHE C 615 TYR 0.025 0.001 TYR F 43 ARG 0.005 0.001 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 5.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 286 MET cc_start: 0.9104 (mmt) cc_final: 0.8873 (mmp) REVERT: E 343 MET cc_start: 0.8068 (tmm) cc_final: 0.7235 (tmm) REVERT: A 42 MET cc_start: 0.8733 (tpp) cc_final: 0.8165 (tpt) REVERT: A 293 PHE cc_start: 0.7306 (m-80) cc_final: 0.7062 (m-10) REVERT: C 309 MET cc_start: 0.8569 (tpt) cc_final: 0.7826 (tpt) REVERT: C 543 MET cc_start: 0.8975 (mtm) cc_final: 0.8654 (mtm) REVERT: C 573 LEU cc_start: 0.9495 (tp) cc_final: 0.9274 (tp) REVERT: D 334 MET cc_start: 0.8636 (mpp) cc_final: 0.6949 (mpp) REVERT: e 47 TRP cc_start: 0.8344 (t60) cc_final: 0.8076 (t60) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.4915 time to fit residues: 241.9185 Evaluate side-chains 256 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 716 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 423 optimal weight: 50.0000 chunk 542 optimal weight: 10.0000 chunk 420 optimal weight: 50.0000 chunk 625 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 chunk 740 optimal weight: 0.9990 chunk 463 optimal weight: 6.9990 chunk 451 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN D 362 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 46758 Z= 0.325 Angle : 0.551 12.200 64552 Z= 0.303 Chirality : 0.041 0.285 8252 Planarity : 0.004 0.055 8749 Dihedral : 4.369 60.325 8047 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.10), residues: 7668 helix: 2.84 (0.07), residues: 4688 sheet: -1.59 (0.22), residues: 553 loop : -1.19 (0.13), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 50 HIS 0.009 0.001 HIS C 166 PHE 0.021 0.001 PHE C 615 TYR 0.022 0.002 TYR D 42 ARG 0.007 0.001 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 5.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8104 (tmm) cc_final: 0.7487 (tmm) REVERT: E 494 GLU cc_start: 0.8968 (pm20) cc_final: 0.8760 (pm20) REVERT: A 42 MET cc_start: 0.8736 (tpp) cc_final: 0.8270 (tpt) REVERT: A 293 PHE cc_start: 0.7404 (m-80) cc_final: 0.7154 (m-10) REVERT: B 212 MET cc_start: 0.8634 (mpp) cc_final: 0.8386 (mpp) REVERT: C 309 MET cc_start: 0.8609 (tpt) cc_final: 0.7932 (tpt) REVERT: C 543 MET cc_start: 0.9159 (mtm) cc_final: 0.8861 (mtm) REVERT: C 573 LEU cc_start: 0.9509 (tp) cc_final: 0.9304 (tp) REVERT: D 334 MET cc_start: 0.8712 (mpp) cc_final: 0.7134 (mpp) REVERT: e 47 TRP cc_start: 0.8359 (t60) cc_final: 0.8107 (t60) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4756 time to fit residues: 231.1195 Evaluate side-chains 253 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 30.0000 chunk 295 optimal weight: 0.3980 chunk 442 optimal weight: 0.0270 chunk 222 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 470 optimal weight: 10.0000 chunk 504 optimal weight: 30.0000 chunk 365 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 581 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 179 GLN F 183 GLN ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN D 87 GLN D 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 46758 Z= 0.140 Angle : 0.478 10.717 64552 Z= 0.254 Chirality : 0.039 0.199 8252 Planarity : 0.004 0.050 8749 Dihedral : 4.028 59.044 8047 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.10), residues: 7668 helix: 3.07 (0.07), residues: 4680 sheet: -1.39 (0.22), residues: 568 loop : -1.07 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 50 HIS 0.010 0.001 HIS C 167 PHE 0.015 0.001 PHE E 138 TYR 0.018 0.001 TYR C 345 ARG 0.005 0.001 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 5.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8078 (tmm) cc_final: 0.7318 (tmm) REVERT: F 388 MET cc_start: 0.9367 (pmm) cc_final: 0.9136 (pmm) REVERT: A 42 MET cc_start: 0.8679 (tpp) cc_final: 0.8244 (tpt) REVERT: A 293 PHE cc_start: 0.7274 (m-80) cc_final: 0.7054 (m-10) REVERT: C 309 MET cc_start: 0.8516 (tpt) cc_final: 0.7816 (tpt) REVERT: C 543 MET cc_start: 0.8988 (mtm) cc_final: 0.8678 (mtm) REVERT: C 573 LEU cc_start: 0.9480 (tp) cc_final: 0.9276 (tp) REVERT: D 334 MET cc_start: 0.8597 (mpp) cc_final: 0.6852 (mpp) REVERT: e 47 TRP cc_start: 0.8309 (t60) cc_final: 0.8065 (t60) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.4935 time to fit residues: 240.7081 Evaluate side-chains 258 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 30.0000 chunk 709 optimal weight: 50.0000 chunk 647 optimal weight: 7.9990 chunk 689 optimal weight: 0.5980 chunk 708 optimal weight: 40.0000 chunk 415 optimal weight: 50.0000 chunk 300 optimal weight: 20.0000 chunk 541 optimal weight: 20.0000 chunk 211 optimal weight: 0.2980 chunk 623 optimal weight: 5.9990 chunk 652 optimal weight: 40.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 576 HIS F 179 GLN ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN D 362 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 46758 Z= 0.465 Angle : 0.654 17.990 64552 Z= 0.361 Chirality : 0.043 0.226 8252 Planarity : 0.005 0.059 8749 Dihedral : 4.501 56.820 8047 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.10), residues: 7668 helix: 2.72 (0.07), residues: 4683 sheet: -1.66 (0.22), residues: 546 loop : -1.30 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 795 HIS 0.008 0.002 HIS G 178 PHE 0.022 0.002 PHE B 83 TYR 0.029 0.002 TYR M 209 ARG 0.010 0.001 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 5.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8087 (tmm) cc_final: 0.7488 (tmm) REVERT: A 293 PHE cc_start: 0.7436 (m-80) cc_final: 0.7037 (m-80) REVERT: B 212 MET cc_start: 0.8715 (mpp) cc_final: 0.7723 (mpp) REVERT: B 278 MET cc_start: 0.8732 (mmp) cc_final: 0.8487 (mmp) REVERT: C 309 MET cc_start: 0.8611 (tpt) cc_final: 0.7954 (tpt) REVERT: C 343 MET cc_start: 0.8198 (tpp) cc_final: 0.7988 (tpp) REVERT: C 543 MET cc_start: 0.9143 (mtm) cc_final: 0.8827 (mtm) REVERT: C 573 LEU cc_start: 0.9480 (tp) cc_final: 0.9270 (tp) REVERT: D 305 MET cc_start: 0.8903 (ttm) cc_final: 0.8606 (ttp) REVERT: D 334 MET cc_start: 0.8770 (mpp) cc_final: 0.7341 (mpp) REVERT: e 47 TRP cc_start: 0.8377 (t60) cc_final: 0.8110 (t60) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4973 time to fit residues: 243.0204 Evaluate side-chains 254 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 687 optimal weight: 50.0000 chunk 452 optimal weight: 40.0000 chunk 729 optimal weight: 0.9990 chunk 445 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 507 optimal weight: 10.0000 chunk 765 optimal weight: 20.0000 chunk 704 optimal weight: 0.9990 chunk 609 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 183 GLN ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN D 362 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 46758 Z= 0.375 Angle : 0.585 13.170 64552 Z= 0.323 Chirality : 0.041 0.233 8252 Planarity : 0.004 0.060 8749 Dihedral : 4.526 58.773 8047 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.10), residues: 7668 helix: 2.74 (0.07), residues: 4668 sheet: -1.79 (0.21), residues: 586 loop : -1.28 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 459 HIS 0.007 0.001 HIS C 166 PHE 0.020 0.001 PHE E 240 TYR 0.025 0.002 TYR B 43 ARG 0.014 0.001 ARG E 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15336 Ramachandran restraints generated. 7668 Oldfield, 0 Emsley, 7668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8132 (tmm) cc_final: 0.7475 (tmm) REVERT: A 293 PHE cc_start: 0.7431 (m-80) cc_final: 0.7030 (m-80) REVERT: B 212 MET cc_start: 0.8652 (mpp) cc_final: 0.8385 (mpp) REVERT: B 278 MET cc_start: 0.8676 (mmp) cc_final: 0.8436 (mmp) REVERT: C 298 MET cc_start: 0.9042 (ptp) cc_final: 0.8813 (ptp) REVERT: C 309 MET cc_start: 0.8552 (tpt) cc_final: 0.7906 (tpt) REVERT: C 543 MET cc_start: 0.9181 (mtm) cc_final: 0.8837 (mtm) REVERT: C 573 LEU cc_start: 0.9456 (tp) cc_final: 0.9198 (tp) REVERT: D 305 MET cc_start: 0.8931 (ttm) cc_final: 0.8609 (ttp) REVERT: D 334 MET cc_start: 0.8752 (mpp) cc_final: 0.7251 (mpp) REVERT: e 47 TRP cc_start: 0.8359 (t60) cc_final: 0.8118 (t60) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.4878 time to fit residues: 237.5440 Evaluate side-chains 255 residues out of total 6423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 20.0000 chunk 483 optimal weight: 5.9990 chunk 649 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 561 optimal weight: 0.0980 chunk 89 optimal weight: 7.9990 chunk 169 optimal weight: 0.0060 chunk 610 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 626 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN D 87 GLN D 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.055313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042722 restraints weight = 447304.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042172 restraints weight = 325361.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042233 restraints weight = 283005.558| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 46758 Z= 0.150 Angle : 0.485 10.567 64552 Z= 0.258 Chirality : 0.040 0.222 8252 Planarity : 0.004 0.052 8749 Dihedral : 4.086 58.011 8047 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.10), residues: 7668 helix: 3.12 (0.07), residues: 4674 sheet: -1.45 (0.21), residues: 584 loop : -1.08 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 50 HIS 0.004 0.001 HIS C 549 PHE 0.015 0.001 PHE E 138 TYR 0.020 0.001 TYR D 42 ARG 0.010 0.001 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6861.54 seconds wall clock time: 125 minutes 41.03 seconds (7541.03 seconds total)