Starting phenix.real_space_refine on Mon Mar 25 04:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwa_26826/03_2024/7uwa_26826.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.118 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 28831 2.51 5 N 8573 2.21 5 O 8702 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 "E ASP 532": "OD1" <-> "OD2" Residue "F TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "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 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "K ASP 196": "OD1" <-> "OD2" Residue "L ASP 96": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46194 Number of models: 1 Model: "" Number of chains: 31 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 Chain: "P" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2137 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 1 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 1796 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 28, 'TYR:plan': 13, 'ASN:plan1': 13, 'TRP:plan': 8, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 27, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 717 Time building chain proxies: 26.04, per 1000 atoms: 0.56 Number of scatterers: 46194 At special positions: 0 Unit cell: (150.381, 182.721, 266.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 8702 8.00 N 8573 7.00 C 28831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.62 Conformation dependent library (CDL) restraints added in 10.3 seconds 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14428 Finding SS restraints... Secondary structure from input PDB file: 292 helices and 39 sheets defined 66.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... 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: 4.278A pdb=" N ILE E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 368 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 415 through 419 removed outlier: 4.188A 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: 3.706A 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: 4.010A 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 556 removed outlier: 3.553A pdb=" N GLN E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 578 Processing helix chain 'E' and resid 578 through 591 removed outlier: 4.084A 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 137 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 266 Proline residue: F 253 - end of helix Processing helix chain 'F' and resid 277 through 292 removed outlier: 4.025A pdb=" N TYR F 281 " --> pdb=" O ASP F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 314 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 Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 392 through 418 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 239 Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.664A pdb=" N SER A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.602A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.602A 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: 4.256A pdb=" N GLU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.823A 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: 4.719A pdb=" N PHE A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 561 Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 578 through 588 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: 3.964A pdb=" N ARG B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.047A 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 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 450 through 465 removed outlier: 3.640A pdb=" N SER B 454 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 3.986A 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 258 through 269 Processing helix chain 'C' and resid 282 through 293 Processing helix chain 'C' and resid 307 through 311 removed outlier: 4.118A 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 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 325 through 343 Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.866A pdb=" N TRP C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.974A pdb=" N ARG C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.207A 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: 3.589A 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: 4.281A 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: 4.581A 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: 3.758A 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: 3.752A 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 230 removed outlier: 4.027A pdb=" N GLY D 230 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'D' and resid 247 through 265 removed outlier: 3.619A pdb=" N ILE D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Proline residue: D 253 - end of helix removed outlier: 3.992A 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 Processing helix chain 'D' and resid 302 through 303 No H-bonds generated for 'chain 'D' and resid 302 through 303' Processing helix chain 'D' and resid 304 through 314 removed outlier: 3.606A 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: 4.166A pdb=" N TYR D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 removed outlier: 3.533A 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: 3.782A pdb=" N LEU D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 481 removed outlier: 3.870A pdb=" N LEU D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 481 " --> pdb=" O THR D 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 76 removed outlier: 4.845A pdb=" N GLY M 59 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 3.837A 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: 4.533A pdb=" N ALA M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU M 144 " --> pdb=" O VAL M 140 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU M 174 " --> pdb=" O VAL M 170 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN M 175 " --> pdb=" O ASN M 171 " (cutoff:3.500A) Proline residue: M 179 - end of helix removed outlier: 4.480A pdb=" N GLU M 194 " --> pdb=" O GLY M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 29 removed outlier: 4.034A pdb=" N GLY N 26 " --> pdb=" O ASP N 22 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU N 29 " --> pdb=" O THR N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.770A 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: 3.834A pdb=" N PHE N 83 " --> pdb=" O MET N 80 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP N 86 " --> pdb=" O PHE N 83 " (cutoff:3.500A) removed outlier: 3.664A 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: 4.058A pdb=" N UNK b 290 " --> pdb=" O UNK b 286 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK b 291 " --> pdb=" O UNK b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 304 removed outlier: 4.076A pdb=" N UNK b 303 " --> pdb=" O UNK b 299 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK b 304 " --> pdb=" O UNK b 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 304' Processing helix chain 'c' and resid 12 through 19 removed outlier: 4.028A pdb=" N VAL c 18 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS c 19 " --> pdb=" O ARG c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 56 removed outlier: 3.620A pdb=" N PHE c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA c 33 " --> pdb=" O GLY c 29 " (cutoff:3.500A) removed outlier: 4.513A 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: 3.555A 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: 3.559A 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 removed outlier: 3.504A pdb=" N ASN d 108 " --> pdb=" O HIS d 104 " (cutoff:3.500A) 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: 3.623A pdb=" N PHE d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 176 removed outlier: 3.581A 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 226 Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 252 through 258 removed outlier: 4.457A pdb=" N CYS d 258 " --> pdb=" O GLU d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.688A pdb=" N GLY d 266 " --> pdb=" O ASP d 262 " (cutoff:3.500A) removed outlier: 3.525A 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: 3.603A pdb=" N VAL g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 removed outlier: 3.851A pdb=" N LYS g 53 " --> pdb=" O GLU g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 78 Processing helix chain 'g' and resid 87 through 126 removed outlier: 3.775A pdb=" N ALA g 118 " --> pdb=" O ILE g 114 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG g 121 " --> pdb=" O ASP g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 159 removed outlier: 3.691A pdb=" N GLY g 159 " --> pdb=" O SER g 155 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 47 Processing helix chain 'h' and resid 47 through 54 removed outlier: 3.676A pdb=" N VAL h 51 " --> pdb=" O ARG h 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET h 52 " --> pdb=" O PRO h 48 " (cutoff:3.500A) removed outlier: 3.953A 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: 4.220A pdb=" N GLY h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG h 121 " --> pdb=" O ASP h 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA h 124 " --> pdb=" O VAL h 120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN h 125 " --> pdb=" O ARG h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 157 removed outlier: 3.500A pdb=" N ALA h 144 " --> pdb=" O ALA h 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 44 removed outlier: 4.079A pdb=" N PHE i 13 " --> pdb=" O THR i 9 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.753A 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: 3.837A pdb=" N TYR i 92 " --> pdb=" O LEU i 88 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.918A pdb=" N LEU i 143 " --> pdb=" O PHE i 139 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA i 144 " --> pdb=" O ALA i 140 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.688A pdb=" N LEU j 16 " --> pdb=" O PHE j 12 " (cutoff:3.500A) removed outlier: 3.525A 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: 4.495A pdb=" N VAL j 58 " --> pdb=" O SER j 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE j 79 " --> pdb=" O ILE j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 126 removed outlier: 3.534A pdb=" N GLY j 91 " --> pdb=" O TYR j 87 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA j 124 " --> pdb=" O VAL j 120 " (cutoff:3.500A) Processing helix chain 'j' and resid 126 through 157 removed outlier: 3.820A pdb=" N LEU j 135 " --> pdb=" O VAL j 131 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.958A pdb=" N MET k 52 " --> pdb=" O PRO k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 79 removed outlier: 3.920A pdb=" N ILE k 79 " --> pdb=" O ILE k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 126 removed outlier: 3.837A pdb=" N GLY k 91 " --> pdb=" O TYR k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 160 removed outlier: 3.984A pdb=" N VAL k 131 " --> pdb=" O PRO k 127 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA k 142 " --> pdb=" O ILE k 138 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU k 143 " --> pdb=" O PHE k 139 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA k 144 " --> pdb=" O ALA k 140 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 47 removed outlier: 3.659A pdb=" N PHE l 13 " --> pdb=" O THR l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.507A pdb=" N MET l 52 " --> pdb=" O PRO l 48 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS l 53 " --> pdb=" O GLU l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 79 removed outlier: 3.530A pdb=" N VAL l 59 " --> pdb=" O ILE l 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU l 64 " --> pdb=" O MET l 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 126 removed outlier: 4.045A 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: 3.529A pdb=" N PHE m 13 " --> pdb=" O THR m 9 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER m 42 " --> pdb=" O VAL m 38 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.720A pdb=" N PHE m 130 " --> pdb=" O GLN m 126 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU m 143 " --> pdb=" O PHE m 139 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA m 144 " --> pdb=" O ALA m 140 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU m 145 " --> pdb=" O GLU m 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 47 removed outlier: 3.721A pdb=" N GLY n 39 " --> pdb=" O LYS n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 76 removed outlier: 3.730A pdb=" N MET n 52 " --> pdb=" O PRO n 48 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL n 56 " --> pdb=" O MET n 52 " (cutoff:3.500A) Proline residue: n 57 - end of helix removed outlier: 3.794A pdb=" N ALA n 72 " --> pdb=" O GLY n 68 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL n 73 " --> pdb=" O LEU n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 123 removed outlier: 3.958A pdb=" N GLY n 91 " --> pdb=" O TYR n 87 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA n 118 " --> pdb=" O ILE n 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 158 removed outlier: 3.851A pdb=" N PHE n 130 " --> pdb=" O GLN n 126 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL n 131 " --> pdb=" O PRO n 127 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA n 140 " --> pdb=" O ILE n 136 " (cutoff:3.500A) removed outlier: 4.165A 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 45 removed outlier: 4.096A pdb=" N LEU o 22 " --> pdb=" O ALA o 18 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR o 31 " --> pdb=" O MET o 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY o 32 " --> pdb=" O GLY o 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER o 42 " --> pdb=" O VAL o 38 " (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: 3.560A pdb=" N UNK r 339 " --> pdb=" O UNK r 335 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK r 350 " --> pdb=" O UNK r 346 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK r 351 " --> pdb=" O UNK r 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 45 removed outlier: 3.738A pdb=" N VAL G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 55 removed outlier: 3.769A pdb=" N LYS G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 105 removed outlier: 3.805A pdb=" N ILE G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 126 removed outlier: 3.509A pdb=" N LYS G 111 " --> pdb=" O HIS G 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.635A 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 removed outlier: 3.716A pdb=" N LYS G 215 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 15 through 107 removed outlier: 3.538A pdb=" N LYS H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASP H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 106 removed outlier: 3.732A pdb=" N ASP I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 126 Processing helix chain 'I' and resid 138 through 157 removed outlier: 4.929A pdb=" N GLU I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYS I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 removed outlier: 4.372A pdb=" N GLY I 177 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 4.276A 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: 3.509A pdb=" N ALA J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS J 22 " --> pdb=" O GLN J 18 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 106 removed outlier: 3.837A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 104 removed outlier: 3.666A pdb=" N ALA K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.531A 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: 4.285A pdb=" N GLU K 147 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER K 148 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU K 157 " --> pdb=" O TYR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 226 Proline residue: K 218 - end of helix removed outlier: 3.741A pdb=" N SER K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 107 removed outlier: 3.618A pdb=" N GLU L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASP L 96 " --> pdb=" O LYS L 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.510A pdb=" N LEU O 23 " --> pdb=" O TRP O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 48 through 58 Processing helix chain 'O' and resid 58 through 81 Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.842A pdb=" N GLY O 85 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 3.899A 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: 3.770A pdb=" N THR O 103 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 109 removed outlier: 3.825A pdb=" N GLU O 109 " --> pdb=" O VAL O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 153 removed outlier: 3.504A pdb=" N ASP O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP O 134 " --> pdb=" O ALA O 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP O 135 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE O 153 " --> pdb=" O GLN O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 169 removed outlier: 3.657A pdb=" N SER O 167 " --> pdb=" O ARG O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 241 removed outlier: 3.520A pdb=" N PHE O 236 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 309 removed outlier: 4.233A pdb=" N LEU O 278 " --> pdb=" O LEU O 274 " (cutoff:3.500A) removed outlier: 4.537A 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 'a' and resid 33 through 44 removed outlier: 4.231A pdb=" N HIS a 37 " --> pdb=" O ILE a 33 " (cutoff:3.500A) removed outlier: 4.710A 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: 3.708A pdb=" N ARG a 218 " --> pdb=" O PHE a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 267 Processing helix chain 'a' and resid 276 through 336 removed outlier: 3.993A pdb=" N THR a 311 " --> pdb=" O ASN a 307 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU a 321 " --> pdb=" O GLU a 317 " (cutoff:3.500A) Processing helix chain 'a' and resid 354 through 357 Processing helix chain 'a' and resid 358 through 371 removed outlier: 4.076A pdb=" N ALA a 362 " --> pdb=" O GLN a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 407 removed outlier: 4.406A pdb=" N ALA a 399 " --> pdb=" O LYS a 395 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE a 400 " --> pdb=" O PHE a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 433 removed outlier: 3.835A 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 removed outlier: 3.504A pdb=" N SER a 458 " --> pdb=" O LYS a 454 " (cutoff:3.500A) Processing helix chain 'a' and resid 463 through 471 removed outlier: 3.764A pdb=" N MET a 467 " --> pdb=" O ASP a 463 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 490 removed outlier: 3.554A 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: 4.070A pdb=" N ILE a 586 " --> pdb=" O TRP a 582 " (cutoff:3.500A) Proline residue: a 587 - end of helix removed outlier: 4.295A pdb=" N ILE a 590 " --> pdb=" O ILE a 586 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE a 591 " --> pdb=" O PRO a 587 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU a 592 " --> pdb=" O GLN a 588 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASN a 593 " --> pdb=" O ILE a 589 " (cutoff:3.500A) removed outlier: 4.054A 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 659 Proline residue: a 655 - end of helix removed outlier: 3.988A pdb=" N LEU a 658 " --> pdb=" O VAL a 654 " (cutoff:3.500A) 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: 3.664A 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 57 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.809A pdb=" N ARG P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 24 removed outlier: 3.512A pdb=" N TYR P 21 " --> pdb=" O PRO P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 47 removed outlier: 4.442A pdb=" N ASP P 39 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 54 Processing helix chain 'P' and resid 54 through 68 removed outlier: 4.320A pdb=" N ARG P 59 " --> pdb=" O PRO P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 86 removed outlier: 3.985A pdb=" N TYR P 76 " --> pdb=" O GLU P 72 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU P 83 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N MET P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 99 Processing helix chain 'P' and resid 101 through 112 Proline residue: P 108 - end of helix removed outlier: 3.991A pdb=" N ARG P 111 " --> pdb=" O GLU P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 133 removed outlier: 4.258A pdb=" N GLU P 122 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER P 133 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 165 Processing helix chain 'P' and resid 166 through 173 Processing helix chain 'P' and resid 181 through 194 removed outlier: 3.675A pdb=" N VAL P 185 " --> pdb=" O ARG P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 202 Processing helix chain 'P' and resid 202 through 212 removed outlier: 3.528A pdb=" N LYS P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 217 removed outlier: 3.922A pdb=" N SER P 217 " --> pdb=" O THR P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 241 removed outlier: 3.531A pdb=" N GLN P 226 " --> pdb=" O GLN P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 251 Processing helix chain 'P' and resid 253 through 263 Processing helix chain 'P' and resid 266 through 280 Processing helix chain 'P' and resid 284 through 305 Proline residue: P 296 - end of helix removed outlier: 3.835A pdb=" N VAL P 299 " --> pdb=" O LEU P 295 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN P 300 " --> pdb=" O PRO P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 327 Processing helix chain 'P' and resid 333 through 340 Processing helix chain 'P' and resid 348 through 353 removed outlier: 3.522A pdb=" N LYS P 352 " --> pdb=" O SER P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 365 removed outlier: 3.570A pdb=" N ASN P 363 " --> pdb=" O ASP P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 381 removed outlier: 3.553A pdb=" N THR P 381 " --> pdb=" O THR P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 384 through 402 Processing helix chain 'P' and resid 402 through 412 Processing helix chain 'P' and resid 412 through 420 removed outlier: 4.213A pdb=" N GLU P 416 " --> pdb=" O LEU P 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 445 removed outlier: 3.883A pdb=" N THR P 430 " --> pdb=" O ASN P 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 23 through 28 removed outlier: 5.687A pdb=" N VAL E 24 " --> pdb=" O ASP E 35 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP E 35 " --> pdb=" O VAL E 24 " (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: 6.129A pdb=" N PHE E 102 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR E 318 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 273 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.610A 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 159 removed outlier: 4.704A pdb=" N GLU E 137 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 148 through 149 removed outlier: 6.886A pdb=" N GLU E 195 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL E 181 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL E 193 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 228 through 229 removed outlier: 4.767A 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: 6.639A pdb=" N VAL E 413 " --> pdb=" O CYS E 248 " (cutoff:3.500A) removed outlier: 5.460A 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: 3.745A 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: 6.700A 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: 4.440A 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: 6.576A 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: 6.710A pdb=" N VAL B 69 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL B 63 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 7.040A 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: 6.019A pdb=" N ILE C 57 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN C 68 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.721A 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 69 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: 6.989A pdb=" N VAL D 69 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL D 63 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.159A 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: 5.330A 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 189 through 194 removed outlier: 3.735A 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: 6.454A pdb=" N ILE F 207 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE F 238 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE F 209 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN F 240 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA F 211 " --> pdb=" O ASN F 240 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA F 206 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE F 274 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 208 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR F 276 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA F 210 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL F 271 " --> pdb=" O THR F 327 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE F 329 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 273 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE F 331 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU F 275 " --> pdb=" O ILE F 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.662A pdb=" N TRP A 211 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AB7, 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=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AB9, first strand: chain 'A' and resid 148 through 150 removed outlier: 5.699A pdb=" N VAL A 178 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A 197 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 194 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 154 through 161 removed outlier: 3.635A pdb=" N ALA A 156 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AC3, first strand: chain 'B' and resid 94 through 97 Processing sheet with id=AC4, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.411A pdb=" N PHE B 106 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE B 209 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN B 240 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 211 " --> pdb=" O ASN B 240 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B 212 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 271 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 157 through 158 removed outlier: 4.661A pdb=" N ILE B 157 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 332 through 333 removed outlier: 6.092A pdb=" N LEU B 165 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR B 356 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.648A pdb=" N GLU C 137 " --> pdb=" O PHE C 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AD1, first strand: chain 'C' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 223 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=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 228 through 229 removed outlier: 4.807A pdb=" N SER C 242 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 86 through 88 removed outlier: 4.025A pdb=" N MET D 19 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 190 " --> pdb=" O ASN G 203 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 95 removed outlier: 3.687A pdb=" N LEU D 125 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 137 through 138 removed outlier: 3.986A pdb=" N ARG D 318 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AD8, first strand: chain 'D' and resid 235 through 241 removed outlier: 6.647A pdb=" N VAL D 208 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR D 276 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA D 210 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 271 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE D 329 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL D 273 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 96 through 102 removed outlier: 3.747A pdb=" N GLU M 111 " --> pdb=" O ARG M 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG M 98 " --> pdb=" O LYS M 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 129 through 131 removed outlier: 3.952A pdb=" N ILE G 165 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 344 through 352 removed outlier: 3.638A pdb=" N VAL a 27 " --> pdb=" O GLY a 349 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER a 351 " --> pdb=" O GLN a 25 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE a 377 " --> pdb=" O ILE a 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 195 through 197 removed outlier: 3.569A pdb=" N TYR a 250 " --> pdb=" O GLY a 195 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL a 248 " --> pdb=" O ILE a 197 " (cutoff:3.500A) 3878 hydrogen bonds defined for protein. 11424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.09 Time building geometry restraints manager: 20.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8590 1.33 - 1.45: 10697 1.45 - 1.57: 27363 1.57 - 1.69: 0 1.69 - 1.82: 146 Bond restraints: 46796 Sorted by residual: bond pdb=" C THR D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.334 1.364 -0.030 8.40e-03 1.42e+04 1.31e+01 bond pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" C PRO D 253 " pdb=" O PRO D 253 " ideal model delta sigma weight residual 1.234 1.203 0.031 1.00e-02 1.00e+04 9.36e+00 bond pdb=" N VAL A 260 " pdb=" CA VAL A 260 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N LEU F 373 " pdb=" CA LEU F 373 " ideal model delta sigma weight residual 1.461 1.489 -0.027 9.20e-03 1.18e+04 8.88e+00 ... (remaining 46791 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.13: 935 105.13 - 112.42: 25550 112.42 - 119.70: 12789 119.70 - 126.98: 24938 126.98 - 134.27: 393 Bond angle restraints: 64605 Sorted by residual: angle pdb=" C THR A 354 " pdb=" CA THR A 354 " pdb=" CB THR A 354 " ideal model delta sigma weight residual 109.83 119.61 -9.78 9.90e-01 1.02e+00 9.77e+01 angle pdb=" N PRO D 253 " pdb=" CA PRO D 253 " pdb=" C PRO D 253 " ideal model delta sigma weight residual 114.68 106.48 8.20 1.04e+00 9.25e-01 6.22e+01 angle pdb=" N ILE A 261 " pdb=" CA ILE A 261 " pdb=" C ILE A 261 " ideal model delta sigma weight residual 110.62 103.46 7.16 1.02e+00 9.61e-01 4.93e+01 angle pdb=" N SER A 355 " pdb=" CA SER A 355 " pdb=" C SER A 355 " ideal model delta sigma weight residual 112.68 104.00 8.68 1.33e+00 5.65e-01 4.26e+01 angle pdb=" N ARG D 254 " pdb=" CA ARG D 254 " pdb=" C ARG D 254 " ideal model delta sigma weight residual 112.93 104.50 8.43 1.33e+00 5.65e-01 4.02e+01 ... (remaining 64600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 26291 17.32 - 34.63: 872 34.63 - 51.95: 157 51.95 - 69.27: 27 69.27 - 86.59: 13 Dihedral angle restraints: 27360 sinusoidal: 5013 harmonic: 22347 Sorted by residual: dihedral pdb=" C THR A 354 " pdb=" N THR A 354 " pdb=" CA THR A 354 " pdb=" CB THR A 354 " ideal model delta harmonic sigma weight residual -122.00 -137.24 15.24 0 2.50e+00 1.60e-01 3.72e+01 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 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" N THR A 354 " pdb=" C THR A 354 " pdb=" CA THR A 354 " pdb=" CB THR A 354 " ideal model delta harmonic sigma weight residual 123.40 135.05 -11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 27357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 7936 0.097 - 0.193: 301 0.193 - 0.290: 18 0.290 - 0.387: 3 0.387 - 0.484: 1 Chirality restraints: 8259 Sorted by residual: chirality pdb=" CA THR A 354 " pdb=" N THR A 354 " pdb=" C THR A 354 " pdb=" CB THR A 354 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA ILE D 132 " pdb=" N ILE D 132 " pdb=" C ILE D 132 " pdb=" CB ILE D 132 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 8256 not shown) Planarity restraints: 8757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 620 " 0.045 2.00e-02 2.50e+03 8.60e-02 7.39e+01 pdb=" C ASP C 620 " -0.149 2.00e-02 2.50e+03 pdb=" O ASP C 620 " 0.055 2.00e-02 2.50e+03 pdb=" N GLU C 621 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 514 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C THR C 514 " -0.046 2.00e-02 2.50e+03 pdb=" O THR C 514 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 515 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 107 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO C 108 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " -0.029 5.00e-02 4.00e+02 ... (remaining 8754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4793 2.74 - 3.28: 50998 3.28 - 3.82: 82538 3.82 - 4.36: 81558 4.36 - 4.90: 141331 Nonbonded interactions: 361218 Sorted by model distance: nonbonded pdb=" OG1 THR A 318 " pdb=" OD1 ASN A 320 " model vdw 2.202 2.440 nonbonded pdb=" ND2 ASN C 320 " pdb=" O GLU D 314 " model vdw 2.212 2.520 nonbonded pdb=" O LYS C 132 " pdb=" NZ LYS C 190 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR C 120 " pdb=" OE1 GLU D 261 " model vdw 2.219 2.440 nonbonded pdb=" O MET F 388 " pdb=" OG1 THR F 389 " model vdw 2.227 2.440 ... (remaining 361213 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.700 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 125.230 Find NCS groups from input model: 3.450 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.051 46796 Z= 0.215 Angle : 0.615 10.163 64605 Z= 0.393 Chirality : 0.043 0.484 8259 Planarity : 0.004 0.086 8757 Dihedral : 10.201 86.586 12932 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.05 % Allowed : 1.13 % Favored : 97.82 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 7676 helix: 2.89 (0.08), residues: 4571 sheet: -1.18 (0.22), residues: 562 loop : -0.96 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 50 HIS 0.005 0.001 HIS C 166 PHE 0.018 0.001 PHE C 293 TYR 0.016 0.001 TYR I 110 ARG 0.008 0.001 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 5.313 Fit side-chains revert: symmetry clash REVERT: E 343 MET cc_start: 0.8164 (ppp) cc_final: 0.7802 (ppp) REVERT: F 212 MET cc_start: 0.8672 (mpp) cc_final: 0.8456 (mpp) REVERT: F 373 LEU cc_start: 0.9074 (tp) cc_final: 0.8789 (tp) REVERT: A 293 PHE cc_start: 0.7441 (m-10) cc_final: 0.6963 (m-10) REVERT: B 278 MET cc_start: 0.9084 (mmp) cc_final: 0.8200 (mmp) REVERT: D 132 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (tt) REVERT: D 278 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (mmm) REVERT: D 305 MET cc_start: 0.8795 (ttm) cc_final: 0.8586 (ttp) REVERT: D 318 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: D 334 MET cc_start: 0.9138 (mpp) cc_final: 0.8192 (mpp) REVERT: D 362 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8601 (tm-30) outliers start: 25 outliers final: 6 residues processed: 296 average time/residue: 0.5044 time to fit residues: 263.1949 Evaluate side-chains 265 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 649 optimal weight: 30.0000 chunk 582 optimal weight: 30.0000 chunk 323 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 393 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 602 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 366 optimal weight: 40.0000 chunk 448 optimal weight: 20.0000 chunk 698 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 145 GLN A 86 HIS B 71 GLN ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 46796 Z= 0.398 Angle : 0.599 9.887 64605 Z= 0.335 Chirality : 0.041 0.184 8259 Planarity : 0.004 0.054 8757 Dihedral : 4.489 56.688 8055 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7676 helix: 2.65 (0.07), residues: 4677 sheet: -1.23 (0.22), residues: 578 loop : -1.22 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 542 HIS 0.018 0.002 HIS D 341 PHE 0.016 0.001 PHE A 388 TYR 0.022 0.002 TYR F 43 ARG 0.014 0.001 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 5.040 Fit side-chains revert: symmetry clash REVERT: E 343 MET cc_start: 0.8295 (ppp) cc_final: 0.7984 (ppp) REVERT: A 293 PHE cc_start: 0.7472 (m-10) cc_final: 0.7061 (m-10) REVERT: B 62 GLU cc_start: 0.8328 (pp20) cc_final: 0.8098 (tm-30) REVERT: B 278 MET cc_start: 0.9136 (mmp) cc_final: 0.8489 (mmp) REVERT: B 294 GLU cc_start: 0.8588 (pm20) cc_final: 0.8342 (pm20) REVERT: C 309 MET cc_start: 0.8449 (tpt) cc_final: 0.8239 (tpp) REVERT: C 543 MET cc_start: 0.9069 (mtm) cc_final: 0.8800 (mtm) REVERT: D 305 MET cc_start: 0.9138 (ttm) cc_final: 0.8920 (ttp) REVERT: D 334 MET cc_start: 0.9256 (mpp) cc_final: 0.7897 (mpp) REVERT: D 362 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8785 (tm-30) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.4894 time to fit residues: 238.3339 Evaluate side-chains 257 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 388 optimal weight: 50.0000 chunk 216 optimal weight: 2.9990 chunk 581 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 chunk 699 optimal weight: 7.9990 chunk 755 optimal weight: 30.0000 chunk 623 optimal weight: 9.9990 chunk 693 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 561 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 549 HIS B 71 GLN C 167 HIS ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 46796 Z= 0.308 Angle : 0.537 10.179 64605 Z= 0.298 Chirality : 0.041 0.235 8259 Planarity : 0.004 0.076 8757 Dihedral : 4.417 60.786 8055 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.10), residues: 7676 helix: 2.70 (0.07), residues: 4687 sheet: -1.32 (0.22), residues: 584 loop : -1.22 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 542 HIS 0.011 0.001 HIS H 104 PHE 0.015 0.001 PHE E 240 TYR 0.019 0.002 TYR M 209 ARG 0.009 0.001 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 5.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8266 (ppp) cc_final: 0.7824 (ppp) REVERT: B 278 MET cc_start: 0.9085 (mmp) cc_final: 0.8543 (mmp) REVERT: B 294 GLU cc_start: 0.8602 (pm20) cc_final: 0.8320 (pm20) REVERT: C 543 MET cc_start: 0.9106 (mtm) cc_final: 0.8754 (mtm) REVERT: D 334 MET cc_start: 0.9282 (mpp) cc_final: 0.8037 (mpp) REVERT: D 362 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8797 (tm-30) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.5004 time to fit residues: 242.0341 Evaluate side-chains 255 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 691 optimal weight: 9.9990 chunk 525 optimal weight: 7.9990 chunk 363 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 469 optimal weight: 40.0000 chunk 702 optimal weight: 9.9990 chunk 743 optimal weight: 30.0000 chunk 366 optimal weight: 0.0000 chunk 665 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46796 Z= 0.221 Angle : 0.488 10.328 64605 Z= 0.268 Chirality : 0.040 0.209 8259 Planarity : 0.004 0.060 8757 Dihedral : 4.265 63.710 8055 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.10), residues: 7676 helix: 2.88 (0.07), residues: 4686 sheet: -1.35 (0.22), residues: 591 loop : -1.13 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 50 HIS 0.015 0.001 HIS G 178 PHE 0.019 0.001 PHE C 293 TYR 0.021 0.001 TYR E 377 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 5.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8205 (ppp) cc_final: 0.7720 (ppp) REVERT: E 576 HIS cc_start: 0.7007 (p-80) cc_final: 0.6223 (m170) REVERT: F 36 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8413 (mmmt) REVERT: A 42 MET cc_start: 0.8921 (tpp) cc_final: 0.8518 (tpt) REVERT: B 294 GLU cc_start: 0.8606 (pm20) cc_final: 0.8313 (pm20) REVERT: D 305 MET cc_start: 0.8856 (ttm) cc_final: 0.8639 (ttp) REVERT: D 334 MET cc_start: 0.9229 (mpp) cc_final: 0.8084 (mpp) REVERT: D 362 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8798 (tm-30) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.4804 time to fit residues: 236.3241 Evaluate side-chains 258 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 619 optimal weight: 0.0470 chunk 421 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 553 optimal weight: 8.9990 chunk 306 optimal weight: 0.0030 chunk 634 optimal weight: 50.0000 chunk 513 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 667 optimal weight: 50.0000 chunk 187 optimal weight: 0.6980 overall best weight: 2.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN D 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46796 Z= 0.196 Angle : 0.479 10.341 64605 Z= 0.260 Chirality : 0.039 0.193 8259 Planarity : 0.004 0.053 8757 Dihedral : 4.156 64.380 8055 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.10), residues: 7676 helix: 2.96 (0.07), residues: 4691 sheet: -1.38 (0.22), residues: 582 loop : -1.09 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 50 HIS 0.006 0.001 HIS G 178 PHE 0.018 0.001 PHE C 615 TYR 0.021 0.001 TYR M 209 ARG 0.007 0.000 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8333 (ppp) cc_final: 0.7981 (ppp) REVERT: B 294 GLU cc_start: 0.8701 (pm20) cc_final: 0.8458 (pm20) REVERT: C 543 MET cc_start: 0.9181 (mtm) cc_final: 0.8783 (mtm) REVERT: D 305 MET cc_start: 0.8893 (ttm) cc_final: 0.8663 (ttp) REVERT: D 334 MET cc_start: 0.9202 (mpp) cc_final: 0.8150 (mpp) REVERT: D 362 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8799 (tm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.4840 time to fit residues: 238.4305 Evaluate side-chains 259 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 250 optimal weight: 2.9990 chunk 669 optimal weight: 5.9990 chunk 146 optimal weight: 0.0980 chunk 436 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 744 optimal weight: 8.9990 chunk 617 optimal weight: 9.9990 chunk 344 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 390 optimal weight: 0.4980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN D 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 46796 Z= 0.156 Angle : 0.458 10.442 64605 Z= 0.247 Chirality : 0.039 0.151 8259 Planarity : 0.004 0.049 8757 Dihedral : 4.003 64.119 8055 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.10), residues: 7676 helix: 3.10 (0.07), residues: 4684 sheet: -1.31 (0.22), residues: 583 loop : -1.02 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 50 HIS 0.017 0.001 HIS H 104 PHE 0.014 0.001 PHE E 138 TYR 0.021 0.001 TYR M 209 ARG 0.009 0.000 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8321 (ppp) cc_final: 0.7958 (ppp) REVERT: B 294 GLU cc_start: 0.8730 (pm20) cc_final: 0.8365 (pm20) REVERT: C 543 MET cc_start: 0.9125 (mtm) cc_final: 0.8788 (mtm) REVERT: D 305 MET cc_start: 0.8876 (ttm) cc_final: 0.8610 (ttm) REVERT: D 334 MET cc_start: 0.9156 (mpp) cc_final: 0.8112 (mpp) REVERT: D 362 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8814 (tm-30) REVERT: K 93 MET cc_start: 0.8335 (mmm) cc_final: 0.7992 (tpt) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.4955 time to fit residues: 246.9765 Evaluate side-chains 261 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 5.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 717 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 423 optimal weight: 20.0000 chunk 543 optimal weight: 20.0000 chunk 420 optimal weight: 5.9990 chunk 626 optimal weight: 50.0000 chunk 415 optimal weight: 5.9990 chunk 741 optimal weight: 0.0870 chunk 463 optimal weight: 40.0000 chunk 451 optimal weight: 7.9990 chunk 342 optimal weight: 50.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN G 85 GLN G 91 ASN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN K 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 46796 Z= 0.290 Angle : 0.521 10.073 64605 Z= 0.286 Chirality : 0.040 0.175 8259 Planarity : 0.004 0.051 8757 Dihedral : 4.147 63.337 8055 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.10), residues: 7676 helix: 3.02 (0.07), residues: 4675 sheet: -1.39 (0.22), residues: 593 loop : -1.10 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.005 0.001 HIS G 178 PHE 0.017 0.001 PHE C 293 TYR 0.017 0.001 TYR F 43 ARG 0.010 0.001 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 5.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8274 (ppp) cc_final: 0.7835 (ppp) REVERT: B 294 GLU cc_start: 0.8658 (pm20) cc_final: 0.8417 (pm20) REVERT: C 543 MET cc_start: 0.9310 (mtm) cc_final: 0.8751 (mtm) REVERT: D 305 MET cc_start: 0.8836 (ttm) cc_final: 0.8589 (ttm) REVERT: D 334 MET cc_start: 0.9249 (mpp) cc_final: 0.8299 (mpp) REVERT: D 362 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8868 (tm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.4790 time to fit residues: 232.8668 Evaluate side-chains 260 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 458 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 442 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 471 optimal weight: 6.9990 chunk 504 optimal weight: 40.0000 chunk 366 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 582 optimal weight: 30.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 46796 Z= 0.290 Angle : 0.523 10.196 64605 Z= 0.287 Chirality : 0.040 0.237 8259 Planarity : 0.004 0.051 8757 Dihedral : 4.232 63.818 8055 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.10), residues: 7676 helix: 2.98 (0.07), residues: 4674 sheet: -1.49 (0.21), residues: 608 loop : -1.14 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 542 HIS 0.005 0.001 HIS G 178 PHE 0.017 0.001 PHE E 240 TYR 0.022 0.001 TYR F 43 ARG 0.009 0.001 ARG B 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8265 (ppp) cc_final: 0.7807 (ppp) REVERT: B 62 GLU cc_start: 0.8412 (pp20) cc_final: 0.8112 (pp20) REVERT: B 294 GLU cc_start: 0.8693 (pm20) cc_final: 0.8451 (pm20) REVERT: C 309 MET cc_start: 0.8751 (tpp) cc_final: 0.8389 (tpt) REVERT: C 543 MET cc_start: 0.9307 (mtm) cc_final: 0.8689 (mtm) REVERT: D 305 MET cc_start: 0.8816 (ttm) cc_final: 0.8589 (ttm) REVERT: D 334 MET cc_start: 0.9260 (mpp) cc_final: 0.8319 (mpp) REVERT: D 362 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8871 (tm-30) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.4701 time to fit residues: 227.2672 Evaluate side-chains 258 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 674 optimal weight: 4.9990 chunk 710 optimal weight: 20.0000 chunk 647 optimal weight: 7.9990 chunk 690 optimal weight: 6.9990 chunk 709 optimal weight: 40.0000 chunk 415 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 542 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 624 optimal weight: 10.0000 chunk 653 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 71 GLN D 328 GLN D 399 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 46796 Z= 0.321 Angle : 0.556 10.057 64605 Z= 0.306 Chirality : 0.041 0.214 8259 Planarity : 0.004 0.061 8757 Dihedral : 4.374 64.574 8055 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.10), residues: 7676 helix: 2.90 (0.07), residues: 4664 sheet: -1.44 (0.22), residues: 570 loop : -1.24 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 542 HIS 0.008 0.001 HIS E 576 PHE 0.022 0.001 PHE K 213 TYR 0.044 0.002 TYR B 43 ARG 0.016 0.001 ARG G 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 5.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8204 (ppp) cc_final: 0.7766 (ppp) REVERT: E 576 HIS cc_start: 0.7204 (p-80) cc_final: 0.6991 (m170) REVERT: A 293 PHE cc_start: 0.7333 (m-10) cc_final: 0.7038 (m-10) REVERT: B 62 GLU cc_start: 0.8405 (pp20) cc_final: 0.8127 (pp20) REVERT: C 309 MET cc_start: 0.8941 (tpp) cc_final: 0.8529 (tpt) REVERT: C 543 MET cc_start: 0.9355 (mtm) cc_final: 0.8911 (mtm) REVERT: D 19 MET cc_start: 0.8811 (mmp) cc_final: 0.8506 (mmp) REVERT: D 334 MET cc_start: 0.9293 (mpp) cc_final: 0.8392 (mpp) REVERT: D 362 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8870 (tm-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.5027 time to fit residues: 245.5438 Evaluate side-chains 256 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 5.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 688 optimal weight: 40.0000 chunk 453 optimal weight: 20.0000 chunk 730 optimal weight: 10.0000 chunk 445 optimal weight: 20.0000 chunk 346 optimal weight: 0.8980 chunk 507 optimal weight: 50.0000 chunk 766 optimal weight: 50.0000 chunk 705 optimal weight: 6.9990 chunk 610 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 471 optimal weight: 0.0060 overall best weight: 3.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 46796 Z= 0.283 Angle : 0.530 10.169 64605 Z= 0.290 Chirality : 0.040 0.206 8259 Planarity : 0.004 0.068 8757 Dihedral : 4.323 65.379 8055 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.10), residues: 7676 helix: 2.94 (0.07), residues: 4674 sheet: -1.59 (0.21), residues: 602 loop : -1.20 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.005 0.001 HIS G 178 PHE 0.021 0.001 PHE C 293 TYR 0.025 0.001 TYR D 43 ARG 0.010 0.001 ARG G 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15352 Ramachandran restraints generated. 7676 Oldfield, 0 Emsley, 7676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 343 MET cc_start: 0.8248 (ppp) cc_final: 0.7797 (ppp) REVERT: A 293 PHE cc_start: 0.7320 (m-10) cc_final: 0.7021 (m-10) REVERT: B 62 GLU cc_start: 0.8382 (pp20) cc_final: 0.8086 (pp20) REVERT: B 278 MET cc_start: 0.8794 (mmp) cc_final: 0.8549 (mmp) REVERT: B 294 GLU cc_start: 0.8617 (pm20) cc_final: 0.8356 (pm20) REVERT: C 309 MET cc_start: 0.8918 (tpp) cc_final: 0.8492 (tpt) REVERT: C 543 MET cc_start: 0.9267 (mtm) cc_final: 0.8871 (mtm) REVERT: D 305 MET cc_start: 0.8694 (ttm) cc_final: 0.8443 (ttp) REVERT: D 334 MET cc_start: 0.9315 (mpp) cc_final: 0.8392 (mpp) REVERT: D 362 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8883 (tm-30) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.4868 time to fit residues: 236.8523 Evaluate side-chains 260 residues out of total 6430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 769 random chunks: chunk 374 optimal weight: 50.0000 chunk 484 optimal weight: 30.0000 chunk 649 optimal weight: 40.0000 chunk 186 optimal weight: 4.9990 chunk 562 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 611 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 627 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.066955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037771 restraints weight = 353787.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.036841 restraints weight = 301000.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036491 restraints weight = 347600.667| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 46796 Z= 0.274 Angle : 0.524 10.137 64605 Z= 0.286 Chirality : 0.040 0.204 8259 Planarity : 0.004 0.054 8757 Dihedral : 4.293 65.759 8055 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 7676 helix: 2.96 (0.07), residues: 4665 sheet: -1.62 (0.21), residues: 614 loop : -1.17 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.005 0.001 HIS G 178 PHE 0.020 0.001 PHE C 293 TYR 0.028 0.001 TYR D 43 ARG 0.012 0.001 ARG G 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7056.54 seconds wall clock time: 128 minutes 52.39 seconds (7732.39 seconds total)