Starting phenix.real_space_refine on Mon Mar 11 13:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tms_26001/03_2024/7tms_26001_updated.pdb" } resolution = 3.8 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= 0.078 sd= 1.456 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 232 5.16 5 C 36713 2.51 5 N 9869 2.21 5 O 10836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 292": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E GLU 303": "OE1" <-> "OE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 576": "OD1" <-> "OD2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 323": "OE1" <-> "OE2" Residue "F ASP 361": "OD1" <-> "OD2" Residue "F GLU 389": "OE1" <-> "OE2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "G TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 58": "OE1" <-> "OE2" Residue "a TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 721": "OE1" <-> "OE2" Residue "c PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 174": "OD1" <-> "OD2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 96": "OD1" <-> "OD2" Residue "d GLU 171": "OE1" <-> "OE2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 240": "OD1" <-> "OD2" Residue "d TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 274": "OE1" <-> "OE2" Residue "d TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 319": "OE1" <-> "OE2" Residue "d TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 46": "OE1" <-> "OE2" Residue "h PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 3": "OE1" <-> "OE2" Residue "j TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 3": "OE1" <-> "OE2" Residue "m TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 157": "OD1" <-> "OD2" Residue "n PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57652 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4542 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3677 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4547 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3694 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4578 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3731 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1325 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 235 Chain: "H" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 556 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 155 Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1346 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 248 Chain: "J" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 562 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "K" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1263 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 6, 'TRANS': 217} Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 658 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 16, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 272 Chain: "L" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 556 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 150 Chain: "M" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1463 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 219} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 587 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 201 Chain: "O" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1808 Classifications: {'peptide': 357} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 303} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 1094 Unresolved non-hydrogen angles: 1400 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 20, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 600 Chain: "P" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 2229 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 394} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 1367 Unresolved non-hydrogen angles: 1740 Unresolved non-hydrogen dihedrals: 1101 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 29, 'TYR:plan': 9, 'ASN:plan1': 23, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 695 Chain: "a" Number of atoms: 5362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5362 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 763 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 362 Chain: "b" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1464 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 333} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 510 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1128 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "j" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "k" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1129 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "m" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "n" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1130 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1123 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.51, per 1000 atoms: 0.44 Number of scatterers: 57652 At special positions: 0 Unit cell: (142.998, 188.662, 261.963, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 232 16.00 P 2 15.00 O 10836 8.00 N 9869 7.00 C 36713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.64 Conformation dependent library (CDL) restraints added in 8.6 seconds 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 283 helices and 38 sheets defined 58.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 287 through 299 removed outlier: 3.507A pdb=" N PHE A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 326 through 344 removed outlier: 4.547A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.542A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.564A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 4.304A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 4.064A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 219 through 231 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 249 through 269 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 396 through 418 removed outlier: 4.061A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 442 removed outlier: 3.712A pdb=" N GLU B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 4.543A pdb=" N ILE B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 Processing helix chain 'C' and resid 112 through 118 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 261 through 271 removed outlier: 4.590A pdb=" N SER C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 removed outlier: 3.506A pdb=" N VAL C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 326 through 344 removed outlier: 4.227A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 382 through 394 removed outlier: 4.428A pdb=" N GLY C 385 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.763A pdb=" N LYS C 469 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 502 removed outlier: 4.116A pdb=" N LEU C 501 " --> pdb=" O GLN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 540 through 562 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.465A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 593 through 614 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 250 through 268 removed outlier: 3.808A pdb=" N THR D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Proline residue: D 256 - end of helix removed outlier: 3.525A pdb=" N ALA D 267 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR D 268 " --> pdb=" O TYR D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 316 removed outlier: 4.345A pdb=" N TYR D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.694A pdb=" N ILE D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 396 through 420 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.267A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 478 through 484 Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 287 through 299 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 326 through 344 removed outlier: 3.710A pdb=" N GLU E 330 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 384 through 394 removed outlier: 4.007A pdb=" N ARG E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 466 through 474 removed outlier: 3.584A pdb=" N LYS E 469 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP E 472 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 502 Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 562 Processing helix chain 'E' and resid 567 through 573 removed outlier: 3.763A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 removed outlier: 4.423A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE E 586 " --> pdb=" O SER E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 593 through 614 Processing helix chain 'F' and resid 12 through 15 No H-bonds generated for 'chain 'F' and resid 12 through 15' Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 156 through 159 No H-bonds generated for 'chain 'F' and resid 156 through 159' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 219 through 231 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 250 through 268 removed outlier: 3.827A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix removed outlier: 4.275A pdb=" N TYR F 268 " --> pdb=" O TYR F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.368A pdb=" N TYR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.867A pdb=" N LYS F 384 " --> pdb=" O ARG F 381 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 385 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.725A pdb=" N VAL F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 442 Processing helix chain 'F' and resid 454 through 467 removed outlier: 4.044A pdb=" N ILE F 467 " --> pdb=" O SER F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 478 through 484 removed outlier: 3.592A pdb=" N GLU F 483 " --> pdb=" O LYS F 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 15 No H-bonds generated for 'chain 'G' and resid 13 through 15' Processing helix chain 'G' and resid 19 through 112 Processing helix chain 'G' and resid 114 through 132 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 146 through 163 removed outlier: 4.902A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 215 through 223 Processing helix chain 'H' and resid 4 through 103 removed outlier: 3.662A pdb=" N LYS H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 112 Processing helix chain 'I' and resid 114 through 132 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 146 through 151 Processing helix chain 'I' and resid 153 through 163 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'I' and resid 215 through 222 Processing helix chain 'J' and resid 3 through 102 removed outlier: 4.306A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 66 removed outlier: 4.332A pdb=" N LYS K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU K 27 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS K 65 " --> pdb=" O ASN K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 112 removed outlier: 4.244A pdb=" N GLN K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN K 74 " --> pdb=" O MET K 70 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 146 through 163 removed outlier: 3.692A pdb=" N GLU K 150 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 213 Processing helix chain 'K' and resid 215 through 222 Processing helix chain 'L' and resid 3 through 103 removed outlier: 3.686A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 74 removed outlier: 4.240A pdb=" N GLN M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 86 removed outlier: 3.884A pdb=" N SER M 86 " --> pdb=" O GLN M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 103 No H-bonds generated for 'chain 'M' and resid 101 through 103' Processing helix chain 'M' and resid 119 through 121 No H-bonds generated for 'chain 'M' and resid 119 through 121' Processing helix chain 'M' and resid 126 through 171 Processing helix chain 'M' and resid 173 through 223 Proline residue: M 179 - end of helix removed outlier: 4.135A pdb=" N SER M 190 " --> pdb=" O ALA M 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 74 through 77 No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.817A pdb=" N SER N 83 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'O' and resid 30 through 35 Processing helix chain 'O' and resid 58 through 89 Processing helix chain 'O' and resid 91 through 94 No H-bonds generated for 'chain 'O' and resid 91 through 94' Processing helix chain 'O' and resid 97 through 99 No H-bonds generated for 'chain 'O' and resid 97 through 99' Processing helix chain 'O' and resid 107 through 112 Processing helix chain 'O' and resid 127 through 164 Processing helix chain 'O' and resid 205 through 211 removed outlier: 3.778A pdb=" N GLU O 211 " --> pdb=" O GLU O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 216 Processing helix chain 'O' and resid 240 through 251 removed outlier: 6.365A pdb=" N GLN O 244 " --> pdb=" O LYS O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 315 removed outlier: 3.861A pdb=" N HIS O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG O 290 " --> pdb=" O VAL O 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 346 Processing helix chain 'P' and resid 7 through 9 No H-bonds generated for 'chain 'P' and resid 7 through 9' Processing helix chain 'P' and resid 11 through 22 removed outlier: 5.162A pdb=" N ILE P 16 " --> pdb=" O PHE P 13 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE P 20 " --> pdb=" O ARG P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.513A pdb=" N ARG P 32 " --> pdb=" O ASP P 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 28 through 32' Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 75 through 86 Proline residue: P 79 - end of helix removed outlier: 3.514A pdb=" N SER P 85 " --> pdb=" O HIS P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 105 Processing helix chain 'P' and resid 110 through 118 removed outlier: 4.109A pdb=" N PHE P 117 " --> pdb=" O THR P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 131 removed outlier: 3.610A pdb=" N GLU P 125 " --> pdb=" O LYS P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 151 removed outlier: 3.808A pdb=" N LEU P 140 " --> pdb=" O PHE P 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN P 145 " --> pdb=" O ILE P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 168 through 175 Processing helix chain 'P' and resid 180 through 195 removed outlier: 4.302A pdb=" N VAL P 185 " --> pdb=" O ASP P 181 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU P 189 " --> pdb=" O VAL P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 205 removed outlier: 3.721A pdb=" N ASP P 201 " --> pdb=" O GLU P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 211 through 220 Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 257 through 266 removed outlier: 3.773A pdb=" N GLU P 262 " --> pdb=" O VAL P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 280 removed outlier: 4.363A pdb=" N LEU P 275 " --> pdb=" O PHE P 271 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS P 276 " --> pdb=" O LEU P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 297 Processing helix chain 'P' and resid 308 through 314 Processing helix chain 'P' and resid 319 through 327 Processing helix chain 'P' and resid 333 through 354 removed outlier: 3.988A pdb=" N GLN P 351 " --> pdb=" O GLU P 347 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU P 353 " --> pdb=" O GLU P 349 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR P 354 " --> pdb=" O TYR P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 364 Processing helix chain 'P' and resid 372 through 379 removed outlier: 5.429A pdb=" N ASN P 377 " --> pdb=" O HIS P 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY P 378 " --> pdb=" O VAL P 375 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P 379 " --> pdb=" O ASP P 376 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 407 removed outlier: 5.719A pdb=" N ASP P 390 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN P 391 " --> pdb=" O LYS P 388 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE P 394 " --> pdb=" O ASN P 391 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG P 407 " --> pdb=" O ALA P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 433 Processing helix chain 'P' and resid 435 through 443 Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.676A pdb=" N MET P 451 " --> pdb=" O LYS P 447 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 476 Processing helix chain 'a' and resid 26 through 35 Processing helix chain 'a' and resid 56 through 78 Processing helix chain 'a' and resid 86 through 94 removed outlier: 3.529A pdb=" N LYS a 90 " --> pdb=" O GLY a 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU a 92 " --> pdb=" O THR a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 143 removed outlier: 3.505A pdb=" N LEU a 121 " --> pdb=" O GLU a 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP a 129 " --> pdb=" O ASP a 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU a 139 " --> pdb=" O ASN a 136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN a 140 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG a 142 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 206 removed outlier: 3.629A pdb=" N VAL a 196 " --> pdb=" O ARG a 193 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA a 197 " --> pdb=" O ASP a 194 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL a 206 " --> pdb=" O LEU a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 255 Processing helix chain 'a' and resid 267 through 326 removed outlier: 3.727A pdb=" N ASP a 283 " --> pdb=" O LYS a 279 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS a 304 " --> pdb=" O TYR a 300 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 311 " --> pdb=" O ASP a 307 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG a 315 " --> pdb=" O GLN a 311 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU a 316 " --> pdb=" O ASP a 312 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 317 " --> pdb=" O VAL a 313 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA a 318 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS a 325 " --> pdb=" O GLU a 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER a 326 " --> pdb=" O ILE a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 360 removed outlier: 5.443A pdb=" N ALA a 347 " --> pdb=" O ASP a 344 " (cutoff:3.500A) Processing helix chain 'a' and resid 388 through 397 removed outlier: 4.291A pdb=" N TYR a 397 " --> pdb=" O ILE a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 423 removed outlier: 4.301A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 426 through 440 removed outlier: 3.626A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 448 removed outlier: 4.129A pdb=" N LYS a 448 " --> pdb=" O LYS a 444 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 459 Processing helix chain 'a' and resid 462 through 479 Processing helix chain 'a' and resid 520 through 522 No H-bonds generated for 'chain 'a' and resid 520 through 522' Processing helix chain 'a' and resid 528 through 561 removed outlier: 3.681A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 595 removed outlier: 4.979A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix removed outlier: 4.614A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 601 No H-bonds generated for 'chain 'a' and resid 598 through 601' Processing helix chain 'a' and resid 611 through 615 Processing helix chain 'a' and resid 630 through 650 removed outlier: 3.994A pdb=" N GLN a 634 " --> pdb=" O GLN a 630 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL a 635 " --> pdb=" O ALA a 631 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE a 636 " --> pdb=" O LYS a 632 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU a 637 " --> pdb=" O VAL a 633 " (cutoff:3.500A) Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 711 through 754 removed outlier: 3.638A pdb=" N ILE a 717 " --> pdb=" O ILE a 713 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU a 734 " --> pdb=" O THR a 730 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG a 735 " --> pdb=" O ALA a 731 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU a 736 " --> pdb=" O SER a 732 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) Processing helix chain 'a' and resid 764 through 802 Processing helix chain 'a' and resid 806 through 809 No H-bonds generated for 'chain 'a' and resid 806 through 809' Processing helix chain 'b' and resid 221 through 246 removed outlier: 3.707A pdb=" N ASN b 246 " --> pdb=" O SER b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 254 Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 47 through 53 Processing helix chain 'c' and resid 56 through 92 removed outlier: 3.731A pdb=" N VAL c 68 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER c 85 " --> pdb=" O ILE c 81 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG c 92 " --> pdb=" O GLY c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 122 removed outlier: 4.791A pdb=" N THR c 98 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS c 99 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE c 102 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL c 109 " --> pdb=" O PHE c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 176 Processing helix chain 'c' and resid 178 through 207 removed outlier: 3.650A pdb=" N VAL c 182 " --> pdb=" O SER c 178 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 8 Processing helix chain 'd' and resid 11 through 23 Processing helix chain 'd' and resid 27 through 34 Processing helix chain 'd' and resid 39 through 47 Processing helix chain 'd' and resid 52 through 55 removed outlier: 4.639A pdb=" N LEU d 55 " --> pdb=" O GLY d 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 52 through 55' Processing helix chain 'd' and resid 65 through 85 Processing helix chain 'd' and resid 90 through 111 removed outlier: 3.830A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 129 through 131 No H-bonds generated for 'chain 'd' and resid 129 through 131' Processing helix chain 'd' and resid 134 through 141 Proline residue: d 137 - end of helix Processing helix chain 'd' and resid 145 through 153 Processing helix chain 'd' and resid 159 through 165 Processing helix chain 'd' and resid 180 through 199 Processing helix chain 'd' and resid 204 through 226 removed outlier: 4.208A pdb=" N THR d 210 " --> pdb=" O GLU d 206 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 241 Processing helix chain 'd' and resid 253 through 258 Processing helix chain 'd' and resid 262 through 271 removed outlier: 3.621A pdb=" N ASN d 271 " --> pdb=" O ALA d 267 " (cutoff:3.500A) Processing helix chain 'd' and resid 273 through 275 No H-bonds generated for 'chain 'd' and resid 273 through 275' Processing helix chain 'd' and resid 284 through 301 Processing helix chain 'd' and resid 306 through 331 removed outlier: 3.664A pdb=" N LYS d 314 " --> pdb=" O ALA d 311 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 340 removed outlier: 5.322A pdb=" N ASN d 339 " --> pdb=" O GLU d 336 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN d 340 " --> pdb=" O ARG d 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 Processing helix chain 'e' and resid 30 through 53 removed outlier: 3.683A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 32 removed outlier: 5.126A pdb=" N ILE f 23 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU f 24 " --> pdb=" O VAL f 21 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE f 27 " --> pdb=" O LEU f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 72 removed outlier: 3.607A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE f 71 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN f 72 " --> pdb=" O PHE f 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 43 removed outlier: 3.776A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 49 No H-bonds generated for 'chain 'g' and resid 47 through 49' Processing helix chain 'g' and resid 52 through 77 removed outlier: 3.740A pdb=" N VAL g 55 " --> pdb=" O LYS g 52 " (cutoff:3.500A) Proline residue: g 56 - end of helix removed outlier: 4.014A pdb=" N TYR g 76 " --> pdb=" O LEU g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 121 removed outlier: 3.891A pdb=" N GLN g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 123 through 154 removed outlier: 3.729A pdb=" N VAL g 127 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU g 139 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 5 No H-bonds generated for 'chain 'h' and resid 3 through 5' Processing helix chain 'h' and resid 9 through 42 removed outlier: 3.718A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 47 through 49 No H-bonds generated for 'chain 'h' and resid 47 through 49' Processing helix chain 'h' and resid 51 through 77 removed outlier: 3.627A pdb=" N ILE h 54 " --> pdb=" O PHE h 51 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL h 55 " --> pdb=" O LYS h 52 " (cutoff:3.500A) Proline residue: h 56 - end of helix removed outlier: 3.550A pdb=" N CYS h 75 " --> pdb=" O VAL h 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR h 76 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 119 Processing helix chain 'h' and resid 123 through 155 removed outlier: 3.815A pdb=" N PHE h 126 " --> pdb=" O PRO h 123 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL h 127 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL h 138 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR h 155 " --> pdb=" O SER h 152 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 43 Proline residue: i 10 - end of helix removed outlier: 3.558A pdb=" N ALA i 20 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE i 23 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR i 24 " --> pdb=" O ILE i 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS i 34 " --> pdb=" O GLY i 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER i 35 " --> pdb=" O THR i 32 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS i 43 " --> pdb=" O CYS i 40 " (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 51 through 77 removed outlier: 4.357A pdb=" N VAL i 55 " --> pdb=" O LYS i 52 " (cutoff:3.500A) Proline residue: i 56 - end of helix removed outlier: 3.766A pdb=" N TYR i 76 " --> pdb=" O LEU i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 121 removed outlier: 3.597A pdb=" N SER i 120 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 155 removed outlier: 3.872A pdb=" N VAL i 127 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE i 132 " --> pdb=" O MET i 129 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL i 138 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN i 151 " --> pdb=" O LEU i 148 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA i 154 " --> pdb=" O ASN i 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR i 155 " --> pdb=" O SER i 152 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 5 No H-bonds generated for 'chain 'j' and resid 3 through 5' Processing helix chain 'j' and resid 7 through 43 Proline residue: j 10 - end of helix removed outlier: 3.867A pdb=" N ALA j 20 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE j 23 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR j 24 " --> pdb=" O ILE j 21 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS j 43 " --> pdb=" O CYS j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 76 removed outlier: 4.344A pdb=" N PHE j 51 " --> pdb=" O ASP j 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE j 54 " --> pdb=" O PHE j 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL j 55 " --> pdb=" O LYS j 52 " (cutoff:3.500A) Proline residue: j 56 - end of helix Processing helix chain 'j' and resid 84 through 119 Processing helix chain 'j' and resid 124 through 155 removed outlier: 4.173A pdb=" N VAL j 138 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU j 150 " --> pdb=" O ALA j 147 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR j 155 " --> pdb=" O SER j 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 43 Proline residue: k 10 - end of helix removed outlier: 3.818A pdb=" N ALA k 20 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE k 23 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR k 24 " --> pdb=" O ILE k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 51 removed outlier: 4.228A pdb=" N PHE k 51 " --> pdb=" O ASP k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 77 removed outlier: 3.701A pdb=" N TYR k 76 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 121 removed outlier: 3.853A pdb=" N SER k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN k 121 " --> pdb=" O ARG k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 123 through 155 removed outlier: 3.714A pdb=" N VAL k 127 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL k 138 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR k 155 " --> pdb=" O SER k 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 5 No H-bonds generated for 'chain 'l' and resid 3 through 5' Processing helix chain 'l' and resid 9 through 43 removed outlier: 3.912A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 50 Processing helix chain 'l' and resid 55 through 76 Processing helix chain 'l' and resid 84 through 121 removed outlier: 4.085A pdb=" N GLN l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 3.674A pdb=" N VAL l 127 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL l 138 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER l 152 " --> pdb=" O LEU l 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 45 removed outlier: 3.795A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU m 45 " --> pdb=" O ALA m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 77 removed outlier: 4.200A pdb=" N PHE m 51 " --> pdb=" O ASP m 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS m 52 " --> pdb=" O LEU m 49 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL m 55 " --> pdb=" O LYS m 52 " (cutoff:3.500A) Proline residue: m 56 - end of helix Processing helix chain 'm' and resid 84 through 121 removed outlier: 3.906A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 123 through 152 removed outlier: 3.901A pdb=" N PHE m 126 " --> pdb=" O PRO m 123 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL m 127 " --> pdb=" O ARG m 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 42 Proline residue: n 10 - end of helix removed outlier: 5.009A pdb=" N PHE n 23 " --> pdb=" O ALA n 20 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR n 24 " --> pdb=" O ILE n 21 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS n 34 " --> pdb=" O GLY n 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS n 40 " --> pdb=" O VAL n 37 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 77 removed outlier: 4.961A pdb=" N VAL n 55 " --> pdb=" O PHE n 51 " (cutoff:3.500A) Proline residue: n 56 - end of helix Processing helix chain 'n' and resid 84 through 121 removed outlier: 3.556A pdb=" N GLN n 121 " --> pdb=" O ARG n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 123 through 153 removed outlier: 3.595A pdb=" N VAL n 127 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU n 139 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 11 No H-bonds generated for 'chain 'o' and resid 9 through 11' Processing helix chain 'o' and resid 15 through 49 Processing helix chain 'o' and resid 56 through 82 removed outlier: 4.621A pdb=" N ILE o 61 " --> pdb=" O MET o 57 " (cutoff:3.500A) Proline residue: o 62 - end of helix Processing helix chain 'o' and resid 92 through 127 Processing helix chain 'o' and resid 131 through 163 removed outlier: 3.820A pdb=" N PHE o 134 " --> pdb=" O PRO o 131 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL o 135 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL o 146 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR o 150 " --> pdb=" O LEU o 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER o 163 " --> pdb=" O THR o 160 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.366A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 97 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 removed outlier: 6.691A pdb=" N ILE A 172 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER A 160 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N HIS A 170 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 251 through 255 removed outlier: 8.167A pdb=" N THR A 252 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 412 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 254 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 414 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.695A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU A 199 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER A 207 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.745A pdb=" N VAL A 399 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.782A pdb=" N ILE B 40 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL B 34 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 78 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 67 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 102 through 104 Processing sheet with id= I, first strand: chain 'B' and resid 357 through 359 Processing sheet with id= J, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.393A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 93 through 96 Processing sheet with id= L, first strand: chain 'C' and resid 189 through 191 removed outlier: 4.761A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE C 172 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER C 160 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS C 170 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 437 through 439 removed outlier: 8.044A pdb=" N THR C 252 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 412 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE C 254 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 414 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.585A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 185 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE C 197 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE C 209 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 199 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER C 207 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 223 through 226 removed outlier: 6.660A pdb=" N VAL C 399 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.739A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 69 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN D 78 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 67 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.642A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 111 through 114 removed outlier: 3.842A pdb=" N ARG D 111 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 210 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE D 241 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN D 243 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA D 214 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 215 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER D 328 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR D 276 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR D 330 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU D 278 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 332 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 357 through 359 Processing sheet with id= T, first strand: chain 'E' and resid 26 through 31 removed outlier: 6.466A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 62 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= V, first strand: chain 'E' and resid 189 through 191 Processing sheet with id= W, first strand: chain 'E' and resid 206 through 209 removed outlier: 6.305A pdb=" N GLU E 201 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE E 182 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 251 through 255 removed outlier: 7.838A pdb=" N THR E 252 " --> pdb=" O VAL E 410 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE E 412 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE E 254 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA E 414 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.520A pdb=" N VAL E 399 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 31 through 35 removed outlier: 6.626A pdb=" N ILE F 40 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 41 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.577A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 112 through 114 removed outlier: 6.245A pdb=" N LEU F 240 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET F 215 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER F 328 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR F 276 " --> pdb=" O SER F 328 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR F 330 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU F 278 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE F 332 " --> pdb=" O LEU F 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 357 through 359 Processing sheet with id= AD, first strand: chain 'G' and resid 171 through 174 Processing sheet with id= AE, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.934A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN I 201 " --> pdb=" O VAL I 188 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.856A pdb=" N ALA K 137 " --> pdb=" O GLU K 171 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 92 through 95 Processing sheet with id= AH, first strand: chain 'M' and resid 99 through 101 Processing sheet with id= AI, first strand: chain 'O' and resid 11 through 14 Processing sheet with id= AJ, first strand: chain 'a' and resid 335 through 342 removed outlier: 3.583A pdb=" N GLY a 339 " --> pdb=" O VAL a 17 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL a 17 " --> pdb=" O GLY a 339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE a 367 " --> pdb=" O TYR a 20 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 187 through 191 Processing sheet with id= AL, first strand: chain 'a' and resid 222 through 224 removed outlier: 3.543A pdb=" N LYS a 231 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU a 229 " --> pdb=" O ASP a 224 " (cutoff:3.500A) 3741 hydrogen bonds defined for protein. 8892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.28 Time building geometry restraints manager: 22.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11488 1.33 - 1.45: 13290 1.45 - 1.57: 33488 1.57 - 1.69: 3 1.69 - 1.82: 377 Bond restraints: 58646 Sorted by residual: bond pdb=" CG1 ILE m 22 " pdb=" CD1 ILE m 22 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.30e+00 bond pdb=" CG1 ILE E 333 " pdb=" CD1 ILE E 333 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.82e+00 bond pdb=" CG GLN a 68 " pdb=" CD GLN a 68 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.57e+00 bond pdb=" CG1 ILE i 132 " pdb=" CD1 ILE i 132 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.42e+00 bond pdb=" CG1 ILE n 89 " pdb=" CD1 ILE n 89 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.91e+00 ... (remaining 58641 not shown) Histogram of bond angle deviations from ideal: 97.70 - 105.36: 1070 105.36 - 113.01: 32151 113.01 - 120.67: 27040 120.67 - 128.32: 19490 128.32 - 135.98: 250 Bond angle restraints: 80001 Sorted by residual: angle pdb=" C ILE A 27 " pdb=" N TYR A 28 " pdb=" CA TYR A 28 " ideal model delta sigma weight residual 122.16 129.69 -7.53 1.32e+00 5.74e-01 3.25e+01 angle pdb=" C THR O 30 " pdb=" CA THR O 30 " pdb=" CB THR O 30 " ideal model delta sigma weight residual 117.23 109.66 7.57 1.36e+00 5.41e-01 3.10e+01 angle pdb=" C THR B 392 " pdb=" CA THR B 392 " pdb=" CB THR B 392 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.61e+01 angle pdb=" C THR d 197 " pdb=" N GLU d 198 " pdb=" CA GLU d 198 " ideal model delta sigma weight residual 121.80 110.93 10.87 2.16e+00 2.14e-01 2.53e+01 angle pdb=" N ARG d 297 " pdb=" CA ARG d 297 " pdb=" C ARG d 297 " ideal model delta sigma weight residual 111.28 106.56 4.72 1.09e+00 8.42e-01 1.88e+01 ... (remaining 79996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 34447 35.74 - 71.49: 359 71.49 - 107.23: 46 107.23 - 142.98: 0 142.98 - 178.72: 1 Dihedral angle restraints: 34853 sinusoidal: 11196 harmonic: 23657 Sorted by residual: dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 121.28 178.72 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA MET B 472 " pdb=" C MET B 472 " pdb=" N LEU B 473 " pdb=" CA LEU B 473 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE F 353 " pdb=" C ILE F 353 " pdb=" N THR F 354 " pdb=" CA THR F 354 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 34850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 7489 0.052 - 0.104: 1774 0.104 - 0.156: 279 0.156 - 0.208: 18 0.208 - 0.261: 7 Chirality restraints: 9567 Sorted by residual: chirality pdb=" CA TRP c 147 " pdb=" N TRP c 147 " pdb=" C TRP c 147 " pdb=" CB TRP c 147 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE E 104 " pdb=" CA ILE E 104 " pdb=" CG1 ILE E 104 " pdb=" CG2 ILE E 104 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA MET i 59 " pdb=" N MET i 59 " pdb=" C MET i 59 " pdb=" CB MET i 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 9564 not shown) Planarity restraints: 10420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 594 " 0.039 2.00e-02 2.50e+03 3.36e-02 2.83e+01 pdb=" CG TRP a 594 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP a 594 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP a 594 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 594 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP a 594 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 594 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 594 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 594 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP a 594 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 737 " 0.042 2.00e-02 2.50e+03 3.24e-02 2.63e+01 pdb=" CG TRP a 737 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP a 737 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP a 737 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP a 737 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 737 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 737 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 737 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 737 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP a 737 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR d 249 " -0.056 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO d 250 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO d 250 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO d 250 " -0.042 5.00e-02 4.00e+02 ... (remaining 10417 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5865 2.74 - 3.28: 64848 3.28 - 3.82: 103394 3.82 - 4.36: 116572 4.36 - 4.90: 198612 Nonbonded interactions: 489291 Sorted by model distance: nonbonded pdb=" O ILE d 111 " pdb=" OG1 THR d 114 " model vdw 2.199 2.440 nonbonded pdb=" ND2 ASN c 61 " pdb=" O PHE g 88 " model vdw 2.201 2.520 nonbonded pdb=" OG1 THR a 488 " pdb=" NE2 HIS f 35 " model vdw 2.203 2.520 nonbonded pdb=" O LEU B 425 " pdb=" NZ LYS B 430 " model vdw 2.205 2.520 nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.207 2.440 ... (remaining 489286 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 24 through 261 or (resid 262 through 270 and (name N or na \ me CA or name C or name O or name CB )) or resid 271 through 273 or (resid 274 t \ hrough 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ or name OXT)))) selection = (chain 'C' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 or (resid 31 and (name N or name CA or nam \ e C or name O or name CB )) or resid 32 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 284 or (resid 28 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 286 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 354 or (resid 355 through 356 and (name N or name CA or name C o \ r name O or name CB )) or resid 357 through 421 or (resid 422 and (name N or nam \ e CA or name C or name O or name CB )) or resid 423 through 589 or (resid 590 an \ d (name N or name CA or name C or name O or name CB )) or resid 591 through 592 \ or (resid 593 through 595 and (name N or name CA or name C or name O or name CB \ )) or resid 596 through 616)) selection = (chain 'E' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 or (resid 31 and (name N or name CA or nam \ e C or name O or name CB )) or resid 32 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 261 or (resid 26 \ 2 through 270 and (name N or name CA or name C or name O or name CB )) or resid \ 271 through 273 or (resid 274 through 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name CA \ or name C or name O or name CB )) or resid 286 through 308 or (resid 309 and (n \ ame N or name CA or name C or name O or name CB )) or resid 310 through 354 or ( \ resid 355 through 356 and (name N or name CA or name C or name O or name CB )) o \ r resid 357 through 421 or (resid 422 and (name N or name CA or name C or name O \ or name CB )) or resid 423 through 589 or (resid 590 and (name N or name CA or \ name C or name O or name CB )) or resid 591 through 592 or (resid 593 through 59 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 596 through \ 615 or (resid 616 and (name N or name CA or name C or name O or name CB or name \ OXT)))) } ncs_group { reference = (chain 'B' and (resid 14 through 104 or (resid 105 through 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 487)) selection = (chain 'D' and (resid 14 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 105 or (re \ sid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) \ or resid 483 through 487)) selection = (chain 'F' and ((resid 14 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 104 or (r \ esid 105 through 106 and (name N or name CA or name C or name O or name CB )) or \ resid 107 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 204 or (resid 205 and (name N or name CA or n \ ame C or name O or name CB )) or resid 206 through 481 or (resid 482 and (name N \ or name CA or name C or name O or name CB )) or resid 483 through 487)) } ncs_group { reference = (chain 'G' and (resid 9 through 91 or (resid 92 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name CB )) or resid 121 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 39 or (resid 140 through 141 and (name N or name CA or name C or name O or name \ CB )) or resid 142 or (resid 143 and (name N or name CA or name C or name O or n \ ame CB )) or resid 144 or (resid 145 through 152 and (name N or name CA or name \ C or name O or name CB )) or resid 153 through 156 or (resid 157 through 159 and \ (name N or name CA or name C or name O or name CB )) or resid 160 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 168 or (resid 169 through 177 and (name N or name CA or name C or nam \ e O or name CB )) or resid 178 or (resid 179 through 185 and (name N or name CA \ or name C or name O or name CB )) or resid 186 through 187 or (resid 188 through \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 or (r \ esid 207 through 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 217 or (resid 218 and (name N or name CA or name C or name O \ or name CB )) or resid 219 or (resid 220 through 222 and (name N or name CA or n \ ame C or name O or name CB )) or resid 223 through 228)) selection = (chain 'I' and (resid 9 through 84 or (resid 85 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 108 and (name N or name \ CA or name C or name O or name CB )) or (resid 109 through 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB )) or resid 121 through 125 or (resid \ 126 and (name N or name CA or name C or name O or name CB )) or resid 127 throug \ h 139 or (resid 140 through 141 and (name N or name CA or name C or name O or na \ me CB )) or resid 142 through 147 or (resid 148 through 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 155 or (resid 156 thro \ ugh 159 and (name N or name CA or name C or name O or name CB )) or resid 160 th \ rough 162 or (resid 163 through 165 and (name N or name CA or name C or name O o \ r name CB )) or resid 166 through 168 or (resid 169 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 180 or (resid 181 \ through 185 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 86 through 205 and (name N or name CA or name C or name O or name CB )) or resid \ 206 or (resid 207 through 215 and (name N or name CA or name C or name O or nam \ e CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or name C \ or name O or name CB )) or resid 219 or (resid 220 through 222 and (name N or na \ me CA or name C or name O or name CB )) or resid 223 through 228)) selection = (chain 'K' and (resid 9 through 99 or (resid 100 through 108 and (name N or name \ CA or name C or name O or name CB )) or (resid 109 through 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 144 or (resid 145 \ through 152 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 3 through 171 or (resid 172 through 177 and (name N or name CA or name C or name \ O or name CB )) or resid 178 through 196 or (resid 197 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 through 221 or (resid \ 222 and (name N or name CA or name C or name O or name CB )) or resid 223 throug \ h 228)) } ncs_group { reference = (chain 'H' and resid 2 through 112) selection = (chain 'J' and ((resid 2 through 62 and (name N or name CA or name C or name O o \ r name CB )) or (resid 63 through 104 and (name N or name CA or name C or name O \ or name CB )) or resid 105 through 112)) selection = (chain 'L' and (resid 2 through 109 or (resid 110 through 112 and (name N or nam \ e CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'g' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 159)) selection = (chain 'h' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'i' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'j' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'k' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 81 or (resid 82 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'l' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 129 or (res \ id 130 through 131 and (name N or name CA or name C or name O or name CB )) or r \ esid 132 through 140 or (resid 141 and (name N or name CA or name C or name O or \ name CB )) or resid 142 through 152 or (resid 153 through 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'm' and (resid 1 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 79 or (resid 80 through 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 85 or (resi \ d 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 129 or (resid 130 through 131 and (name N or name CA or name C or name O or na \ me CB )) or resid 132 through 140 or (resid 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 159)) selection = (chain 'n' and (resid 1 through 79 or (resid 80 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 85 or (resid 86 and (nam \ e N or name CA or name C or name O or name CB )) or resid 87 through 140 or (res \ id 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 152 or (resid 153 through 154 and (name N or name CA or name C or name O or \ name CB )) or resid 155 through 159)) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 9.010 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 125.990 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.004 0.090 58646 Z= 0.267 Angle : 0.661 10.873 80001 Z= 0.356 Chirality : 0.045 0.261 9567 Planarity : 0.005 0.087 10420 Dihedral : 12.966 178.719 19647 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8154 helix: 1.74 (0.07), residues: 4700 sheet: -1.23 (0.20), residues: 625 loop : -0.29 (0.12), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP a 594 HIS 0.009 0.001 HIS o 98 PHE 0.040 0.002 PHE o 96 TYR 0.043 0.002 TYR k 142 ARG 0.014 0.001 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1790 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1786 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8443 (p0) cc_final: 0.8210 (p0) REVERT: A 123 TYR cc_start: 0.8230 (m-80) cc_final: 0.7301 (m-80) REVERT: A 276 ASP cc_start: 0.8333 (m-30) cc_final: 0.8117 (m-30) REVERT: A 487 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7782 (pt0) REVERT: A 523 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 69 GLU cc_start: 0.7318 (tp30) cc_final: 0.6899 (tp30) REVERT: B 182 GLU cc_start: 0.7722 (mp0) cc_final: 0.6957 (mp0) REVERT: B 412 ASP cc_start: 0.7786 (m-30) cc_final: 0.7044 (m-30) REVERT: B 434 GLU cc_start: 0.8048 (pp20) cc_final: 0.7553 (pp20) REVERT: B 441 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8046 (mtmm) REVERT: B 456 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 472 MET cc_start: 0.5247 (mtm) cc_final: 0.4913 (mtm) REVERT: C 108 ILE cc_start: 0.9049 (mm) cc_final: 0.8737 (mm) REVERT: C 118 GLU cc_start: 0.7726 (tp30) cc_final: 0.7304 (tp30) REVERT: C 192 THR cc_start: 0.8441 (p) cc_final: 0.8211 (p) REVERT: C 285 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6977 (mm-30) REVERT: C 292 GLU cc_start: 0.8038 (tp30) cc_final: 0.6898 (tp30) REVERT: C 360 TRP cc_start: 0.8710 (t60) cc_final: 0.8352 (t60) REVERT: C 442 ASP cc_start: 0.7576 (t0) cc_final: 0.7239 (t0) REVERT: C 444 LYS cc_start: 0.8342 (mttp) cc_final: 0.8020 (mttp) REVERT: C 504 LYS cc_start: 0.8877 (mttt) cc_final: 0.8639 (mmtp) REVERT: C 540 ILE cc_start: 0.8834 (tp) cc_final: 0.8598 (tt) REVERT: D 51 GLU cc_start: 0.7890 (tt0) cc_final: 0.7645 (tt0) REVERT: D 74 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7134 (ttm110) REVERT: D 146 TYR cc_start: 0.8463 (t80) cc_final: 0.8169 (t80) REVERT: D 477 SER cc_start: 0.8824 (p) cc_final: 0.8593 (p) REVERT: E 124 ILE cc_start: 0.9131 (mm) cc_final: 0.8927 (mm) REVERT: E 129 ASP cc_start: 0.7526 (p0) cc_final: 0.7325 (p0) REVERT: E 362 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7585 (mt-10) REVERT: E 373 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7968 (mt-10) REVERT: E 425 ASP cc_start: 0.8558 (t70) cc_final: 0.8166 (t0) REVERT: E 500 GLN cc_start: 0.7823 (pp30) cc_final: 0.7484 (pp30) REVERT: E 522 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7702 (mtmt) REVERT: F 18 GLN cc_start: 0.6198 (mp10) cc_final: 0.5960 (mp10) REVERT: F 42 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7031 (mm-30) REVERT: F 98 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7698 (mt-10) REVERT: F 150 MET cc_start: 0.8079 (ttt) cc_final: 0.7788 (ttt) REVERT: F 220 GLU cc_start: 0.7792 (tp30) cc_final: 0.7163 (tp30) REVERT: F 297 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7175 (mt-10) REVERT: F 326 ASN cc_start: 0.8372 (m110) cc_final: 0.7895 (m110) REVERT: F 363 GLN cc_start: 0.7979 (mp10) cc_final: 0.7434 (mp10) REVERT: F 389 GLU cc_start: 0.8084 (tp30) cc_final: 0.7811 (tp30) REVERT: F 412 ASP cc_start: 0.7479 (m-30) cc_final: 0.6981 (m-30) REVERT: F 482 ASP cc_start: 0.7854 (m-30) cc_final: 0.7579 (m-30) REVERT: G 140 LYS cc_start: 0.7975 (tttp) cc_final: 0.7759 (tttm) REVERT: J 46 TYR cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: K 197 ILE cc_start: 0.8994 (mt) cc_final: 0.8771 (mt) REVERT: M 40 THR cc_start: 0.7878 (t) cc_final: 0.7621 (t) REVERT: M 42 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7757 (tpt-90) REVERT: M 55 GLN cc_start: 0.8666 (mp10) cc_final: 0.8440 (mp10) REVERT: M 182 GLU cc_start: 0.7741 (tp30) cc_final: 0.7509 (tp30) REVERT: a 31 TYR cc_start: 0.8228 (t80) cc_final: 0.7968 (t80) REVERT: a 41 PHE cc_start: 0.8247 (m-80) cc_final: 0.7795 (m-80) REVERT: a 53 ARG cc_start: 0.6312 (mpt180) cc_final: 0.5794 (mmt180) REVERT: a 57 ASN cc_start: 0.8705 (p0) cc_final: 0.8453 (p0) REVERT: a 60 ARG cc_start: 0.8871 (ptt90) cc_final: 0.8450 (ptt90) REVERT: a 285 TYR cc_start: 0.9079 (m-80) cc_final: 0.8859 (m-80) REVERT: a 312 ASP cc_start: 0.7258 (m-30) cc_final: 0.6954 (m-30) REVERT: a 344 ASP cc_start: 0.7709 (p0) cc_final: 0.7286 (p0) REVERT: a 437 LEU cc_start: 0.9062 (mt) cc_final: 0.8747 (mt) REVERT: a 465 ILE cc_start: 0.8602 (mt) cc_final: 0.8322 (mm) REVERT: a 529 LEU cc_start: 0.8639 (pt) cc_final: 0.7953 (pt) REVERT: a 536 LYS cc_start: 0.9186 (ptmt) cc_final: 0.8947 (ptmt) REVERT: a 737 TRP cc_start: 0.7778 (t60) cc_final: 0.7487 (t60) REVERT: a 753 MET cc_start: 0.7206 (ptm) cc_final: 0.6885 (tmm) REVERT: a 759 PHE cc_start: 0.7674 (t80) cc_final: 0.7272 (t80) REVERT: a 773 LEU cc_start: 0.8566 (tp) cc_final: 0.8128 (tp) REVERT: a 774 PHE cc_start: 0.8355 (t80) cc_final: 0.7465 (t80) REVERT: a 776 MET cc_start: 0.8345 (tpp) cc_final: 0.7824 (tpp) REVERT: a 791 THR cc_start: 0.9013 (p) cc_final: 0.8809 (p) REVERT: a 796 HIS cc_start: 0.7908 (m-70) cc_final: 0.7650 (m-70) REVERT: b 235 PHE cc_start: 0.7925 (t80) cc_final: 0.7603 (t80) REVERT: c 27 ILE cc_start: 0.9029 (tp) cc_final: 0.8789 (tp) REVERT: c 37 LEU cc_start: 0.9107 (tp) cc_final: 0.8869 (tp) REVERT: c 58 MET cc_start: 0.8223 (tmm) cc_final: 0.7753 (tmm) REVERT: c 102 ILE cc_start: 0.9278 (tp) cc_final: 0.9050 (tp) REVERT: c 105 ILE cc_start: 0.9244 (mm) cc_final: 0.8994 (mm) REVERT: c 147 TRP cc_start: 0.6559 (m-10) cc_final: 0.5925 (m-10) REVERT: c 158 ILE cc_start: 0.8958 (tp) cc_final: 0.8699 (tp) REVERT: c 197 LEU cc_start: 0.8960 (mt) cc_final: 0.8723 (mp) REVERT: d 6 PHE cc_start: 0.8635 (t80) cc_final: 0.8286 (t80) REVERT: d 79 GLU cc_start: 0.7145 (tp30) cc_final: 0.6800 (tp30) REVERT: d 125 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8425 (tm-30) REVERT: d 186 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8869 (tttp) REVERT: d 189 LEU cc_start: 0.9395 (tp) cc_final: 0.8998 (tp) REVERT: d 215 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7998 (tm-30) REVERT: d 234 ASP cc_start: 0.7866 (t70) cc_final: 0.7658 (t0) REVERT: d 236 ASP cc_start: 0.8350 (p0) cc_final: 0.7711 (p0) REVERT: d 266 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7821 (mtm110) REVERT: d 317 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6675 (tm-30) REVERT: d 344 VAL cc_start: 0.8381 (p) cc_final: 0.8180 (p) REVERT: e 11 PHE cc_start: 0.8427 (t80) cc_final: 0.8061 (t80) REVERT: e 47 MET cc_start: 0.8492 (tmm) cc_final: 0.8290 (tmm) REVERT: e 53 LEU cc_start: 0.8787 (tp) cc_final: 0.8496 (tp) REVERT: f 30 LEU cc_start: 0.9041 (tp) cc_final: 0.8822 (tp) REVERT: g 43 CYS cc_start: 0.7568 (t) cc_final: 0.7365 (t) REVERT: g 68 LEU cc_start: 0.8826 (tp) cc_final: 0.8470 (tp) REVERT: h 65 ILE cc_start: 0.9124 (mm) cc_final: 0.8846 (mm) REVERT: h 77 SER cc_start: 0.8691 (p) cc_final: 0.8444 (p) REVERT: h 106 PHE cc_start: 0.6988 (m-10) cc_final: 0.6623 (m-10) REVERT: h 126 PHE cc_start: 0.8303 (t80) cc_final: 0.8101 (t80) REVERT: h 150 LEU cc_start: 0.8881 (mt) cc_final: 0.8528 (mt) REVERT: h 156 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7359 (tp-100) REVERT: i 17 CYS cc_start: 0.8230 (t) cc_final: 0.8019 (t) REVERT: i 26 LEU cc_start: 0.8707 (mm) cc_final: 0.8408 (mm) REVERT: i 129 MET cc_start: 0.7767 (tmm) cc_final: 0.7534 (tmm) REVERT: j 21 ILE cc_start: 0.8674 (tp) cc_final: 0.8419 (tp) REVERT: j 30 TYR cc_start: 0.7853 (t80) cc_final: 0.7631 (t80) REVERT: j 39 ILE cc_start: 0.8814 (mm) cc_final: 0.8367 (mm) REVERT: j 52 LYS cc_start: 0.8337 (tptt) cc_final: 0.8026 (tppt) REVERT: j 73 LEU cc_start: 0.7948 (tp) cc_final: 0.7458 (tp) REVERT: j 117 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7547 (mmm-85) REVERT: k 11 PHE cc_start: 0.8409 (t80) cc_final: 0.7901 (t80) REVERT: k 39 ILE cc_start: 0.8305 (mm) cc_final: 0.7688 (mt) REVERT: k 49 LEU cc_start: 0.8721 (tp) cc_final: 0.8448 (tp) REVERT: k 73 LEU cc_start: 0.8514 (tp) cc_final: 0.8153 (tp) REVERT: k 82 GLN cc_start: 0.6263 (pp30) cc_final: 0.5747 (pt0) REVERT: k 88 PHE cc_start: 0.7918 (m-80) cc_final: 0.7587 (m-80) REVERT: k 130 ILE cc_start: 0.8636 (mm) cc_final: 0.8292 (mm) REVERT: k 134 ILE cc_start: 0.9066 (mp) cc_final: 0.8858 (mp) REVERT: k 151 ASN cc_start: 0.7767 (t0) cc_final: 0.7346 (t0) REVERT: k 157 ASP cc_start: 0.8026 (p0) cc_final: 0.7825 (p0) REVERT: l 53 ASN cc_start: 0.7575 (m-40) cc_final: 0.7308 (m-40) REVERT: l 88 PHE cc_start: 0.7552 (m-80) cc_final: 0.7297 (m-80) REVERT: l 95 LEU cc_start: 0.8852 (mm) cc_final: 0.8517 (mm) REVERT: l 141 LEU cc_start: 0.8399 (tt) cc_final: 0.8183 (tt) REVERT: l 144 LEU cc_start: 0.8932 (tp) cc_final: 0.8432 (tp) REVERT: l 148 LEU cc_start: 0.8480 (mt) cc_final: 0.8227 (mt) REVERT: l 151 ASN cc_start: 0.8326 (t0) cc_final: 0.8078 (t0) REVERT: m 39 ILE cc_start: 0.8266 (mm) cc_final: 0.7434 (mm) REVERT: m 40 CYS cc_start: 0.8819 (m) cc_final: 0.8521 (m) REVERT: m 43 CYS cc_start: 0.7497 (m) cc_final: 0.7288 (m) REVERT: m 121 GLN cc_start: 0.7933 (mp10) cc_final: 0.7541 (mp10) REVERT: m 129 MET cc_start: 0.7529 (tmm) cc_final: 0.7189 (tmm) REVERT: m 156 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7750 (tm-30) REVERT: n 15 ILE cc_start: 0.8442 (mm) cc_final: 0.8222 (mm) REVERT: n 21 ILE cc_start: 0.8857 (tp) cc_final: 0.8593 (tp) REVERT: n 22 ILE cc_start: 0.8919 (mt) cc_final: 0.8701 (mt) REVERT: n 46 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7867 (ttp80) REVERT: n 58 ILE cc_start: 0.9151 (mm) cc_final: 0.8944 (mm) REVERT: n 133 LEU cc_start: 0.9269 (mm) cc_final: 0.9048 (mt) REVERT: o 64 VAL cc_start: 0.8738 (t) cc_final: 0.8528 (t) REVERT: o 74 LEU cc_start: 0.8792 (tp) cc_final: 0.8309 (tp) REVERT: o 85 SER cc_start: 0.8854 (p) cc_final: 0.8165 (m) REVERT: o 152 MET cc_start: 0.7405 (tmm) cc_final: 0.6935 (tmm) outliers start: 4 outliers final: 0 residues processed: 1787 average time/residue: 0.6031 time to fit residues: 1791.2626 Evaluate side-chains 1595 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1595 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 7.9990 chunk 611 optimal weight: 0.6980 chunk 339 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 412 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 632 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 384 optimal weight: 0.0050 chunk 470 optimal weight: 0.0970 chunk 732 optimal weight: 0.3980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 248 GLN A 267 GLN B 78 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 135 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN a 134 GLN ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 106 ASN ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58646 Z= 0.182 Angle : 0.608 11.049 80001 Z= 0.321 Chirality : 0.043 0.248 9567 Planarity : 0.006 0.070 10420 Dihedral : 4.903 178.620 8735 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 12.34 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8154 helix: 1.52 (0.07), residues: 4702 sheet: -1.32 (0.20), residues: 619 loop : -0.26 (0.12), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP a 594 HIS 0.006 0.001 HIS a 796 PHE 0.033 0.002 PHE o 96 TYR 0.054 0.001 TYR c 22 ARG 0.009 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1687 time to evaluate : 5.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.8262 (m-30) cc_final: 0.8020 (m-30) REVERT: A 523 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 541 TRP cc_start: 0.8656 (p-90) cc_final: 0.8395 (p-90) REVERT: B 69 GLU cc_start: 0.7332 (tp30) cc_final: 0.7070 (tp30) REVERT: B 78 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: B 295 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.8065 (ttp-170) REVERT: B 412 ASP cc_start: 0.7819 (m-30) cc_final: 0.7075 (m-30) REVERT: B 441 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8024 (mtmm) REVERT: B 456 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 40 MET cc_start: 0.8294 (mmm) cc_final: 0.7619 (mmm) REVERT: C 118 GLU cc_start: 0.7729 (tp30) cc_final: 0.7270 (tp30) REVERT: C 285 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6905 (mm-30) REVERT: C 290 MET cc_start: 0.8561 (mmm) cc_final: 0.8265 (tpp) REVERT: C 352 MET cc_start: 0.8614 (ttp) cc_final: 0.8396 (tmm) REVERT: C 442 ASP cc_start: 0.7622 (t0) cc_final: 0.7260 (t70) REVERT: C 504 LYS cc_start: 0.8802 (mttt) cc_final: 0.8487 (mmtp) REVERT: C 540 ILE cc_start: 0.8822 (tp) cc_final: 0.8566 (tt) REVERT: C 608 GLN cc_start: 0.8359 (tp40) cc_final: 0.7983 (tp-100) REVERT: D 51 GLU cc_start: 0.7918 (tt0) cc_final: 0.7651 (tt0) REVERT: D 74 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7300 (ttm110) REVERT: D 223 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7515 (mmm-85) REVERT: D 477 SER cc_start: 0.8839 (p) cc_final: 0.8581 (p) REVERT: E 124 ILE cc_start: 0.9119 (mm) cc_final: 0.8905 (mm) REVERT: E 362 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 378 GLN cc_start: 0.8716 (mt0) cc_final: 0.8204 (mt0) REVERT: E 425 ASP cc_start: 0.8582 (t70) cc_final: 0.8217 (t70) REVERT: E 500 GLN cc_start: 0.7916 (pp30) cc_final: 0.7596 (pp30) REVERT: E 522 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7626 (mtmt) REVERT: F 18 GLN cc_start: 0.6081 (mp10) cc_final: 0.5822 (mp10) REVERT: F 42 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7174 (mm-30) REVERT: F 74 ARG cc_start: 0.8703 (ptm-80) cc_final: 0.8301 (ttp80) REVERT: F 98 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7674 (mt-10) REVERT: F 150 MET cc_start: 0.8242 (ttt) cc_final: 0.8026 (ttt) REVERT: F 220 GLU cc_start: 0.7735 (tp30) cc_final: 0.7101 (tp30) REVERT: F 251 GLU cc_start: 0.7892 (tt0) cc_final: 0.7492 (tt0) REVERT: F 326 ASN cc_start: 0.8352 (m110) cc_final: 0.7889 (m110) REVERT: F 363 GLN cc_start: 0.8070 (mp10) cc_final: 0.7445 (mp10) REVERT: F 389 GLU cc_start: 0.8147 (tp30) cc_final: 0.7761 (tp30) REVERT: F 412 ASP cc_start: 0.7452 (m-30) cc_final: 0.7108 (m-30) REVERT: F 428 GLU cc_start: 0.7270 (tp30) cc_final: 0.7000 (tp30) REVERT: F 482 ASP cc_start: 0.7799 (m-30) cc_final: 0.7527 (m-30) REVERT: G 134 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8230 (mm-30) REVERT: G 166 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8322 (mmm-85) REVERT: G 198 GLU cc_start: 0.7710 (pm20) cc_final: 0.7343 (pm20) REVERT: I 105 GLU cc_start: 0.8053 (mp0) cc_final: 0.7801 (mp0) REVERT: J 46 TYR cc_start: 0.8095 (t80) cc_final: 0.7837 (t80) REVERT: K 197 ILE cc_start: 0.8948 (mt) cc_final: 0.8735 (mt) REVERT: M 34 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7500 (mtp-110) REVERT: M 42 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7742 (tpt-90) REVERT: M 55 GLN cc_start: 0.8494 (mp10) cc_final: 0.8282 (mp10) REVERT: M 62 GLN cc_start: 0.6569 (pp30) cc_final: 0.6158 (pt0) REVERT: M 182 GLU cc_start: 0.7735 (tp30) cc_final: 0.7017 (tp30) REVERT: M 221 MET cc_start: 0.4057 (ppp) cc_final: 0.3645 (ppp) REVERT: a 41 PHE cc_start: 0.8094 (m-80) cc_final: 0.7660 (m-80) REVERT: a 60 ARG cc_start: 0.8837 (ptt90) cc_final: 0.8333 (ptt90) REVERT: a 68 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7823 (mm110) REVERT: a 211 LEU cc_start: 0.8428 (pt) cc_final: 0.8132 (pp) REVERT: a 285 TYR cc_start: 0.9075 (m-80) cc_final: 0.8803 (m-80) REVERT: a 312 ASP cc_start: 0.7322 (m-30) cc_final: 0.7036 (m-30) REVERT: a 344 ASP cc_start: 0.7851 (p0) cc_final: 0.7373 (p0) REVERT: a 369 GLN cc_start: 0.7133 (tp-100) cc_final: 0.6916 (tp-100) REVERT: a 465 ILE cc_start: 0.8646 (mt) cc_final: 0.8435 (mm) REVERT: a 537 MET cc_start: 0.8194 (mmt) cc_final: 0.7697 (mmt) REVERT: a 737 TRP cc_start: 0.7684 (t60) cc_final: 0.7438 (t60) REVERT: a 753 MET cc_start: 0.7030 (ptm) cc_final: 0.6703 (tmm) REVERT: a 759 PHE cc_start: 0.7570 (t80) cc_final: 0.7202 (t80) REVERT: a 773 LEU cc_start: 0.8536 (tp) cc_final: 0.8061 (tp) REVERT: a 774 PHE cc_start: 0.8067 (t80) cc_final: 0.7660 (t80) REVERT: a 776 MET cc_start: 0.8298 (tpp) cc_final: 0.7834 (tpp) REVERT: b 235 PHE cc_start: 0.7940 (t80) cc_final: 0.7604 (t80) REVERT: b 246 ASN cc_start: 0.8383 (m-40) cc_final: 0.8034 (t0) REVERT: c 27 ILE cc_start: 0.9044 (tp) cc_final: 0.8659 (tp) REVERT: c 58 MET cc_start: 0.8100 (tmm) cc_final: 0.7875 (tmm) REVERT: c 158 ILE cc_start: 0.8934 (tp) cc_final: 0.8620 (tp) REVERT: c 183 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8538 (mtmm) REVERT: d 79 GLU cc_start: 0.7261 (tp30) cc_final: 0.6683 (tp30) REVERT: d 85 ASP cc_start: 0.7603 (p0) cc_final: 0.7359 (p0) REVERT: d 125 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8480 (tm-30) REVERT: d 189 LEU cc_start: 0.9352 (tp) cc_final: 0.9122 (tp) REVERT: d 215 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8100 (tm-30) REVERT: d 314 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8366 (mmmm) REVERT: d 317 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7292 (tm-30) REVERT: d 336 GLU cc_start: 0.8054 (pm20) cc_final: 0.7815 (pm20) REVERT: e 47 MET cc_start: 0.8586 (tmm) cc_final: 0.8318 (tmm) REVERT: e 53 LEU cc_start: 0.8781 (tp) cc_final: 0.8455 (tp) REVERT: f 30 LEU cc_start: 0.9325 (tp) cc_final: 0.9002 (tp) REVERT: g 134 ILE cc_start: 0.9081 (mm) cc_final: 0.8838 (mt) REVERT: g 137 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7881 (mm-30) REVERT: h 52 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8590 (tttm) REVERT: h 65 ILE cc_start: 0.9113 (mm) cc_final: 0.8876 (mm) REVERT: h 77 SER cc_start: 0.8605 (p) cc_final: 0.8355 (p) REVERT: h 106 PHE cc_start: 0.7033 (m-10) cc_final: 0.6751 (m-10) REVERT: h 129 MET cc_start: 0.8425 (tmm) cc_final: 0.8218 (tmm) REVERT: i 26 LEU cc_start: 0.8835 (mm) cc_final: 0.8598 (mm) REVERT: j 73 LEU cc_start: 0.8301 (tp) cc_final: 0.7999 (tp) REVERT: j 91 LEU cc_start: 0.8875 (tp) cc_final: 0.8487 (tt) REVERT: j 149 LEU cc_start: 0.8469 (tp) cc_final: 0.8149 (tt) REVERT: k 11 PHE cc_start: 0.8486 (t80) cc_final: 0.8195 (t80) REVERT: k 30 TYR cc_start: 0.8620 (t80) cc_final: 0.8420 (t80) REVERT: k 49 LEU cc_start: 0.8502 (tp) cc_final: 0.8232 (tp) REVERT: k 82 GLN cc_start: 0.6185 (pp30) cc_final: 0.5760 (pt0) REVERT: k 85 TYR cc_start: 0.8558 (t80) cc_final: 0.8344 (t80) REVERT: k 88 PHE cc_start: 0.7897 (m-80) cc_final: 0.7662 (m-80) REVERT: k 130 ILE cc_start: 0.9000 (mm) cc_final: 0.8780 (mm) REVERT: k 157 ASP cc_start: 0.8018 (p0) cc_final: 0.7758 (p0) REVERT: l 30 TYR cc_start: 0.8321 (t80) cc_final: 0.8111 (t80) REVERT: l 88 PHE cc_start: 0.7588 (m-80) cc_final: 0.7215 (m-80) REVERT: l 95 LEU cc_start: 0.8786 (mm) cc_final: 0.8472 (mm) REVERT: l 121 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7491 (mm-40) REVERT: l 144 LEU cc_start: 0.9024 (tp) cc_final: 0.8677 (tp) REVERT: l 148 LEU cc_start: 0.8780 (mt) cc_final: 0.8521 (mt) REVERT: m 8 TYR cc_start: 0.8489 (p90) cc_final: 0.8287 (p90) REVERT: m 39 ILE cc_start: 0.8262 (mm) cc_final: 0.7374 (mm) REVERT: m 40 CYS cc_start: 0.8829 (m) cc_final: 0.8550 (m) REVERT: m 43 CYS cc_start: 0.7593 (m) cc_final: 0.7340 (m) REVERT: m 80 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8043 (tm-30) REVERT: m 121 GLN cc_start: 0.7824 (mp10) cc_final: 0.7494 (mp10) REVERT: m 129 MET cc_start: 0.7888 (tmm) cc_final: 0.7623 (tmm) REVERT: m 156 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7869 (tm-30) REVERT: n 21 ILE cc_start: 0.8650 (tp) cc_final: 0.8412 (tp) REVERT: n 22 ILE cc_start: 0.8893 (mt) cc_final: 0.8631 (mt) REVERT: n 59 MET cc_start: 0.8498 (tpp) cc_final: 0.8202 (mmm) REVERT: n 117 ARG cc_start: 0.7924 (mmt180) cc_final: 0.7657 (mmt180) REVERT: n 122 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8600 (tm-30) REVERT: o 74 LEU cc_start: 0.8613 (tp) cc_final: 0.8325 (tp) REVERT: o 85 SER cc_start: 0.8924 (p) cc_final: 0.8325 (m) REVERT: o 152 MET cc_start: 0.7769 (tmm) cc_final: 0.7401 (tmm) outliers start: 94 outliers final: 55 residues processed: 1705 average time/residue: 0.5544 time to fit residues: 1577.0465 Evaluate side-chains 1661 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1605 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 65 ILE Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain k residue 17 CYS Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 106 PHE Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 75 CYS Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 144 LEU Chi-restraints excluded: chain o residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 40.0000 chunk 227 optimal weight: 0.3980 chunk 609 optimal weight: 7.9990 chunk 499 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 734 optimal weight: 0.7980 chunk 793 optimal weight: 4.9990 chunk 653 optimal weight: 0.0020 chunk 728 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 588 optimal weight: 10.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 78 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 135 ASN D 339 ASN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN E 608 GLN K 122 GLN ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 715 GLN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 213 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 121 GLN l 151 ASN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58646 Z= 0.185 Angle : 0.575 10.375 80001 Z= 0.303 Chirality : 0.042 0.199 9567 Planarity : 0.005 0.072 10420 Dihedral : 4.770 177.245 8735 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 15.50 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8154 helix: 1.37 (0.08), residues: 4715 sheet: -1.35 (0.19), residues: 637 loop : -0.26 (0.12), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 594 HIS 0.005 0.001 HIS o 98 PHE 0.037 0.002 PHE o 96 TYR 0.043 0.001 TYR c 22 ARG 0.009 0.000 ARG M 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1801 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1667 time to evaluate : 5.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: A 205 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8305 (tmtt) REVERT: A 276 ASP cc_start: 0.8246 (m-30) cc_final: 0.8004 (m-30) REVERT: A 523 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 541 TRP cc_start: 0.8625 (p-90) cc_final: 0.8234 (p-90) REVERT: B 69 GLU cc_start: 0.7253 (tp30) cc_final: 0.6975 (tp30) REVERT: B 182 GLU cc_start: 0.7819 (mp0) cc_final: 0.7357 (mp0) REVERT: B 412 ASP cc_start: 0.7736 (m-30) cc_final: 0.7039 (m-30) REVERT: B 441 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7846 (mtmt) REVERT: B 456 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 40 MET cc_start: 0.8249 (mmm) cc_final: 0.7607 (mmm) REVERT: C 118 GLU cc_start: 0.7723 (tp30) cc_final: 0.7270 (tp30) REVERT: C 285 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6910 (mm-30) REVERT: C 290 MET cc_start: 0.8559 (mmm) cc_final: 0.8303 (tpp) REVERT: C 292 GLU cc_start: 0.7900 (tp30) cc_final: 0.6762 (tp30) REVERT: C 442 ASP cc_start: 0.7730 (t0) cc_final: 0.7458 (t0) REVERT: C 540 ILE cc_start: 0.8816 (tp) cc_final: 0.8551 (tt) REVERT: C 556 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 608 GLN cc_start: 0.8363 (tp40) cc_final: 0.7980 (tp-100) REVERT: D 51 GLU cc_start: 0.7920 (tt0) cc_final: 0.7631 (tt0) REVERT: D 74 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7156 (ttm110) REVERT: D 146 TYR cc_start: 0.8318 (t80) cc_final: 0.7918 (t80) REVERT: D 223 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7511 (mmm-85) REVERT: D 477 SER cc_start: 0.8861 (p) cc_final: 0.8614 (p) REVERT: E 362 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7531 (mt-10) REVERT: E 378 GLN cc_start: 0.8748 (mt0) cc_final: 0.8473 (mt0) REVERT: E 500 GLN cc_start: 0.7950 (pp30) cc_final: 0.7589 (pp30) REVERT: E 522 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7682 (mtmt) REVERT: F 42 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7263 (mm-30) REVERT: F 74 ARG cc_start: 0.8685 (ptm-80) cc_final: 0.8455 (ttp-170) REVERT: F 98 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7683 (mt-10) REVERT: F 106 GLU cc_start: 0.7916 (mp0) cc_final: 0.6886 (mp0) REVERT: F 150 MET cc_start: 0.8237 (ttt) cc_final: 0.7979 (ttt) REVERT: F 220 GLU cc_start: 0.7739 (tp30) cc_final: 0.7104 (tp30) REVERT: F 251 GLU cc_start: 0.7873 (tt0) cc_final: 0.7648 (tt0) REVERT: F 326 ASN cc_start: 0.8359 (m110) cc_final: 0.7896 (m110) REVERT: F 363 GLN cc_start: 0.8017 (mp10) cc_final: 0.7379 (mp10) REVERT: F 389 GLU cc_start: 0.8126 (tp30) cc_final: 0.7684 (tp30) REVERT: F 398 ASP cc_start: 0.8030 (m-30) cc_final: 0.7828 (m-30) REVERT: F 412 ASP cc_start: 0.7520 (m-30) cc_final: 0.7032 (m-30) REVERT: F 428 GLU cc_start: 0.7270 (tp30) cc_final: 0.7067 (tp30) REVERT: F 482 ASP cc_start: 0.7799 (m-30) cc_final: 0.7499 (m-30) REVERT: G 134 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8226 (mm-30) REVERT: G 140 LYS cc_start: 0.8101 (tttm) cc_final: 0.7765 (tttm) REVERT: I 105 GLU cc_start: 0.8193 (mp0) cc_final: 0.7898 (mp0) REVERT: J 46 TYR cc_start: 0.8087 (t80) cc_final: 0.7838 (t80) REVERT: M 34 ARG cc_start: 0.7915 (ptm160) cc_final: 0.7668 (ptm160) REVERT: M 182 GLU cc_start: 0.7726 (tp30) cc_final: 0.7482 (tp30) REVERT: a 8 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8458 (tt) REVERT: a 14 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5556 (ptp) REVERT: a 31 TYR cc_start: 0.7986 (t80) cc_final: 0.7713 (t80) REVERT: a 41 PHE cc_start: 0.8078 (m-80) cc_final: 0.7567 (m-80) REVERT: a 60 ARG cc_start: 0.8808 (ptt90) cc_final: 0.8348 (ptt90) REVERT: a 67 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8393 (ttp-110) REVERT: a 68 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7962 (mm110) REVERT: a 285 TYR cc_start: 0.9093 (m-80) cc_final: 0.8860 (m-80) REVERT: a 324 ASN cc_start: 0.8562 (t0) cc_final: 0.8358 (m-40) REVERT: a 344 ASP cc_start: 0.7936 (p0) cc_final: 0.7442 (p0) REVERT: a 369 GLN cc_start: 0.7049 (tp-100) cc_final: 0.6825 (tp-100) REVERT: a 465 ILE cc_start: 0.8667 (mt) cc_final: 0.8444 (mm) REVERT: a 474 TYR cc_start: 0.7578 (t80) cc_final: 0.6683 (t80) REVERT: a 478 LEU cc_start: 0.8584 (mt) cc_final: 0.7036 (mt) REVERT: a 537 MET cc_start: 0.8335 (mmt) cc_final: 0.7838 (mmm) REVERT: a 579 MET cc_start: 0.8142 (ppp) cc_final: 0.7250 (ppp) REVERT: a 745 GLN cc_start: 0.8062 (tp40) cc_final: 0.7814 (tp40) REVERT: a 753 MET cc_start: 0.7061 (ptm) cc_final: 0.6754 (tmm) REVERT: a 759 PHE cc_start: 0.7574 (t80) cc_final: 0.7090 (t80) REVERT: a 769 MET cc_start: 0.8271 (mtp) cc_final: 0.7589 (mtp) REVERT: a 773 LEU cc_start: 0.8551 (tp) cc_final: 0.8117 (tp) REVERT: a 774 PHE cc_start: 0.8055 (t80) cc_final: 0.7688 (t80) REVERT: a 776 MET cc_start: 0.8254 (tpp) cc_final: 0.7751 (tpp) REVERT: a 778 PHE cc_start: 0.8634 (t80) cc_final: 0.8428 (t80) REVERT: a 787 LEU cc_start: 0.8543 (tt) cc_final: 0.8302 (tt) REVERT: b 235 PHE cc_start: 0.7944 (t80) cc_final: 0.7582 (t80) REVERT: b 246 ASN cc_start: 0.8316 (m-40) cc_final: 0.8025 (t0) REVERT: c 27 ILE cc_start: 0.8988 (tp) cc_final: 0.8704 (tp) REVERT: c 58 MET cc_start: 0.8111 (tmm) cc_final: 0.7885 (tmm) REVERT: c 106 PHE cc_start: 0.7965 (m-80) cc_final: 0.7133 (t80) REVERT: c 158 ILE cc_start: 0.8939 (tp) cc_final: 0.8606 (tp) REVERT: c 213 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: d 70 GLU cc_start: 0.8625 (tt0) cc_final: 0.8326 (tm-30) REVERT: d 79 GLU cc_start: 0.7262 (tp30) cc_final: 0.7049 (tp30) REVERT: d 97 TYR cc_start: 0.8403 (m-80) cc_final: 0.8192 (m-80) REVERT: d 125 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8591 (tm-30) REVERT: d 126 ARG cc_start: 0.8297 (ttt180) cc_final: 0.7882 (ttm-80) REVERT: d 191 ASP cc_start: 0.7555 (t0) cc_final: 0.6458 (t0) REVERT: d 251 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8185 (pp) REVERT: d 285 GLU cc_start: 0.6634 (tt0) cc_final: 0.6364 (tt0) REVERT: d 317 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7598 (tm-30) REVERT: d 334 GLN cc_start: 0.7921 (mt0) cc_final: 0.7494 (mt0) REVERT: d 336 GLU cc_start: 0.8049 (pm20) cc_final: 0.7837 (pm20) REVERT: e 47 MET cc_start: 0.8588 (tmm) cc_final: 0.8008 (tmm) REVERT: e 53 LEU cc_start: 0.8748 (tp) cc_final: 0.8389 (tp) REVERT: f 30 LEU cc_start: 0.9302 (tp) cc_final: 0.8947 (tp) REVERT: g 91 LEU cc_start: 0.9057 (tp) cc_final: 0.8622 (tp) REVERT: g 129 MET cc_start: 0.7798 (tmm) cc_final: 0.7548 (tmm) REVERT: h 65 ILE cc_start: 0.9091 (mm) cc_final: 0.8836 (mm) REVERT: h 77 SER cc_start: 0.8586 (p) cc_final: 0.8276 (p) REVERT: h 106 PHE cc_start: 0.7020 (m-80) cc_final: 0.6732 (m-10) REVERT: i 11 PHE cc_start: 0.8066 (t80) cc_final: 0.7699 (t80) REVERT: i 129 MET cc_start: 0.8029 (tmm) cc_final: 0.7730 (tmm) REVERT: j 73 LEU cc_start: 0.8403 (tp) cc_final: 0.8048 (tp) REVERT: j 117 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: k 11 PHE cc_start: 0.8445 (t80) cc_final: 0.8076 (t80) REVERT: k 53 ASN cc_start: 0.8086 (p0) cc_final: 0.7755 (p0) REVERT: k 90 GLN cc_start: 0.8571 (mt0) cc_final: 0.8174 (mt0) REVERT: k 157 ASP cc_start: 0.8036 (p0) cc_final: 0.7731 (p0) REVERT: l 48 ASP cc_start: 0.8384 (p0) cc_final: 0.8117 (p0) REVERT: l 88 PHE cc_start: 0.7696 (m-80) cc_final: 0.7358 (m-80) REVERT: l 95 LEU cc_start: 0.8798 (mm) cc_final: 0.8465 (mm) REVERT: l 117 ARG cc_start: 0.8420 (mmt90) cc_final: 0.8106 (mmt-90) REVERT: l 144 LEU cc_start: 0.8997 (tp) cc_final: 0.8607 (tp) REVERT: l 148 LEU cc_start: 0.8807 (mt) cc_final: 0.8529 (mt) REVERT: m 39 ILE cc_start: 0.8383 (mm) cc_final: 0.7405 (mm) REVERT: m 40 CYS cc_start: 0.8911 (m) cc_final: 0.8618 (m) REVERT: m 43 CYS cc_start: 0.7508 (m) cc_final: 0.7242 (m) REVERT: m 90 GLN cc_start: 0.8359 (mt0) cc_final: 0.8046 (mt0) REVERT: m 121 GLN cc_start: 0.7854 (mp10) cc_final: 0.7596 (mp10) REVERT: m 129 MET cc_start: 0.7856 (tmm) cc_final: 0.7406 (tmm) REVERT: m 133 LEU cc_start: 0.8557 (mt) cc_final: 0.8323 (mm) REVERT: m 156 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7883 (tm-30) REVERT: n 21 ILE cc_start: 0.8587 (tp) cc_final: 0.8346 (tp) REVERT: n 22 ILE cc_start: 0.8881 (mt) cc_final: 0.8612 (mt) REVERT: n 59 MET cc_start: 0.8606 (tpp) cc_final: 0.8289 (mmm) REVERT: n 110 ILE cc_start: 0.9028 (mm) cc_final: 0.8772 (mm) REVERT: n 117 ARG cc_start: 0.7886 (mmt180) cc_final: 0.7444 (mmt180) REVERT: n 122 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8130 (tm-30) REVERT: o 51 PHE cc_start: 0.8611 (m-80) cc_final: 0.8250 (m-80) REVERT: o 83 ASN cc_start: 0.8001 (p0) cc_final: 0.7671 (p0) REVERT: o 85 SER cc_start: 0.8931 (p) cc_final: 0.8371 (m) REVERT: o 130 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8519 (tm-30) REVERT: o 152 MET cc_start: 0.7940 (tmm) cc_final: 0.7614 (tmm) outliers start: 134 outliers final: 84 residues processed: 1703 average time/residue: 0.5973 time to fit residues: 1712.8945 Evaluate side-chains 1706 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1617 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 586 LEU Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 213 GLN Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 126 PHE Chi-restraints excluded: chain j residue 137 GLU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 106 PHE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 151 ASN Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 19 SER Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 79 LEU Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 128 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 2.9990 chunk 551 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 350 optimal weight: 0.8980 chunk 492 optimal weight: 9.9990 chunk 736 optimal weight: 0.9990 chunk 780 optimal weight: 2.9990 chunk 384 optimal weight: 8.9990 chunk 698 optimal weight: 5.9990 chunk 210 optimal weight: 0.0980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 78 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 135 ASN D 232 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 HIS E 346 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 162 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 151 ASN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 58646 Z= 0.249 Angle : 0.584 11.011 80001 Z= 0.308 Chirality : 0.043 0.296 9567 Planarity : 0.005 0.073 10420 Dihedral : 4.792 179.335 8735 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 3.12 % Allowed : 17.94 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 8154 helix: 1.32 (0.08), residues: 4720 sheet: -1.35 (0.19), residues: 622 loop : -0.27 (0.12), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP a 737 HIS 0.005 0.001 HIS o 98 PHE 0.037 0.002 PHE o 96 TYR 0.040 0.001 TYR c 22 ARG 0.009 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1657 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: A 205 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8311 (tmtt) REVERT: A 276 ASP cc_start: 0.8301 (m-30) cc_final: 0.8076 (m-30) REVERT: A 523 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 541 TRP cc_start: 0.8687 (p-90) cc_final: 0.8460 (p-90) REVERT: B 69 GLU cc_start: 0.7272 (tp30) cc_final: 0.6940 (tp30) REVERT: B 412 ASP cc_start: 0.7731 (m-30) cc_final: 0.7044 (m-30) REVERT: C 40 MET cc_start: 0.8208 (mmm) cc_final: 0.7721 (mmm) REVERT: C 118 GLU cc_start: 0.7751 (tp30) cc_final: 0.7188 (tp30) REVERT: C 285 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6924 (mm-30) REVERT: C 290 MET cc_start: 0.8482 (mmm) cc_final: 0.8207 (tpp) REVERT: C 292 GLU cc_start: 0.7814 (tp30) cc_final: 0.6891 (tp30) REVERT: C 442 ASP cc_start: 0.7753 (t0) cc_final: 0.7438 (t70) REVERT: C 509 ASP cc_start: 0.8067 (t0) cc_final: 0.7838 (t0) REVERT: C 540 ILE cc_start: 0.8851 (tp) cc_final: 0.8578 (tt) REVERT: C 608 GLN cc_start: 0.8390 (tp40) cc_final: 0.7983 (tp-100) REVERT: D 51 GLU cc_start: 0.7937 (tt0) cc_final: 0.7629 (tt0) REVERT: D 74 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7295 (ttm110) REVERT: D 146 TYR cc_start: 0.8479 (t80) cc_final: 0.8024 (t80) REVERT: D 400 SER cc_start: 0.8219 (t) cc_final: 0.7922 (p) REVERT: D 477 SER cc_start: 0.8856 (p) cc_final: 0.8604 (p) REVERT: E 362 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 500 GLN cc_start: 0.7966 (pp30) cc_final: 0.7596 (pp30) REVERT: E 522 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7691 (mtmt) REVERT: F 98 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7713 (mt-10) REVERT: F 150 MET cc_start: 0.8266 (ttt) cc_final: 0.8026 (ttt) REVERT: F 231 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7636 (mt-10) REVERT: F 236 GLU cc_start: 0.8415 (pt0) cc_final: 0.8033 (pm20) REVERT: F 251 GLU cc_start: 0.7924 (tt0) cc_final: 0.7678 (tt0) REVERT: F 311 ASP cc_start: 0.7265 (t0) cc_final: 0.6964 (t0) REVERT: F 326 ASN cc_start: 0.8401 (m110) cc_final: 0.7923 (m110) REVERT: F 363 GLN cc_start: 0.7990 (mp10) cc_final: 0.7332 (mp10) REVERT: F 389 GLU cc_start: 0.8153 (tp30) cc_final: 0.7821 (tp30) REVERT: F 398 ASP cc_start: 0.8029 (m-30) cc_final: 0.7824 (m-30) REVERT: F 412 ASP cc_start: 0.7489 (m-30) cc_final: 0.7036 (m-30) REVERT: F 428 GLU cc_start: 0.7441 (tp30) cc_final: 0.7228 (tp30) REVERT: F 482 ASP cc_start: 0.7860 (m-30) cc_final: 0.7545 (m-30) REVERT: G 134 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8224 (mm-30) REVERT: I 105 GLU cc_start: 0.8244 (mp0) cc_final: 0.7895 (mp0) REVERT: J 46 TYR cc_start: 0.8053 (t80) cc_final: 0.7784 (t80) REVERT: M 182 GLU cc_start: 0.7820 (tp30) cc_final: 0.7541 (tp30) REVERT: M 221 MET cc_start: 0.3893 (ppp) cc_final: 0.3508 (ppp) REVERT: a 8 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8559 (tt) REVERT: a 14 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5683 (ptp) REVERT: a 31 TYR cc_start: 0.8015 (t80) cc_final: 0.7724 (t80) REVERT: a 38 LEU cc_start: 0.7712 (mm) cc_final: 0.7323 (tt) REVERT: a 41 PHE cc_start: 0.8135 (m-80) cc_final: 0.7639 (m-80) REVERT: a 60 ARG cc_start: 0.8806 (ptt90) cc_final: 0.8362 (ptt90) REVERT: a 67 ARG cc_start: 0.8772 (ttp-110) cc_final: 0.8364 (ttp-110) REVERT: a 68 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8061 (mm110) REVERT: a 211 LEU cc_start: 0.8423 (pt) cc_final: 0.8135 (pp) REVERT: a 285 TYR cc_start: 0.9092 (m-80) cc_final: 0.8845 (m-80) REVERT: a 344 ASP cc_start: 0.7966 (p0) cc_final: 0.7465 (p0) REVERT: a 369 GLN cc_start: 0.6980 (tp-100) cc_final: 0.6689 (tp-100) REVERT: a 465 ILE cc_start: 0.8678 (mt) cc_final: 0.8458 (mm) REVERT: a 537 MET cc_start: 0.8309 (mmt) cc_final: 0.8032 (mmt) REVERT: a 577 LEU cc_start: 0.8454 (pp) cc_final: 0.8204 (pp) REVERT: a 579 MET cc_start: 0.8106 (ppp) cc_final: 0.7295 (ppp) REVERT: a 594 TRP cc_start: 0.7516 (m-10) cc_final: 0.7266 (m-90) REVERT: a 611 MET cc_start: 0.7394 (tpp) cc_final: 0.7175 (tmm) REVERT: a 737 TRP cc_start: 0.7888 (t60) cc_final: 0.7671 (t60) REVERT: a 753 MET cc_start: 0.7100 (ptm) cc_final: 0.6797 (tmm) REVERT: a 759 PHE cc_start: 0.7632 (t80) cc_final: 0.7138 (t80) REVERT: a 769 MET cc_start: 0.8308 (mtp) cc_final: 0.7593 (mtp) REVERT: a 773 LEU cc_start: 0.8607 (tp) cc_final: 0.8207 (tp) REVERT: a 776 MET cc_start: 0.8312 (tpp) cc_final: 0.7774 (tpp) REVERT: a 818 GLU cc_start: 0.7275 (mp0) cc_final: 0.7003 (mp0) REVERT: b 223 LEU cc_start: 0.9084 (tp) cc_final: 0.8833 (tt) REVERT: b 235 PHE cc_start: 0.7953 (t80) cc_final: 0.7591 (t80) REVERT: b 246 ASN cc_start: 0.8371 (m-40) cc_final: 0.8102 (t0) REVERT: c 27 ILE cc_start: 0.8988 (tp) cc_final: 0.8715 (tp) REVERT: c 58 MET cc_start: 0.8143 (tmm) cc_final: 0.7858 (tmm) REVERT: c 106 PHE cc_start: 0.7958 (m-80) cc_final: 0.7214 (t80) REVERT: c 158 ILE cc_start: 0.8863 (tp) cc_final: 0.8544 (tp) REVERT: d 79 GLU cc_start: 0.7290 (tp30) cc_final: 0.7061 (tp30) REVERT: d 97 TYR cc_start: 0.8404 (m-80) cc_final: 0.8110 (m-80) REVERT: d 247 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7304 (ptmm) REVERT: d 314 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8496 (mmmm) REVERT: d 317 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7684 (tm-30) REVERT: d 334 GLN cc_start: 0.7963 (mt0) cc_final: 0.7601 (mt0) REVERT: e 33 TRP cc_start: 0.7650 (m-90) cc_final: 0.6746 (m-90) REVERT: e 44 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7396 (mmm) REVERT: f 30 LEU cc_start: 0.9322 (tp) cc_final: 0.8942 (tp) REVERT: f 62 TYR cc_start: 0.8277 (m-10) cc_final: 0.7981 (m-80) REVERT: g 156 GLN cc_start: 0.7263 (pp30) cc_final: 0.6993 (pp30) REVERT: h 65 ILE cc_start: 0.9129 (mm) cc_final: 0.8766 (mm) REVERT: h 77 SER cc_start: 0.8512 (p) cc_final: 0.8271 (p) REVERT: h 133 LEU cc_start: 0.8536 (mt) cc_final: 0.8273 (mt) REVERT: i 129 MET cc_start: 0.8068 (tmm) cc_final: 0.7801 (tmm) REVERT: j 73 LEU cc_start: 0.8371 (tp) cc_final: 0.7988 (tp) REVERT: j 151 ASN cc_start: 0.8810 (t0) cc_final: 0.8590 (t0) REVERT: k 11 PHE cc_start: 0.8468 (t80) cc_final: 0.8038 (t80) REVERT: k 53 ASN cc_start: 0.8063 (p0) cc_final: 0.7815 (p0) REVERT: k 157 ASP cc_start: 0.8058 (p0) cc_final: 0.7776 (p0) REVERT: l 48 ASP cc_start: 0.8457 (p0) cc_final: 0.8202 (p0) REVERT: l 88 PHE cc_start: 0.7888 (m-80) cc_final: 0.7456 (m-80) REVERT: l 95 LEU cc_start: 0.8807 (mm) cc_final: 0.8463 (mm) REVERT: l 117 ARG cc_start: 0.8384 (mmt90) cc_final: 0.8145 (mmt-90) REVERT: l 144 LEU cc_start: 0.8942 (tp) cc_final: 0.8627 (tp) REVERT: l 148 LEU cc_start: 0.8891 (mt) cc_final: 0.8647 (mt) REVERT: m 39 ILE cc_start: 0.8330 (mm) cc_final: 0.7510 (mm) REVERT: m 43 CYS cc_start: 0.7618 (m) cc_final: 0.7347 (m) REVERT: m 70 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (m) REVERT: m 80 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8143 (tm-30) REVERT: m 121 GLN cc_start: 0.7959 (mp10) cc_final: 0.7649 (mp10) REVERT: m 129 MET cc_start: 0.7893 (tmm) cc_final: 0.7576 (tmm) REVERT: m 156 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7896 (tm-30) REVERT: n 21 ILE cc_start: 0.8567 (tp) cc_final: 0.8336 (tp) REVERT: n 22 ILE cc_start: 0.8886 (mt) cc_final: 0.8623 (mt) REVERT: n 49 LEU cc_start: 0.8064 (mt) cc_final: 0.7820 (mt) REVERT: n 59 MET cc_start: 0.8702 (tpp) cc_final: 0.8374 (mmm) REVERT: n 72 VAL cc_start: 0.8882 (m) cc_final: 0.8562 (p) REVERT: n 110 ILE cc_start: 0.9036 (mm) cc_final: 0.8751 (mm) REVERT: n 117 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7447 (mmt180) REVERT: n 122 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8043 (tm-30) REVERT: n 144 LEU cc_start: 0.9425 (tt) cc_final: 0.9217 (tt) REVERT: o 51 PHE cc_start: 0.8542 (m-80) cc_final: 0.8159 (m-80) REVERT: o 83 ASN cc_start: 0.8006 (p0) cc_final: 0.7649 (p0) REVERT: o 147 LEU cc_start: 0.9252 (tp) cc_final: 0.9004 (tp) REVERT: o 152 MET cc_start: 0.7998 (tmm) cc_final: 0.7675 (tmm) outliers start: 159 outliers final: 110 residues processed: 1706 average time/residue: 0.5615 time to fit residues: 1599.9432 Evaluate side-chains 1738 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1623 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 597 ASP Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 133 LEU Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 19 SER Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 79 LEU Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 138 VAL Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 0.0370 chunk 442 optimal weight: 50.0000 chunk 11 optimal weight: 5.9990 chunk 580 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 665 optimal weight: 1.9990 chunk 539 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 398 optimal weight: 20.0000 chunk 700 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 135 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 401 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 756 GLN c 61 ASN c 132 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 244 ASN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 151 ASN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 58646 Z= 0.340 Angle : 0.624 18.072 80001 Z= 0.330 Chirality : 0.044 0.245 9567 Planarity : 0.005 0.074 10420 Dihedral : 4.908 169.967 8735 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.77 % Favored : 96.22 % Rotamer: Outliers : 3.98 % Allowed : 18.92 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8154 helix: 1.22 (0.08), residues: 4725 sheet: -1.45 (0.20), residues: 604 loop : -0.36 (0.12), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 737 HIS 0.005 0.001 HIS o 98 PHE 0.036 0.002 PHE n 88 TYR 0.035 0.002 TYR a 474 ARG 0.010 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1854 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1651 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: A 205 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8353 (tmtt) REVERT: A 276 ASP cc_start: 0.8336 (m-30) cc_final: 0.8111 (m-30) REVERT: A 487 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7808 (pt0) REVERT: A 523 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 541 TRP cc_start: 0.8730 (p-90) cc_final: 0.8483 (p-90) REVERT: B 69 GLU cc_start: 0.7300 (tp30) cc_final: 0.6973 (tp30) REVERT: B 290 GLU cc_start: 0.7884 (tt0) cc_final: 0.7639 (tt0) REVERT: B 323 GLU cc_start: 0.7297 (tp30) cc_final: 0.7068 (tp30) REVERT: B 412 ASP cc_start: 0.7736 (m-30) cc_final: 0.7106 (m-30) REVERT: B 441 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7529 (mppt) REVERT: C 40 MET cc_start: 0.8318 (mmm) cc_final: 0.7845 (mmm) REVERT: C 118 GLU cc_start: 0.7798 (tp30) cc_final: 0.7218 (tp30) REVERT: C 285 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6901 (mm-30) REVERT: C 290 MET cc_start: 0.8462 (mmm) cc_final: 0.8066 (tpp) REVERT: C 442 ASP cc_start: 0.7887 (t0) cc_final: 0.7539 (t0) REVERT: C 540 ILE cc_start: 0.8869 (tp) cc_final: 0.8602 (tt) REVERT: C 608 GLN cc_start: 0.8459 (tp40) cc_final: 0.8019 (tp-100) REVERT: D 51 GLU cc_start: 0.7944 (tt0) cc_final: 0.7591 (tt0) REVERT: D 74 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7305 (ttm110) REVERT: D 400 SER cc_start: 0.8232 (t) cc_final: 0.7909 (p) REVERT: D 411 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8351 (mmmt) REVERT: D 477 SER cc_start: 0.8810 (p) cc_final: 0.8587 (p) REVERT: E 130 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8766 (p) REVERT: E 500 GLN cc_start: 0.7978 (pp30) cc_final: 0.7553 (pp30) REVERT: E 522 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7787 (mtmt) REVERT: F 42 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7104 (mm-30) REVERT: F 74 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.8085 (mtm180) REVERT: F 98 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7762 (mt-10) REVERT: F 231 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7631 (mt-10) REVERT: F 236 GLU cc_start: 0.8425 (pt0) cc_final: 0.8042 (pm20) REVERT: F 251 GLU cc_start: 0.7970 (tt0) cc_final: 0.7711 (tt0) REVERT: F 311 ASP cc_start: 0.7445 (t0) cc_final: 0.7160 (t0) REVERT: F 326 ASN cc_start: 0.8436 (m110) cc_final: 0.7942 (m110) REVERT: F 363 GLN cc_start: 0.7964 (mp10) cc_final: 0.7325 (mp10) REVERT: F 389 GLU cc_start: 0.8188 (tp30) cc_final: 0.7810 (tp30) REVERT: F 412 ASP cc_start: 0.7538 (m-30) cc_final: 0.7062 (m-30) REVERT: F 428 GLU cc_start: 0.7421 (tp30) cc_final: 0.7189 (tp30) REVERT: F 482 ASP cc_start: 0.7924 (m-30) cc_final: 0.7558 (m-30) REVERT: J 46 TYR cc_start: 0.8013 (t80) cc_final: 0.7724 (t80) REVERT: M 34 ARG cc_start: 0.7947 (ptm160) cc_final: 0.7709 (ptm160) REVERT: M 182 GLU cc_start: 0.7779 (tp30) cc_final: 0.7511 (tp30) REVERT: M 221 MET cc_start: 0.3971 (ppp) cc_final: 0.3570 (ppp) REVERT: a 8 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8638 (tt) REVERT: a 14 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5729 (ptp) REVERT: a 31 TYR cc_start: 0.8160 (t80) cc_final: 0.7918 (t80) REVERT: a 38 LEU cc_start: 0.7837 (mm) cc_final: 0.7401 (tt) REVERT: a 53 ARG cc_start: 0.6145 (mpt180) cc_final: 0.5322 (mmt-90) REVERT: a 60 ARG cc_start: 0.8799 (ptt90) cc_final: 0.8390 (ptt90) REVERT: a 67 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8543 (ttp-110) REVERT: a 68 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7991 (mm110) REVERT: a 134 GLN cc_start: 0.8780 (mt0) cc_final: 0.8491 (mm-40) REVERT: a 211 LEU cc_start: 0.8525 (pt) cc_final: 0.8229 (pp) REVERT: a 285 TYR cc_start: 0.9090 (m-80) cc_final: 0.8859 (m-80) REVERT: a 324 ASN cc_start: 0.8793 (t0) cc_final: 0.8080 (m110) REVERT: a 344 ASP cc_start: 0.8060 (p0) cc_final: 0.7580 (p0) REVERT: a 465 ILE cc_start: 0.8693 (mt) cc_final: 0.8459 (mm) REVERT: a 474 TYR cc_start: 0.7524 (t80) cc_final: 0.6961 (t80) REVERT: a 537 MET cc_start: 0.8233 (mmt) cc_final: 0.7221 (mpp) REVERT: a 579 MET cc_start: 0.8352 (ppp) cc_final: 0.7658 (ppp) REVERT: a 594 TRP cc_start: 0.7603 (m-10) cc_final: 0.7241 (m-90) REVERT: a 611 MET cc_start: 0.7463 (tpp) cc_final: 0.7203 (tmm) REVERT: a 753 MET cc_start: 0.7211 (ptm) cc_final: 0.6902 (tmm) REVERT: a 759 PHE cc_start: 0.7704 (t80) cc_final: 0.7187 (t80) REVERT: a 769 MET cc_start: 0.8323 (mtp) cc_final: 0.7612 (mtp) REVERT: a 773 LEU cc_start: 0.8598 (tp) cc_final: 0.8130 (tp) REVERT: a 774 PHE cc_start: 0.8195 (t80) cc_final: 0.7913 (t80) REVERT: a 776 MET cc_start: 0.8339 (tpp) cc_final: 0.7795 (tpp) REVERT: a 818 GLU cc_start: 0.7388 (mp0) cc_final: 0.7079 (mp0) REVERT: b 223 LEU cc_start: 0.9109 (tp) cc_final: 0.8841 (tt) REVERT: b 235 PHE cc_start: 0.7993 (t80) cc_final: 0.7613 (t80) REVERT: b 246 ASN cc_start: 0.8565 (m-40) cc_final: 0.8279 (m-40) REVERT: c 27 ILE cc_start: 0.8999 (tp) cc_final: 0.8710 (tp) REVERT: c 58 MET cc_start: 0.8201 (tmm) cc_final: 0.7996 (tmm) REVERT: c 117 ILE cc_start: 0.9276 (tp) cc_final: 0.8995 (tp) REVERT: c 158 ILE cc_start: 0.8952 (tp) cc_final: 0.8606 (tp) REVERT: d 21 ARG cc_start: 0.8912 (tmt-80) cc_final: 0.8624 (tmt-80) REVERT: d 34 THR cc_start: 0.8316 (m) cc_final: 0.8050 (p) REVERT: d 79 GLU cc_start: 0.7408 (tp30) cc_final: 0.7003 (tp30) REVERT: d 247 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7574 (ptmm) REVERT: d 285 GLU cc_start: 0.6284 (tt0) cc_final: 0.5819 (tt0) REVERT: d 304 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7808 (m-10) REVERT: d 314 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8200 (mmtm) REVERT: d 317 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7778 (tm-30) REVERT: e 46 LEU cc_start: 0.8680 (mm) cc_final: 0.8377 (mm) REVERT: e 53 LEU cc_start: 0.8837 (tp) cc_final: 0.8602 (tp) REVERT: f 62 TYR cc_start: 0.8108 (m-10) cc_final: 0.7849 (m-80) REVERT: g 156 GLN cc_start: 0.7164 (pp30) cc_final: 0.6802 (pp30) REVERT: h 59 MET cc_start: 0.7759 (mtt) cc_final: 0.7426 (mtp) REVERT: h 65 ILE cc_start: 0.9173 (mm) cc_final: 0.8844 (mm) REVERT: h 117 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7614 (mtt-85) REVERT: j 11 PHE cc_start: 0.7432 (t80) cc_final: 0.7095 (t80) REVERT: j 73 LEU cc_start: 0.8385 (tp) cc_final: 0.8055 (tp) REVERT: k 11 PHE cc_start: 0.8633 (t80) cc_final: 0.7912 (t80) REVERT: k 53 ASN cc_start: 0.8100 (p0) cc_final: 0.7838 (p0) REVERT: k 88 PHE cc_start: 0.7681 (m-80) cc_final: 0.7186 (m-80) REVERT: k 149 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8492 (tp) REVERT: k 157 ASP cc_start: 0.8112 (p0) cc_final: 0.7829 (p0) REVERT: l 48 ASP cc_start: 0.8533 (p0) cc_final: 0.8325 (p0) REVERT: l 88 PHE cc_start: 0.7967 (m-80) cc_final: 0.7575 (m-80) REVERT: l 95 LEU cc_start: 0.8823 (mm) cc_final: 0.8497 (mm) REVERT: l 117 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8261 (mmt-90) REVERT: l 144 LEU cc_start: 0.8972 (tp) cc_final: 0.8660 (tp) REVERT: l 148 LEU cc_start: 0.8913 (mt) cc_final: 0.8672 (mt) REVERT: m 39 ILE cc_start: 0.8315 (mm) cc_final: 0.7391 (mm) REVERT: m 59 MET cc_start: 0.8094 (mtt) cc_final: 0.7807 (mtt) REVERT: m 80 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8306 (tm-30) REVERT: m 121 GLN cc_start: 0.8077 (mp10) cc_final: 0.7790 (mp10) REVERT: m 129 MET cc_start: 0.7929 (tmm) cc_final: 0.7572 (tmm) REVERT: m 156 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7805 (tm-30) REVERT: n 22 ILE cc_start: 0.8906 (mt) cc_final: 0.8672 (mt) REVERT: n 59 MET cc_start: 0.8694 (tpp) cc_final: 0.8285 (mmm) REVERT: n 72 VAL cc_start: 0.8928 (m) cc_final: 0.8621 (p) REVERT: n 110 ILE cc_start: 0.9056 (mm) cc_final: 0.8744 (mm) REVERT: n 117 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7640 (mmt180) REVERT: n 144 LEU cc_start: 0.9427 (tt) cc_final: 0.9116 (tt) REVERT: n 148 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9015 (mm) REVERT: o 51 PHE cc_start: 0.8595 (m-80) cc_final: 0.7947 (m-80) REVERT: o 80 ILE cc_start: 0.9135 (mm) cc_final: 0.8914 (mt) REVERT: o 83 ASN cc_start: 0.8141 (p0) cc_final: 0.7818 (p0) REVERT: o 141 LEU cc_start: 0.7952 (tp) cc_final: 0.7636 (tp) REVERT: o 147 LEU cc_start: 0.9252 (tp) cc_final: 0.9006 (tp) REVERT: o 152 MET cc_start: 0.8054 (tmm) cc_final: 0.7747 (tmm) outliers start: 203 outliers final: 150 residues processed: 1722 average time/residue: 0.5901 time to fit residues: 1698.9222 Evaluate side-chains 1757 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1600 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 441 LEU Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 546 ILE Chi-restraints excluded: chain a residue 567 ASP Chi-restraints excluded: chain a residue 596 VAL Chi-restraints excluded: chain a residue 597 ASP Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 93 LYS Chi-restraints excluded: chain d residue 175 MET Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 32 THR Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 17 CYS Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 65 ILE Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 89 ILE Chi-restraints excluded: chain j residue 106 PHE Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 155 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 72 VAL Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 151 ASN Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 119 SER Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 19 SER Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 148 LEU Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 138 VAL Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Chi-restraints excluded: chain o residue 144 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 0.6980 chunk 702 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 457 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 780 optimal weight: 0.9990 chunk 648 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 409 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN D 21 ASN D 135 ASN D 339 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN K 122 GLN ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 151 ASN ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 58646 Z= 0.203 Angle : 0.597 16.198 80001 Z= 0.310 Chirality : 0.043 0.288 9567 Planarity : 0.005 0.074 10420 Dihedral : 4.761 167.878 8735 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 3.28 % Allowed : 21.09 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 8154 helix: 1.30 (0.08), residues: 4707 sheet: -1.44 (0.19), residues: 614 loop : -0.29 (0.12), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP a 737 HIS 0.005 0.001 HIS o 98 PHE 0.034 0.001 PHE o 96 TYR 0.037 0.001 TYR c 22 ARG 0.012 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1835 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1668 time to evaluate : 5.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: A 123 TYR cc_start: 0.8256 (m-80) cc_final: 0.7298 (m-80) REVERT: A 150 ASP cc_start: 0.8424 (m-30) cc_final: 0.7929 (m-30) REVERT: A 205 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8378 (tmtt) REVERT: A 276 ASP cc_start: 0.8293 (m-30) cc_final: 0.8050 (m-30) REVERT: A 487 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7801 (pt0) REVERT: A 523 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 541 TRP cc_start: 0.8743 (p-90) cc_final: 0.8465 (p-90) REVERT: B 69 GLU cc_start: 0.7372 (tp30) cc_final: 0.7024 (tp30) REVERT: B 290 GLU cc_start: 0.7852 (tt0) cc_final: 0.7532 (tt0) REVERT: B 323 GLU cc_start: 0.7230 (tp30) cc_final: 0.7004 (tp30) REVERT: B 412 ASP cc_start: 0.7806 (m-30) cc_final: 0.7077 (m-30) REVERT: B 416 MET cc_start: 0.7157 (mmt) cc_final: 0.6894 (mmt) REVERT: B 441 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7473 (mppt) REVERT: C 40 MET cc_start: 0.8247 (mmm) cc_final: 0.7821 (mmm) REVERT: C 108 ILE cc_start: 0.9096 (mm) cc_final: 0.8810 (mm) REVERT: C 118 GLU cc_start: 0.7757 (tp30) cc_final: 0.7192 (tp30) REVERT: C 285 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 290 MET cc_start: 0.8490 (mmm) cc_final: 0.8119 (tpp) REVERT: C 330 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 360 TRP cc_start: 0.8693 (t60) cc_final: 0.8339 (t60) REVERT: C 442 ASP cc_start: 0.7937 (t0) cc_final: 0.7713 (t0) REVERT: C 540 ILE cc_start: 0.8839 (tp) cc_final: 0.8569 (tt) REVERT: C 608 GLN cc_start: 0.8398 (tp40) cc_final: 0.8057 (tp-100) REVERT: D 74 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7180 (ttm110) REVERT: D 400 SER cc_start: 0.8270 (t) cc_final: 0.7922 (p) REVERT: D 477 SER cc_start: 0.8816 (p) cc_final: 0.8584 (p) REVERT: E 362 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7530 (mt-10) REVERT: E 500 GLN cc_start: 0.7945 (pp30) cc_final: 0.7494 (pp30) REVERT: E 522 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7764 (mtmt) REVERT: F 42 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6999 (mm-30) REVERT: F 74 ARG cc_start: 0.8658 (ptm-80) cc_final: 0.8170 (mtm180) REVERT: F 98 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7714 (mt-10) REVERT: F 231 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7568 (mt-10) REVERT: F 236 GLU cc_start: 0.8391 (pt0) cc_final: 0.8005 (pm20) REVERT: F 251 GLU cc_start: 0.7933 (tt0) cc_final: 0.7528 (tt0) REVERT: F 326 ASN cc_start: 0.8397 (m110) cc_final: 0.7908 (m110) REVERT: F 363 GLN cc_start: 0.7982 (mp10) cc_final: 0.7310 (mp10) REVERT: F 389 GLU cc_start: 0.8142 (tp30) cc_final: 0.7679 (tp30) REVERT: F 412 ASP cc_start: 0.7482 (m-30) cc_final: 0.7083 (m-30) REVERT: F 428 GLU cc_start: 0.7319 (tp30) cc_final: 0.7090 (tp30) REVERT: F 482 ASP cc_start: 0.7898 (m-30) cc_final: 0.7549 (m-30) REVERT: G 134 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8205 (mm-30) REVERT: I 163 LYS cc_start: 0.8918 (mppt) cc_final: 0.8712 (mppt) REVERT: J 46 TYR cc_start: 0.8116 (t80) cc_final: 0.7784 (t80) REVERT: M 34 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7641 (ptm160) REVERT: M 62 GLN cc_start: 0.6382 (pp30) cc_final: 0.5458 (tm-30) REVERT: M 182 GLU cc_start: 0.7777 (tp30) cc_final: 0.7482 (tp30) REVERT: M 221 MET cc_start: 0.4079 (ppp) cc_final: 0.3676 (ppp) REVERT: a 8 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8555 (tt) REVERT: a 14 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5642 (ptp) REVERT: a 31 TYR cc_start: 0.8055 (t80) cc_final: 0.7844 (t80) REVERT: a 38 LEU cc_start: 0.7741 (mm) cc_final: 0.7327 (tt) REVERT: a 60 ARG cc_start: 0.8797 (ptt90) cc_final: 0.8381 (ptt90) REVERT: a 64 ASN cc_start: 0.8796 (t0) cc_final: 0.8261 (t0) REVERT: a 67 ARG cc_start: 0.8830 (ttp-110) cc_final: 0.8445 (ttp-110) REVERT: a 68 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8064 (mm110) REVERT: a 134 GLN cc_start: 0.8751 (mt0) cc_final: 0.8515 (mm-40) REVERT: a 211 LEU cc_start: 0.8451 (pt) cc_final: 0.8162 (pp) REVERT: a 285 TYR cc_start: 0.9072 (m-80) cc_final: 0.8869 (m-80) REVERT: a 316 GLU cc_start: 0.7719 (mp0) cc_final: 0.7466 (mp0) REVERT: a 324 ASN cc_start: 0.8778 (t0) cc_final: 0.8037 (m110) REVERT: a 338 GLU cc_start: 0.7226 (pm20) cc_final: 0.6828 (pt0) REVERT: a 344 ASP cc_start: 0.8023 (p0) cc_final: 0.7600 (p0) REVERT: a 465 ILE cc_start: 0.8628 (mt) cc_final: 0.8376 (mm) REVERT: a 468 MET cc_start: 0.8025 (ptm) cc_final: 0.7750 (ptm) REVERT: a 579 MET cc_start: 0.8137 (ppp) cc_final: 0.7448 (ppp) REVERT: a 594 TRP cc_start: 0.7421 (m-10) cc_final: 0.7092 (m-90) REVERT: a 611 MET cc_start: 0.7203 (tpp) cc_final: 0.6897 (tmm) REVERT: a 753 MET cc_start: 0.7133 (ptm) cc_final: 0.6737 (tmm) REVERT: a 759 PHE cc_start: 0.7561 (t80) cc_final: 0.7129 (t80) REVERT: a 769 MET cc_start: 0.8291 (mtp) cc_final: 0.7589 (mtp) REVERT: a 773 LEU cc_start: 0.8546 (tp) cc_final: 0.8070 (tp) REVERT: a 774 PHE cc_start: 0.8271 (t80) cc_final: 0.7891 (t80) REVERT: a 776 MET cc_start: 0.8276 (tpp) cc_final: 0.7705 (tpp) REVERT: a 818 GLU cc_start: 0.7284 (mp0) cc_final: 0.6986 (mp0) REVERT: b 223 LEU cc_start: 0.9079 (tp) cc_final: 0.8824 (tt) REVERT: b 235 PHE cc_start: 0.7953 (t80) cc_final: 0.7565 (t80) REVERT: b 246 ASN cc_start: 0.8329 (m-40) cc_final: 0.8018 (t0) REVERT: c 58 MET cc_start: 0.8120 (tmm) cc_final: 0.7899 (tmm) REVERT: c 106 PHE cc_start: 0.7916 (m-80) cc_final: 0.7262 (t80) REVERT: c 117 ILE cc_start: 0.9243 (tp) cc_final: 0.8952 (tp) REVERT: c 158 ILE cc_start: 0.8894 (tp) cc_final: 0.8575 (tp) REVERT: d 79 GLU cc_start: 0.7344 (tp30) cc_final: 0.6971 (tp30) REVERT: d 97 TYR cc_start: 0.8421 (m-80) cc_final: 0.8191 (m-80) REVERT: d 191 ASP cc_start: 0.7717 (t0) cc_final: 0.6496 (t0) REVERT: d 234 ASP cc_start: 0.8140 (t70) cc_final: 0.7579 (t0) REVERT: d 236 ASP cc_start: 0.7917 (p0) cc_final: 0.7673 (p0) REVERT: d 304 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: d 310 TRP cc_start: 0.8488 (t-100) cc_final: 0.8270 (t60) REVERT: d 317 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7777 (tm-30) REVERT: d 334 GLN cc_start: 0.7896 (mt0) cc_final: 0.7601 (pt0) REVERT: e 46 LEU cc_start: 0.8665 (mm) cc_final: 0.8343 (mm) REVERT: e 47 MET cc_start: 0.8616 (tmm) cc_final: 0.8270 (tmm) REVERT: e 53 LEU cc_start: 0.8775 (tp) cc_final: 0.8553 (tp) REVERT: f 62 TYR cc_start: 0.8068 (m-10) cc_final: 0.7806 (m-80) REVERT: g 39 ILE cc_start: 0.8985 (pt) cc_final: 0.8640 (tt) REVERT: g 137 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7805 (mm-30) REVERT: g 156 GLN cc_start: 0.7047 (pp30) cc_final: 0.6630 (pp30) REVERT: h 59 MET cc_start: 0.7503 (mtt) cc_final: 0.7253 (mtp) REVERT: h 62 ILE cc_start: 0.8514 (tp) cc_final: 0.8276 (pt) REVERT: h 65 ILE cc_start: 0.9079 (mm) cc_final: 0.8781 (mm) REVERT: h 137 GLU cc_start: 0.8623 (tt0) cc_final: 0.8150 (tt0) REVERT: j 11 PHE cc_start: 0.7347 (t80) cc_final: 0.7047 (t80) REVERT: j 73 LEU cc_start: 0.8331 (tp) cc_final: 0.8065 (tp) REVERT: j 117 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7765 (mmm-85) REVERT: j 149 LEU cc_start: 0.8431 (tp) cc_final: 0.8105 (tt) REVERT: k 11 PHE cc_start: 0.8619 (t80) cc_final: 0.7895 (t80) REVERT: k 53 ASN cc_start: 0.7960 (p0) cc_final: 0.7663 (p0) REVERT: k 157 ASP cc_start: 0.8154 (p0) cc_final: 0.7924 (p0) REVERT: l 34 LYS cc_start: 0.8722 (tptt) cc_final: 0.8408 (mptt) REVERT: l 88 PHE cc_start: 0.7903 (m-80) cc_final: 0.7531 (m-80) REVERT: l 95 LEU cc_start: 0.8781 (mm) cc_final: 0.8424 (mm) REVERT: l 129 MET cc_start: 0.8588 (tpp) cc_final: 0.8120 (tpt) REVERT: l 144 LEU cc_start: 0.8941 (tp) cc_final: 0.8499 (tp) REVERT: l 148 LEU cc_start: 0.8834 (mt) cc_final: 0.8544 (mt) REVERT: m 39 ILE cc_start: 0.8260 (mm) cc_final: 0.7919 (mm) REVERT: m 90 GLN cc_start: 0.8273 (mt0) cc_final: 0.7984 (mt0) REVERT: m 121 GLN cc_start: 0.8000 (mp10) cc_final: 0.7663 (mp10) REVERT: m 129 MET cc_start: 0.7864 (tmm) cc_final: 0.7520 (tmm) REVERT: m 156 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7809 (tm-30) REVERT: n 22 ILE cc_start: 0.8885 (mt) cc_final: 0.8643 (mt) REVERT: n 46 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7720 (ttp80) REVERT: n 59 MET cc_start: 0.8705 (tpp) cc_final: 0.8269 (mmm) REVERT: n 72 VAL cc_start: 0.8913 (m) cc_final: 0.8544 (p) REVERT: n 110 ILE cc_start: 0.8982 (mm) cc_final: 0.8634 (mm) REVERT: n 117 ARG cc_start: 0.7757 (mmt180) cc_final: 0.7263 (mmt180) REVERT: n 122 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8217 (tm-30) REVERT: o 51 PHE cc_start: 0.8558 (m-80) cc_final: 0.8185 (m-80) REVERT: o 80 ILE cc_start: 0.9129 (mm) cc_final: 0.8901 (mt) REVERT: o 83 ASN cc_start: 0.8042 (p0) cc_final: 0.7709 (p0) REVERT: o 85 SER cc_start: 0.8928 (p) cc_final: 0.8249 (m) REVERT: o 130 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8434 (tm-30) REVERT: o 141 LEU cc_start: 0.7837 (tp) cc_final: 0.7530 (tp) REVERT: o 152 MET cc_start: 0.8043 (tmm) cc_final: 0.7742 (tmm) outliers start: 167 outliers final: 125 residues processed: 1721 average time/residue: 0.5623 time to fit residues: 1619.9486 Evaluate side-chains 1754 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1624 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 586 LEU Chi-restraints excluded: chain a residue 597 ASP Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 90 GLN Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 106 PHE Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 106 PHE Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain m residue 153 ARG Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain o residue 79 LEU Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 444 optimal weight: 0.0010 chunk 570 optimal weight: 0.8980 chunk 441 optimal weight: 3.9990 chunk 657 optimal weight: 0.7980 chunk 436 optimal weight: 10.0000 chunk 777 optimal weight: 0.0270 chunk 486 optimal weight: 0.7980 chunk 474 optimal weight: 1.9990 chunk 359 optimal weight: 7.9990 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 135 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 339 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 244 ASN d 271 ASN ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 121 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 58646 Z= 0.185 Angle : 0.592 15.705 80001 Z= 0.307 Chirality : 0.042 0.333 9567 Planarity : 0.005 0.074 10420 Dihedral : 4.668 168.765 8735 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 3.28 % Allowed : 22.12 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 8154 helix: 1.28 (0.08), residues: 4767 sheet: -1.36 (0.19), residues: 640 loop : -0.29 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP a 737 HIS 0.004 0.001 HIS o 98 PHE 0.035 0.001 PHE o 96 TYR 0.038 0.001 TYR k 142 ARG 0.013 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1826 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1659 time to evaluate : 5.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: A 38 GLU cc_start: 0.8026 (tt0) cc_final: 0.7357 (tt0) REVERT: A 123 TYR cc_start: 0.8236 (m-80) cc_final: 0.7238 (m-80) REVERT: A 150 ASP cc_start: 0.8416 (m-30) cc_final: 0.7918 (m-30) REVERT: A 205 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8391 (tmtt) REVERT: A 276 ASP cc_start: 0.8267 (m-30) cc_final: 0.8021 (m-30) REVERT: A 487 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7801 (pt0) REVERT: A 523 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 535 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5880 (t0) REVERT: A 541 TRP cc_start: 0.8803 (p-90) cc_final: 0.8549 (p-90) REVERT: B 69 GLU cc_start: 0.7381 (tp30) cc_final: 0.7022 (tp30) REVERT: B 215 MET cc_start: 0.8540 (mtm) cc_final: 0.8070 (mtm) REVERT: B 412 ASP cc_start: 0.7790 (m-30) cc_final: 0.6986 (m-30) REVERT: B 434 GLU cc_start: 0.8086 (pp20) cc_final: 0.7498 (pp20) REVERT: B 441 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8031 (mtmt) REVERT: C 40 MET cc_start: 0.8243 (mmm) cc_final: 0.7793 (mmm) REVERT: C 108 ILE cc_start: 0.9074 (mm) cc_final: 0.8849 (mm) REVERT: C 118 GLU cc_start: 0.7730 (tp30) cc_final: 0.7182 (tp30) REVERT: C 285 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6960 (mm-30) REVERT: C 290 MET cc_start: 0.8475 (mmm) cc_final: 0.8093 (tpp) REVERT: C 330 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7367 (tm-30) REVERT: C 360 TRP cc_start: 0.8651 (t60) cc_final: 0.8333 (t60) REVERT: C 366 GLU cc_start: 0.7189 (tp30) cc_final: 0.6977 (tp30) REVERT: C 442 ASP cc_start: 0.7937 (t0) cc_final: 0.7724 (t0) REVERT: C 540 ILE cc_start: 0.8837 (tp) cc_final: 0.8556 (tt) REVERT: C 608 GLN cc_start: 0.8414 (tp40) cc_final: 0.8047 (tp-100) REVERT: D 21 ASN cc_start: 0.8485 (t0) cc_final: 0.7586 (p0) REVERT: D 74 ARG cc_start: 0.7620 (ttm110) cc_final: 0.6890 (ttm110) REVERT: D 223 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7537 (mmm-85) REVERT: D 477 SER cc_start: 0.8835 (p) cc_final: 0.8607 (p) REVERT: E 38 GLU cc_start: 0.8133 (pt0) cc_final: 0.7923 (pt0) REVERT: E 362 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7542 (mt-10) REVERT: E 500 GLN cc_start: 0.7932 (pp30) cc_final: 0.7485 (pp30) REVERT: E 522 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7752 (mtmt) REVERT: F 98 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7680 (mt-10) REVERT: F 150 MET cc_start: 0.8329 (ttt) cc_final: 0.8068 (ttt) REVERT: F 231 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7584 (mt-10) REVERT: F 236 GLU cc_start: 0.8404 (pt0) cc_final: 0.8033 (pm20) REVERT: F 326 ASN cc_start: 0.8376 (m110) cc_final: 0.7829 (m110) REVERT: F 363 GLN cc_start: 0.7987 (mp10) cc_final: 0.7328 (mp10) REVERT: F 389 GLU cc_start: 0.8103 (tp30) cc_final: 0.7652 (tp30) REVERT: F 412 ASP cc_start: 0.7492 (m-30) cc_final: 0.7085 (m-30) REVERT: F 428 GLU cc_start: 0.7431 (tp30) cc_final: 0.7145 (tp30) REVERT: F 482 ASP cc_start: 0.7882 (m-30) cc_final: 0.7505 (m-30) REVERT: G 134 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8126 (mm-30) REVERT: G 166 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8071 (ttm110) REVERT: I 105 GLU cc_start: 0.8342 (mp0) cc_final: 0.7941 (mp0) REVERT: J 46 TYR cc_start: 0.8133 (t80) cc_final: 0.7800 (t80) REVERT: M 18 MET cc_start: 0.7784 (mmt) cc_final: 0.7541 (mmt) REVERT: M 34 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7468 (ptm160) REVERT: M 62 GLN cc_start: 0.6290 (pp30) cc_final: 0.5459 (tm-30) REVERT: M 182 GLU cc_start: 0.7766 (tp30) cc_final: 0.7444 (tp30) REVERT: M 221 MET cc_start: 0.4089 (ppp) cc_final: 0.3663 (ppp) REVERT: a 8 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8493 (tt) REVERT: a 14 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.5626 (ptp) REVERT: a 38 LEU cc_start: 0.7656 (mm) cc_final: 0.7291 (tt) REVERT: a 60 ARG cc_start: 0.8788 (ptt90) cc_final: 0.8371 (ptt90) REVERT: a 64 ASN cc_start: 0.8802 (t0) cc_final: 0.8405 (t0) REVERT: a 67 ARG cc_start: 0.8844 (ttp-110) cc_final: 0.8461 (ttp-110) REVERT: a 68 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8152 (mm110) REVERT: a 134 GLN cc_start: 0.8734 (mt0) cc_final: 0.8504 (mm-40) REVERT: a 211 LEU cc_start: 0.8387 (pt) cc_final: 0.8127 (pp) REVERT: a 316 GLU cc_start: 0.7747 (mp0) cc_final: 0.7443 (mp0) REVERT: a 324 ASN cc_start: 0.8746 (t0) cc_final: 0.8013 (m110) REVERT: a 338 GLU cc_start: 0.7020 (pm20) cc_final: 0.6704 (pt0) REVERT: a 344 ASP cc_start: 0.7988 (p0) cc_final: 0.7521 (p0) REVERT: a 369 GLN cc_start: 0.6976 (tp-100) cc_final: 0.6630 (tp-100) REVERT: a 465 ILE cc_start: 0.8636 (mt) cc_final: 0.8374 (mm) REVERT: a 468 MET cc_start: 0.8039 (ptm) cc_final: 0.7837 (ptm) REVERT: a 474 TYR cc_start: 0.7231 (t80) cc_final: 0.6324 (t80) REVERT: a 478 LEU cc_start: 0.8717 (mt) cc_final: 0.8376 (tt) REVERT: a 537 MET cc_start: 0.8321 (mmt) cc_final: 0.7914 (mmt) REVERT: a 579 MET cc_start: 0.8086 (ppp) cc_final: 0.7435 (ppp) REVERT: a 594 TRP cc_start: 0.7427 (m-10) cc_final: 0.7211 (m-90) REVERT: a 611 MET cc_start: 0.7205 (tpp) cc_final: 0.6921 (tmm) REVERT: a 753 MET cc_start: 0.7092 (ptm) cc_final: 0.6698 (tmm) REVERT: a 759 PHE cc_start: 0.7499 (t80) cc_final: 0.7095 (t80) REVERT: a 769 MET cc_start: 0.8295 (mtp) cc_final: 0.7561 (mtp) REVERT: a 773 LEU cc_start: 0.8502 (tp) cc_final: 0.7973 (tp) REVERT: a 774 PHE cc_start: 0.8078 (t80) cc_final: 0.7858 (t80) REVERT: a 776 MET cc_start: 0.8263 (tpp) cc_final: 0.7708 (tpp) REVERT: a 818 GLU cc_start: 0.7222 (mp0) cc_final: 0.6917 (mp0) REVERT: b 223 LEU cc_start: 0.9032 (tp) cc_final: 0.8763 (tt) REVERT: b 235 PHE cc_start: 0.7933 (t80) cc_final: 0.7590 (t80) REVERT: b 246 ASN cc_start: 0.8159 (m-40) cc_final: 0.7891 (t0) REVERT: c 106 PHE cc_start: 0.7892 (m-80) cc_final: 0.7235 (t80) REVERT: c 117 ILE cc_start: 0.9269 (tp) cc_final: 0.8978 (tp) REVERT: c 158 ILE cc_start: 0.8918 (tp) cc_final: 0.8549 (tp) REVERT: d 24 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (mm) REVERT: d 79 GLU cc_start: 0.7333 (tp30) cc_final: 0.7009 (tp30) REVERT: d 125 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8474 (tm-30) REVERT: d 247 LYS cc_start: 0.7720 (ptmm) cc_final: 0.7346 (ptmm) REVERT: d 260 GLN cc_start: 0.8553 (tp40) cc_final: 0.8349 (tp40) REVERT: d 304 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7685 (m-10) REVERT: d 317 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7755 (tm-30) REVERT: e 44 MET cc_start: 0.7985 (tpp) cc_final: 0.7515 (tpp) REVERT: e 46 LEU cc_start: 0.8673 (mm) cc_final: 0.8363 (mm) REVERT: e 53 LEU cc_start: 0.8744 (tp) cc_final: 0.8536 (tp) REVERT: f 62 TYR cc_start: 0.8060 (m-10) cc_final: 0.7814 (m-80) REVERT: g 39 ILE cc_start: 0.8954 (pt) cc_final: 0.8482 (tt) REVERT: g 108 ILE cc_start: 0.9031 (mm) cc_final: 0.8797 (tp) REVERT: g 117 ARG cc_start: 0.8203 (mmt90) cc_final: 0.7911 (mpt-90) REVERT: g 156 GLN cc_start: 0.7005 (pp30) cc_final: 0.6571 (pp30) REVERT: h 59 MET cc_start: 0.7319 (mtt) cc_final: 0.7058 (mtp) REVERT: h 65 ILE cc_start: 0.9084 (mm) cc_final: 0.8816 (mm) REVERT: h 99 LEU cc_start: 0.8889 (mt) cc_final: 0.8655 (mm) REVERT: h 137 GLU cc_start: 0.8398 (tt0) cc_final: 0.8194 (tt0) REVERT: j 11 PHE cc_start: 0.7341 (t80) cc_final: 0.7078 (t80) REVERT: j 34 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8589 (mmtt) REVERT: j 73 LEU cc_start: 0.8420 (tp) cc_final: 0.8142 (tp) REVERT: j 117 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: j 149 LEU cc_start: 0.8326 (tp) cc_final: 0.8110 (tt) REVERT: k 11 PHE cc_start: 0.8568 (t80) cc_final: 0.7948 (t80) REVERT: k 53 ASN cc_start: 0.8032 (p0) cc_final: 0.7819 (p0) REVERT: k 139 LEU cc_start: 0.8171 (mt) cc_final: 0.7935 (mt) REVERT: k 142 TYR cc_start: 0.8029 (m-80) cc_final: 0.7790 (m-80) REVERT: k 157 ASP cc_start: 0.8092 (p0) cc_final: 0.7859 (p0) REVERT: l 34 LYS cc_start: 0.8615 (tptt) cc_final: 0.8161 (mptt) REVERT: l 68 LEU cc_start: 0.8738 (tt) cc_final: 0.8514 (tp) REVERT: l 88 PHE cc_start: 0.7898 (m-80) cc_final: 0.7694 (m-80) REVERT: l 95 LEU cc_start: 0.8751 (mm) cc_final: 0.8444 (mm) REVERT: l 144 LEU cc_start: 0.8896 (tp) cc_final: 0.8620 (tp) REVERT: m 39 ILE cc_start: 0.8284 (mm) cc_final: 0.8058 (mm) REVERT: m 90 GLN cc_start: 0.8236 (mt0) cc_final: 0.7956 (mt0) REVERT: m 121 GLN cc_start: 0.7977 (mp10) cc_final: 0.7626 (mp10) REVERT: m 129 MET cc_start: 0.7856 (tmm) cc_final: 0.7459 (tmm) REVERT: m 156 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7748 (tm-30) REVERT: n 22 ILE cc_start: 0.8871 (mt) cc_final: 0.8653 (mt) REVERT: n 59 MET cc_start: 0.8676 (tpp) cc_final: 0.8289 (mmm) REVERT: n 72 VAL cc_start: 0.8957 (m) cc_final: 0.8610 (p) REVERT: n 122 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8261 (tm-30) REVERT: o 51 PHE cc_start: 0.8545 (m-80) cc_final: 0.8182 (m-80) REVERT: o 80 ILE cc_start: 0.9081 (mm) cc_final: 0.8856 (mt) REVERT: o 83 ASN cc_start: 0.8042 (p0) cc_final: 0.7692 (p0) REVERT: o 85 SER cc_start: 0.8942 (p) cc_final: 0.8277 (m) REVERT: o 130 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8421 (tm-30) REVERT: o 141 LEU cc_start: 0.7817 (tp) cc_final: 0.7537 (tp) REVERT: o 152 MET cc_start: 0.7987 (tmm) cc_final: 0.7715 (tmm) outliers start: 167 outliers final: 127 residues processed: 1713 average time/residue: 0.5489 time to fit residues: 1570.5455 Evaluate side-chains 1747 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1613 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 482 ILE Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 535 TYR Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain a residue 827 MET Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 66 SER Chi-restraints excluded: chain d residue 93 LYS Chi-restraints excluded: chain d residue 175 MET Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain d residue 199 GLU Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain f residue 12 CYS Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 65 ILE Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 51 PHE Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 106 PHE Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain o residue 79 LEU Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 464 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 494 optimal weight: 0.3980 chunk 529 optimal weight: 9.9990 chunk 384 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 611 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 207 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 334 GLN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 58646 Z= 0.263 Angle : 0.627 15.275 80001 Z= 0.323 Chirality : 0.044 0.382 9567 Planarity : 0.005 0.076 10420 Dihedral : 4.716 164.095 8735 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.67 % Favored : 96.32 % Rotamer: Outliers : 3.57 % Allowed : 23.02 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 8154 helix: 1.26 (0.08), residues: 4757 sheet: -1.40 (0.19), residues: 611 loop : -0.30 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 737 HIS 0.004 0.001 HIS o 98 PHE 0.032 0.002 PHE a 417 TYR 0.038 0.002 TYR c 22 ARG 0.011 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1830 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1648 time to evaluate : 5.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: A 150 ASP cc_start: 0.8410 (m-30) cc_final: 0.7897 (m-30) REVERT: A 205 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8374 (tmtt) REVERT: A 276 ASP cc_start: 0.8308 (m-30) cc_final: 0.8068 (m-30) REVERT: A 487 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7801 (pt0) REVERT: A 523 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 541 TRP cc_start: 0.8799 (p-90) cc_final: 0.8503 (p-90) REVERT: A 552 SER cc_start: 0.8959 (m) cc_final: 0.8563 (p) REVERT: A 602 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7530 (mtmm) REVERT: B 69 GLU cc_start: 0.7346 (tp30) cc_final: 0.6895 (tp30) REVERT: B 290 GLU cc_start: 0.7868 (tt0) cc_final: 0.7508 (tt0) REVERT: B 323 GLU cc_start: 0.7367 (tp30) cc_final: 0.7167 (tp30) REVERT: B 412 ASP cc_start: 0.7804 (m-30) cc_final: 0.7112 (m-30) REVERT: B 434 GLU cc_start: 0.8118 (pp20) cc_final: 0.7506 (pp20) REVERT: C 40 MET cc_start: 0.8249 (mmm) cc_final: 0.7818 (mmm) REVERT: C 118 GLU cc_start: 0.7783 (tp30) cc_final: 0.7220 (tp30) REVERT: C 285 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6912 (mm-30) REVERT: C 290 MET cc_start: 0.8430 (mmm) cc_final: 0.7981 (tpp) REVERT: C 296 GLU cc_start: 0.7067 (mp0) cc_final: 0.6510 (mp0) REVERT: C 330 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7387 (tm-30) REVERT: C 360 TRP cc_start: 0.8684 (t60) cc_final: 0.8351 (t60) REVERT: C 366 GLU cc_start: 0.7295 (tp30) cc_final: 0.6934 (tp30) REVERT: C 442 ASP cc_start: 0.7941 (t0) cc_final: 0.7547 (t0) REVERT: C 540 ILE cc_start: 0.8862 (tp) cc_final: 0.8582 (tt) REVERT: C 601 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 608 GLN cc_start: 0.8463 (tp40) cc_final: 0.8078 (tp-100) REVERT: D 74 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7080 (ttm110) REVERT: D 106 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: D 400 SER cc_start: 0.8200 (t) cc_final: 0.7871 (p) REVERT: D 477 SER cc_start: 0.8857 (p) cc_final: 0.8619 (p) REVERT: E 38 GLU cc_start: 0.8137 (pt0) cc_final: 0.7910 (pt0) REVERT: E 130 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8819 (p) REVERT: E 362 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 500 GLN cc_start: 0.7919 (pp30) cc_final: 0.7475 (pp30) REVERT: E 522 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7759 (mtmt) REVERT: F 74 ARG cc_start: 0.8630 (ptm-80) cc_final: 0.8241 (ttp80) REVERT: F 98 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7707 (mt-10) REVERT: F 236 GLU cc_start: 0.8420 (pt0) cc_final: 0.8049 (pm20) REVERT: F 251 GLU cc_start: 0.7973 (tt0) cc_final: 0.7759 (tt0) REVERT: F 326 ASN cc_start: 0.8418 (m110) cc_final: 0.7869 (m110) REVERT: F 363 GLN cc_start: 0.7988 (mp10) cc_final: 0.7313 (mp10) REVERT: F 389 GLU cc_start: 0.8122 (tp30) cc_final: 0.7664 (tp30) REVERT: F 412 ASP cc_start: 0.7466 (m-30) cc_final: 0.7087 (m-30) REVERT: F 428 GLU cc_start: 0.7436 (tp30) cc_final: 0.7162 (tp30) REVERT: F 482 ASP cc_start: 0.7916 (m-30) cc_final: 0.7512 (m-30) REVERT: G 134 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8204 (mm-30) REVERT: I 105 GLU cc_start: 0.8287 (mp0) cc_final: 0.7873 (mp0) REVERT: J 46 TYR cc_start: 0.8133 (t80) cc_final: 0.7788 (t80) REVERT: K 136 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8357 (mmmt) REVERT: M 34 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7731 (ptm160) REVERT: M 182 GLU cc_start: 0.7765 (tp30) cc_final: 0.7445 (tp30) REVERT: M 221 MET cc_start: 0.4076 (ppp) cc_final: 0.3672 (ppp) REVERT: a 8 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8597 (tt) REVERT: a 14 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5653 (ptp) REVERT: a 38 LEU cc_start: 0.7696 (mm) cc_final: 0.7324 (tt) REVERT: a 41 PHE cc_start: 0.8206 (m-80) cc_final: 0.7731 (m-80) REVERT: a 60 ARG cc_start: 0.8786 (ptt90) cc_final: 0.8382 (ptt90) REVERT: a 64 ASN cc_start: 0.8800 (t0) cc_final: 0.8389 (t0) REVERT: a 67 ARG cc_start: 0.8842 (ttp-110) cc_final: 0.8465 (ttp-110) REVERT: a 68 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8133 (mm110) REVERT: a 134 GLN cc_start: 0.8746 (mt0) cc_final: 0.8448 (mm-40) REVERT: a 338 GLU cc_start: 0.7007 (pm20) cc_final: 0.6719 (pt0) REVERT: a 344 ASP cc_start: 0.8043 (p0) cc_final: 0.7597 (p0) REVERT: a 369 GLN cc_start: 0.6963 (tp-100) cc_final: 0.6628 (tp-100) REVERT: a 465 ILE cc_start: 0.8654 (mt) cc_final: 0.8379 (mm) REVERT: a 468 MET cc_start: 0.8068 (ptm) cc_final: 0.7866 (ptm) REVERT: a 474 TYR cc_start: 0.7472 (t80) cc_final: 0.6439 (t80) REVERT: a 537 MET cc_start: 0.8329 (mmt) cc_final: 0.8095 (mmt) REVERT: a 579 MET cc_start: 0.8025 (ppp) cc_final: 0.7410 (ppp) REVERT: a 594 TRP cc_start: 0.7492 (m-10) cc_final: 0.7074 (m-90) REVERT: a 753 MET cc_start: 0.7164 (ptm) cc_final: 0.6774 (tmm) REVERT: a 759 PHE cc_start: 0.7537 (t80) cc_final: 0.7125 (t80) REVERT: a 769 MET cc_start: 0.8323 (mtp) cc_final: 0.7595 (mtp) REVERT: a 773 LEU cc_start: 0.8622 (tp) cc_final: 0.8074 (tp) REVERT: a 774 PHE cc_start: 0.8203 (t80) cc_final: 0.7967 (t80) REVERT: a 776 MET cc_start: 0.8286 (tpp) cc_final: 0.7711 (tpp) REVERT: a 818 GLU cc_start: 0.7300 (mp0) cc_final: 0.6986 (mp0) REVERT: b 215 LEU cc_start: 0.6363 (mp) cc_final: 0.5976 (mp) REVERT: b 223 LEU cc_start: 0.9048 (tp) cc_final: 0.8792 (tt) REVERT: b 235 PHE cc_start: 0.7983 (t80) cc_final: 0.7635 (t80) REVERT: b 243 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.7673 (t60) REVERT: b 246 ASN cc_start: 0.8237 (m-40) cc_final: 0.7931 (t0) REVERT: c 117 ILE cc_start: 0.9223 (tp) cc_final: 0.9016 (tp) REVERT: c 158 ILE cc_start: 0.9011 (tp) cc_final: 0.8652 (tp) REVERT: d 21 ARG cc_start: 0.8945 (tmt-80) cc_final: 0.8592 (tmt-80) REVERT: d 24 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8881 (mm) REVERT: d 79 GLU cc_start: 0.7436 (tp30) cc_final: 0.7138 (tp30) REVERT: d 125 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8550 (tm-30) REVERT: d 126 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8272 (ttm-80) REVERT: d 247 LYS cc_start: 0.7969 (ptmm) cc_final: 0.7671 (ptmm) REVERT: d 260 GLN cc_start: 0.8567 (tp40) cc_final: 0.8303 (tp40) REVERT: d 261 ASP cc_start: 0.8271 (p0) cc_final: 0.7891 (p0) REVERT: d 285 GLU cc_start: 0.6379 (tt0) cc_final: 0.6090 (tt0) REVERT: d 304 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7778 (m-10) REVERT: d 317 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7838 (tm-30) REVERT: d 332 GLN cc_start: 0.8064 (mm110) cc_final: 0.7699 (mm-40) REVERT: d 334 GLN cc_start: 0.7830 (pt0) cc_final: 0.7469 (pp30) REVERT: e 53 LEU cc_start: 0.8761 (tp) cc_final: 0.8538 (tp) REVERT: f 56 TYR cc_start: 0.8678 (m-10) cc_final: 0.8416 (m-10) REVERT: f 62 TYR cc_start: 0.8130 (m-10) cc_final: 0.7865 (m-80) REVERT: g 108 ILE cc_start: 0.9075 (mm) cc_final: 0.8775 (tp) REVERT: g 137 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7855 (mm-30) REVERT: g 156 GLN cc_start: 0.7003 (pp30) cc_final: 0.6489 (pp30) REVERT: h 65 ILE cc_start: 0.9119 (mm) cc_final: 0.8885 (mm) REVERT: h 99 LEU cc_start: 0.8925 (mt) cc_final: 0.8686 (mm) REVERT: h 144 LEU cc_start: 0.9023 (tp) cc_final: 0.8793 (tp) REVERT: j 11 PHE cc_start: 0.7396 (t80) cc_final: 0.7188 (t80) REVERT: j 73 LEU cc_start: 0.8321 (tp) cc_final: 0.8062 (tp) REVERT: j 117 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7760 (mmm-85) REVERT: j 149 LEU cc_start: 0.8407 (tp) cc_final: 0.8179 (tt) REVERT: k 11 PHE cc_start: 0.8624 (t80) cc_final: 0.7936 (t80) REVERT: k 88 PHE cc_start: 0.7729 (m-80) cc_final: 0.7118 (m-80) REVERT: k 157 ASP cc_start: 0.7903 (p0) cc_final: 0.7494 (p0) REVERT: l 34 LYS cc_start: 0.8658 (tptt) cc_final: 0.8404 (mptt) REVERT: l 95 LEU cc_start: 0.8807 (mm) cc_final: 0.8453 (mm) REVERT: l 144 LEU cc_start: 0.8952 (tp) cc_final: 0.8678 (tp) REVERT: m 39 ILE cc_start: 0.8383 (mm) cc_final: 0.8154 (mm) REVERT: m 90 GLN cc_start: 0.8203 (mt0) cc_final: 0.7801 (mt0) REVERT: m 121 GLN cc_start: 0.8092 (mp10) cc_final: 0.7744 (mp10) REVERT: m 129 MET cc_start: 0.7913 (tmm) cc_final: 0.7572 (tmm) REVERT: m 156 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7770 (tm-30) REVERT: n 22 ILE cc_start: 0.8907 (mt) cc_final: 0.8702 (mt) REVERT: n 59 MET cc_start: 0.8697 (tpp) cc_final: 0.8303 (mmm) REVERT: n 72 VAL cc_start: 0.9010 (m) cc_final: 0.8665 (p) REVERT: n 122 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8383 (tm-30) REVERT: o 51 PHE cc_start: 0.8627 (m-80) cc_final: 0.8060 (m-80) REVERT: o 83 ASN cc_start: 0.7991 (p0) cc_final: 0.7662 (p0) REVERT: o 130 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8452 (tm-30) REVERT: o 141 LEU cc_start: 0.7842 (tp) cc_final: 0.7604 (tp) REVERT: o 149 LEU cc_start: 0.8916 (tp) cc_final: 0.8647 (tp) REVERT: o 152 MET cc_start: 0.8080 (tmm) cc_final: 0.7785 (tmm) outliers start: 182 outliers final: 142 residues processed: 1708 average time/residue: 0.5540 time to fit residues: 1577.7094 Evaluate side-chains 1757 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1606 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 441 LEU Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 482 ILE Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 535 TYR Chi-restraints excluded: chain a residue 546 ILE Chi-restraints excluded: chain a residue 567 ASP Chi-restraints excluded: chain a residue 597 ASP Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain b residue 224 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 93 LYS Chi-restraints excluded: chain d residue 175 MET Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain d residue 199 GLU Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain f residue 12 CYS Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 157 ASP Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 89 ILE Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 54 ILE Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 51 PHE Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 149 LEU Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 153 ARG Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 0.3980 chunk 745 optimal weight: 0.1980 chunk 679 optimal weight: 0.4980 chunk 724 optimal weight: 1.9990 chunk 744 optimal weight: 0.9990 chunk 436 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 569 optimal weight: 8.9990 chunk 222 optimal weight: 0.0010 chunk 654 optimal weight: 5.9990 chunk 685 optimal weight: 0.0670 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 207 ASN K 122 GLN M 27 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 ASN ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 580 GLN ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 58646 Z= 0.182 Angle : 0.634 16.737 80001 Z= 0.322 Chirality : 0.043 0.342 9567 Planarity : 0.005 0.079 10420 Dihedral : 4.638 164.776 8735 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 3.02 % Allowed : 24.08 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8154 helix: 1.28 (0.08), residues: 4766 sheet: -1.40 (0.20), residues: 603 loop : -0.29 (0.12), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP a 737 HIS 0.009 0.001 HIS o 98 PHE 0.046 0.001 PHE c 146 TYR 0.039 0.001 TYR c 22 ARG 0.015 0.001 ARG a 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1650 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: A 123 TYR cc_start: 0.8209 (m-80) cc_final: 0.7139 (m-80) REVERT: A 150 ASP cc_start: 0.8409 (m-30) cc_final: 0.7901 (m-30) REVERT: A 276 ASP cc_start: 0.8235 (m-30) cc_final: 0.8000 (m-30) REVERT: A 292 GLU cc_start: 0.7604 (tt0) cc_final: 0.7372 (tt0) REVERT: A 487 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7782 (pt0) REVERT: A 523 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 535 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5982 (t70) REVERT: A 541 TRP cc_start: 0.8798 (p-90) cc_final: 0.8483 (p-90) REVERT: A 591 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7110 (mtm180) REVERT: A 599 GLU cc_start: 0.7195 (pt0) cc_final: 0.6966 (pt0) REVERT: B 69 GLU cc_start: 0.7191 (tp30) cc_final: 0.6869 (tp30) REVERT: B 215 MET cc_start: 0.8494 (mtm) cc_final: 0.8013 (mtm) REVERT: B 412 ASP cc_start: 0.7824 (m-30) cc_final: 0.7095 (m-30) REVERT: B 434 GLU cc_start: 0.8052 (pp20) cc_final: 0.7505 (pp20) REVERT: B 441 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7752 (mppt) REVERT: C 40 MET cc_start: 0.8206 (mmm) cc_final: 0.7799 (mmm) REVERT: C 118 GLU cc_start: 0.7746 (tp30) cc_final: 0.7274 (tp30) REVERT: C 285 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 290 MET cc_start: 0.8456 (mmm) cc_final: 0.8007 (tpp) REVERT: C 295 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7422 (ptm) REVERT: C 296 GLU cc_start: 0.6970 (mp0) cc_final: 0.6652 (mp0) REVERT: C 330 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 360 TRP cc_start: 0.8633 (t60) cc_final: 0.8321 (t60) REVERT: C 366 GLU cc_start: 0.7122 (tp30) cc_final: 0.6758 (tp30) REVERT: C 442 ASP cc_start: 0.7946 (t0) cc_final: 0.7666 (t0) REVERT: D 21 ASN cc_start: 0.8476 (t0) cc_final: 0.7683 (p0) REVERT: D 74 ARG cc_start: 0.7530 (ttm110) cc_final: 0.6906 (ttm110) REVERT: D 106 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: D 223 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7516 (mmm-85) REVERT: D 477 SER cc_start: 0.8849 (p) cc_final: 0.8615 (p) REVERT: D 483 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7480 (tm-30) REVERT: E 38 GLU cc_start: 0.8113 (pt0) cc_final: 0.7907 (pt0) REVERT: E 362 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 500 GLN cc_start: 0.7884 (pp30) cc_final: 0.7449 (pp30) REVERT: E 522 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7715 (mtmt) REVERT: F 74 ARG cc_start: 0.8643 (ptm-80) cc_final: 0.8285 (ttp80) REVERT: F 98 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7679 (mt-10) REVERT: F 114 ASP cc_start: 0.7821 (m-30) cc_final: 0.7595 (m-30) REVERT: F 150 MET cc_start: 0.8278 (ttt) cc_final: 0.8045 (ttt) REVERT: F 236 GLU cc_start: 0.8404 (pt0) cc_final: 0.8060 (pm20) REVERT: F 301 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7185 (mtp-110) REVERT: F 326 ASN cc_start: 0.8372 (m110) cc_final: 0.7840 (m110) REVERT: F 363 GLN cc_start: 0.8000 (mp10) cc_final: 0.7309 (mp10) REVERT: F 389 GLU cc_start: 0.8060 (tp30) cc_final: 0.7590 (tp30) REVERT: F 412 ASP cc_start: 0.7476 (m-30) cc_final: 0.7093 (m-30) REVERT: F 428 GLU cc_start: 0.7447 (tp30) cc_final: 0.7156 (tp30) REVERT: F 429 ASP cc_start: 0.7566 (m-30) cc_final: 0.7321 (t0) REVERT: F 479 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8270 (mtmt) REVERT: F 482 ASP cc_start: 0.7906 (m-30) cc_final: 0.7509 (m-30) REVERT: G 134 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8119 (mm-30) REVERT: I 105 GLU cc_start: 0.8327 (mp0) cc_final: 0.7909 (mp0) REVERT: J 46 TYR cc_start: 0.8129 (t80) cc_final: 0.7765 (t80) REVERT: K 136 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8347 (mmmt) REVERT: M 5 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7247 (ttt-90) REVERT: M 18 MET cc_start: 0.7796 (mmt) cc_final: 0.7589 (mmt) REVERT: M 34 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7582 (ptm160) REVERT: M 221 MET cc_start: 0.4213 (ppp) cc_final: 0.3824 (ppp) REVERT: a 8 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8420 (tt) REVERT: a 14 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5736 (ptp) REVERT: a 38 LEU cc_start: 0.7551 (mm) cc_final: 0.7233 (tt) REVERT: a 41 PHE cc_start: 0.8111 (m-80) cc_final: 0.7675 (m-80) REVERT: a 60 ARG cc_start: 0.8774 (ptt90) cc_final: 0.8376 (ptt90) REVERT: a 64 ASN cc_start: 0.8816 (t0) cc_final: 0.8412 (t0) REVERT: a 67 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8458 (ttp-110) REVERT: a 68 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8162 (mm110) REVERT: a 134 GLN cc_start: 0.8733 (mt0) cc_final: 0.8453 (mm-40) REVERT: a 211 LEU cc_start: 0.8324 (pt) cc_final: 0.8055 (pp) REVERT: a 324 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.7852 (m110) REVERT: a 338 GLU cc_start: 0.6658 (pm20) cc_final: 0.6377 (pt0) REVERT: a 344 ASP cc_start: 0.7923 (p0) cc_final: 0.7467 (p0) REVERT: a 369 GLN cc_start: 0.6849 (tp-100) cc_final: 0.6526 (tp-100) REVERT: a 465 ILE cc_start: 0.8650 (mt) cc_final: 0.8379 (mm) REVERT: a 468 MET cc_start: 0.7967 (ptm) cc_final: 0.7762 (ptm) REVERT: a 473 MET cc_start: 0.7255 (mmp) cc_final: 0.6575 (mmp) REVERT: a 474 TYR cc_start: 0.6975 (t80) cc_final: 0.6418 (t80) REVERT: a 537 MET cc_start: 0.8216 (mmt) cc_final: 0.7622 (mpp) REVERT: a 579 MET cc_start: 0.7896 (ppp) cc_final: 0.7437 (ppp) REVERT: a 592 TYR cc_start: 0.7759 (t80) cc_final: 0.7479 (t80) REVERT: a 594 TRP cc_start: 0.7533 (m-10) cc_final: 0.7238 (m-90) REVERT: a 627 TYR cc_start: 0.6113 (m-80) cc_final: 0.5816 (m-80) REVERT: a 745 GLN cc_start: 0.7950 (tp40) cc_final: 0.7438 (tp40) REVERT: a 759 PHE cc_start: 0.7358 (t80) cc_final: 0.6971 (t80) REVERT: a 769 MET cc_start: 0.8292 (mtp) cc_final: 0.7561 (mtp) REVERT: a 773 LEU cc_start: 0.8557 (tp) cc_final: 0.8065 (tp) REVERT: a 776 MET cc_start: 0.8249 (tpp) cc_final: 0.7846 (tpp) REVERT: a 818 GLU cc_start: 0.7197 (mp0) cc_final: 0.6907 (mp0) REVERT: b 223 LEU cc_start: 0.8976 (tp) cc_final: 0.8729 (tt) REVERT: b 235 PHE cc_start: 0.7919 (t80) cc_final: 0.7622 (t80) REVERT: b 243 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7545 (t60) REVERT: b 246 ASN cc_start: 0.8079 (m-40) cc_final: 0.7776 (t0) REVERT: c 117 ILE cc_start: 0.9259 (tp) cc_final: 0.9000 (tp) REVERT: c 158 ILE cc_start: 0.8937 (tp) cc_final: 0.8592 (tp) REVERT: d 21 ARG cc_start: 0.8902 (tmt-80) cc_final: 0.8478 (tmt-80) REVERT: d 24 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8861 (mm) REVERT: d 79 GLU cc_start: 0.7428 (tp30) cc_final: 0.7168 (tp30) REVERT: d 125 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8547 (tm-30) REVERT: d 173 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7794 (p0) REVERT: d 186 LYS cc_start: 0.9314 (ttpp) cc_final: 0.8922 (tttp) REVERT: d 190 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7482 (mt-10) REVERT: d 247 LYS cc_start: 0.7814 (ptmm) cc_final: 0.7598 (ptmm) REVERT: d 260 GLN cc_start: 0.8478 (tp40) cc_final: 0.8177 (tp40) REVERT: d 261 ASP cc_start: 0.8157 (p0) cc_final: 0.7786 (p0) REVERT: d 266 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7684 (mtm110) REVERT: d 285 GLU cc_start: 0.6209 (tt0) cc_final: 0.5953 (tt0) REVERT: d 304 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: d 317 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7807 (tm-30) REVERT: d 332 GLN cc_start: 0.8062 (mm110) cc_final: 0.7674 (mm-40) REVERT: e 50 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8672 (mp) REVERT: e 53 LEU cc_start: 0.8729 (tp) cc_final: 0.8526 (tp) REVERT: f 62 TYR cc_start: 0.8177 (m-10) cc_final: 0.7975 (m-80) REVERT: g 11 PHE cc_start: 0.8410 (t80) cc_final: 0.8073 (t80) REVERT: g 15 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8756 (mm) REVERT: g 39 ILE cc_start: 0.8922 (pt) cc_final: 0.7741 (mt) REVERT: g 106 PHE cc_start: 0.8200 (m-80) cc_final: 0.7637 (m-10) REVERT: g 108 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8728 (tp) REVERT: g 117 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8065 (tpp80) REVERT: g 156 GLN cc_start: 0.6953 (pp30) cc_final: 0.6450 (pp30) REVERT: h 59 MET cc_start: 0.7319 (mtp) cc_final: 0.7037 (mtm) REVERT: h 65 ILE cc_start: 0.9059 (mm) cc_final: 0.8821 (mm) REVERT: h 99 LEU cc_start: 0.8906 (mt) cc_final: 0.8668 (mm) REVERT: h 144 LEU cc_start: 0.8968 (tp) cc_final: 0.8753 (tp) REVERT: j 73 LEU cc_start: 0.8381 (tp) cc_final: 0.8111 (tp) REVERT: j 117 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: j 149 LEU cc_start: 0.8147 (tp) cc_final: 0.7946 (tp) REVERT: k 157 ASP cc_start: 0.7812 (p0) cc_final: 0.7391 (p0) REVERT: l 34 LYS cc_start: 0.8667 (tptt) cc_final: 0.8409 (mptt) REVERT: l 88 PHE cc_start: 0.7480 (m-80) cc_final: 0.7218 (t80) REVERT: l 95 LEU cc_start: 0.8860 (mm) cc_final: 0.8478 (mm) REVERT: l 144 LEU cc_start: 0.8890 (tp) cc_final: 0.8634 (tp) REVERT: m 39 ILE cc_start: 0.8370 (mm) cc_final: 0.7981 (mm) REVERT: m 90 GLN cc_start: 0.8083 (mt0) cc_final: 0.7714 (mt0) REVERT: m 121 GLN cc_start: 0.7985 (mp10) cc_final: 0.7640 (mp10) REVERT: m 129 MET cc_start: 0.7937 (tmm) cc_final: 0.7581 (tmm) REVERT: m 152 SER cc_start: 0.8874 (p) cc_final: 0.8647 (p) REVERT: m 156 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7761 (tm-30) REVERT: n 59 MET cc_start: 0.8675 (tpp) cc_final: 0.8287 (mmm) REVERT: n 72 VAL cc_start: 0.8943 (m) cc_final: 0.8630 (p) REVERT: n 122 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8292 (tm-30) REVERT: o 51 PHE cc_start: 0.8567 (m-80) cc_final: 0.8024 (m-80) REVERT: o 83 ASN cc_start: 0.8013 (p0) cc_final: 0.7644 (p0) REVERT: o 88 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7794 (tm-30) REVERT: o 141 LEU cc_start: 0.7736 (tp) cc_final: 0.7487 (tp) REVERT: o 152 MET cc_start: 0.8048 (tmm) cc_final: 0.7719 (tmm) outliers start: 154 outliers final: 109 residues processed: 1697 average time/residue: 0.5594 time to fit residues: 1584.8130 Evaluate side-chains 1713 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1589 time to evaluate : 5.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 324 ASN Chi-restraints excluded: chain a residue 535 TYR Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain a residue 827 MET Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 106 PHE Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 175 MET Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 199 GLU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 119 SER Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain j residue 95 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 54 ILE Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 51 PHE Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 69 VAL Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 125 LEU Chi-restraints excluded: chain m residue 131 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 153 ARG Chi-restraints excluded: chain n residue 144 LEU Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 0.9980 chunk 475 optimal weight: 20.0000 chunk 766 optimal weight: 0.3980 chunk 467 optimal weight: 0.0770 chunk 363 optimal weight: 7.9990 chunk 532 optimal weight: 4.9990 chunk 803 optimal weight: 1.9990 chunk 739 optimal weight: 0.7980 chunk 640 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 494 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 597 HIS B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 168 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 207 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 121 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 58646 Z= 0.196 Angle : 0.649 16.514 80001 Z= 0.328 Chirality : 0.044 0.423 9567 Planarity : 0.005 0.083 10420 Dihedral : 4.640 164.676 8735 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 2.51 % Allowed : 25.27 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8154 helix: 1.28 (0.08), residues: 4758 sheet: -1.28 (0.20), residues: 612 loop : -0.28 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP a 737 HIS 0.005 0.001 HIS o 98 PHE 0.051 0.002 PHE m 88 TYR 0.038 0.001 TYR c 22 ARG 0.016 0.001 ARG a 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16308 Ramachandran restraints generated. 8154 Oldfield, 0 Emsley, 8154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1618 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: A 38 GLU cc_start: 0.7986 (tt0) cc_final: 0.7394 (tt0) REVERT: A 150 ASP cc_start: 0.8410 (m-30) cc_final: 0.7969 (m-30) REVERT: A 276 ASP cc_start: 0.8254 (m-30) cc_final: 0.8008 (m-30) REVERT: A 292 GLU cc_start: 0.7636 (tt0) cc_final: 0.7397 (tt0) REVERT: A 487 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7776 (pt0) REVERT: A 523 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 535 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5987 (t70) REVERT: A 541 TRP cc_start: 0.8792 (p-90) cc_final: 0.8477 (p-90) REVERT: A 552 SER cc_start: 0.8876 (m) cc_final: 0.8607 (p) REVERT: A 591 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7125 (mtm180) REVERT: B 69 GLU cc_start: 0.7334 (tp30) cc_final: 0.6994 (tp30) REVERT: B 412 ASP cc_start: 0.7642 (m-30) cc_final: 0.7067 (m-30) REVERT: B 416 MET cc_start: 0.7023 (mmt) cc_final: 0.6453 (mmt) REVERT: B 434 GLU cc_start: 0.8059 (pp20) cc_final: 0.7525 (pp20) REVERT: C 40 MET cc_start: 0.8203 (mmm) cc_final: 0.7795 (mmm) REVERT: C 118 GLU cc_start: 0.7755 (tp30) cc_final: 0.7197 (tp30) REVERT: C 285 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6913 (mm-30) REVERT: C 290 MET cc_start: 0.8453 (mmm) cc_final: 0.8015 (tpp) REVERT: C 295 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7400 (ptm) REVERT: C 296 GLU cc_start: 0.7003 (mp0) cc_final: 0.6669 (mp0) REVERT: C 330 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 360 TRP cc_start: 0.8641 (t60) cc_final: 0.8332 (t60) REVERT: C 366 GLU cc_start: 0.7125 (tp30) cc_final: 0.6791 (tp30) REVERT: C 442 ASP cc_start: 0.7844 (t0) cc_final: 0.7589 (t0) REVERT: C 608 GLN cc_start: 0.8352 (tp40) cc_final: 0.7988 (tp-100) REVERT: C 609 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 21 ASN cc_start: 0.8463 (t0) cc_final: 0.7674 (p0) REVERT: D 74 ARG cc_start: 0.7508 (ttm110) cc_final: 0.6860 (ttm110) REVERT: D 106 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: D 223 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7552 (mmm-85) REVERT: D 400 SER cc_start: 0.8250 (t) cc_final: 0.7894 (p) REVERT: D 477 SER cc_start: 0.8845 (p) cc_final: 0.8606 (p) REVERT: D 483 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7506 (tm-30) REVERT: E 296 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7449 (mt-10) REVERT: E 362 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7532 (mt-10) REVERT: E 522 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7736 (mtmt) REVERT: F 74 ARG cc_start: 0.8648 (ptm-80) cc_final: 0.8298 (ttp80) REVERT: F 98 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7684 (mt-10) REVERT: F 114 ASP cc_start: 0.7801 (m-30) cc_final: 0.7597 (m-30) REVERT: F 150 MET cc_start: 0.8269 (ttt) cc_final: 0.8041 (ttt) REVERT: F 236 GLU cc_start: 0.8406 (pt0) cc_final: 0.8125 (pm20) REVERT: F 301 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7158 (mtp-110) REVERT: F 326 ASN cc_start: 0.8384 (m110) cc_final: 0.7841 (m110) REVERT: F 363 GLN cc_start: 0.7992 (mp10) cc_final: 0.7268 (mp10) REVERT: F 389 GLU cc_start: 0.8046 (tp30) cc_final: 0.7589 (tp30) REVERT: F 412 ASP cc_start: 0.7476 (m-30) cc_final: 0.7099 (m-30) REVERT: F 428 GLU cc_start: 0.7447 (tp30) cc_final: 0.7193 (tp30) REVERT: F 479 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8265 (mtmt) REVERT: F 482 ASP cc_start: 0.7871 (m-30) cc_final: 0.7463 (m-30) REVERT: G 134 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8112 (mm-30) REVERT: I 105 GLU cc_start: 0.8339 (mp0) cc_final: 0.7911 (mp0) REVERT: J 46 TYR cc_start: 0.8124 (t80) cc_final: 0.7754 (t80) REVERT: K 136 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8365 (mmmt) REVERT: M 5 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7225 (ttt-90) REVERT: M 34 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7257 (ptm160) REVERT: a 8 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8465 (tt) REVERT: a 14 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5740 (ptp) REVERT: a 27 ARG cc_start: 0.8549 (tmt170) cc_final: 0.8341 (tmt170) REVERT: a 38 LEU cc_start: 0.7546 (mm) cc_final: 0.7258 (tt) REVERT: a 41 PHE cc_start: 0.8107 (m-80) cc_final: 0.7688 (m-80) REVERT: a 60 ARG cc_start: 0.8788 (ptt90) cc_final: 0.8387 (ptt90) REVERT: a 68 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8039 (mm110) REVERT: a 134 GLN cc_start: 0.8739 (mt0) cc_final: 0.8474 (mm-40) REVERT: a 211 LEU cc_start: 0.8301 (pt) cc_final: 0.8033 (pp) REVERT: a 338 GLU cc_start: 0.6637 (pm20) cc_final: 0.6379 (pt0) REVERT: a 344 ASP cc_start: 0.7928 (p0) cc_final: 0.7473 (p0) REVERT: a 369 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6461 (tp-100) REVERT: a 465 ILE cc_start: 0.8630 (mt) cc_final: 0.8358 (mm) REVERT: a 473 MET cc_start: 0.7277 (mmp) cc_final: 0.6531 (mmt) REVERT: a 537 MET cc_start: 0.8322 (mmt) cc_final: 0.7730 (mpp) REVERT: a 579 MET cc_start: 0.7798 (ppp) cc_final: 0.7330 (ppp) REVERT: a 594 TRP cc_start: 0.7521 (m-10) cc_final: 0.7129 (m-90) REVERT: a 739 LEU cc_start: 0.8746 (mp) cc_final: 0.8534 (mp) REVERT: a 745 GLN cc_start: 0.7970 (tp40) cc_final: 0.7450 (tp40) REVERT: a 759 PHE cc_start: 0.7334 (t80) cc_final: 0.6950 (t80) REVERT: a 769 MET cc_start: 0.8289 (mtp) cc_final: 0.7561 (mtp) REVERT: a 773 LEU cc_start: 0.8686 (tp) cc_final: 0.8180 (tp) REVERT: a 776 MET cc_start: 0.8283 (tpp) cc_final: 0.7855 (tpp) REVERT: a 818 GLU cc_start: 0.7188 (mp0) cc_final: 0.6884 (mp0) REVERT: b 235 PHE cc_start: 0.7930 (t80) cc_final: 0.7676 (t80) REVERT: b 243 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7561 (t60) REVERT: b 246 ASN cc_start: 0.7988 (m-40) cc_final: 0.7685 (t0) REVERT: c 106 PHE cc_start: 0.7777 (m-80) cc_final: 0.7181 (t80) REVERT: c 117 ILE cc_start: 0.9260 (tp) cc_final: 0.9003 (tp) REVERT: c 158 ILE cc_start: 0.8991 (tp) cc_final: 0.8636 (tp) REVERT: d 24 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8874 (mm) REVERT: d 34 THR cc_start: 0.7978 (m) cc_final: 0.7555 (p) REVERT: d 79 GLU cc_start: 0.7448 (tp30) cc_final: 0.7233 (tp30) REVERT: d 247 LYS cc_start: 0.7940 (ptmm) cc_final: 0.7644 (ptmm) REVERT: d 260 GLN cc_start: 0.8472 (tp40) cc_final: 0.8167 (tp40) REVERT: d 276 ARG cc_start: 0.7539 (ptp-170) cc_final: 0.7332 (ptp-170) REVERT: d 285 GLU cc_start: 0.6216 (tt0) cc_final: 0.5968 (tt0) REVERT: d 304 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7585 (m-10) REVERT: d 317 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7821 (tm-30) REVERT: d 332 GLN cc_start: 0.8073 (mm110) cc_final: 0.7657 (mm-40) REVERT: e 50 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8614 (mp) REVERT: e 53 LEU cc_start: 0.8660 (tp) cc_final: 0.8441 (tp) REVERT: f 56 TYR cc_start: 0.8677 (m-10) cc_final: 0.8402 (m-10) REVERT: g 11 PHE cc_start: 0.8383 (t80) cc_final: 0.8037 (t80) REVERT: g 108 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8695 (tp) REVERT: g 117 ARG cc_start: 0.8288 (tpp80) cc_final: 0.8060 (tpp80) REVERT: g 156 GLN cc_start: 0.6953 (pp30) cc_final: 0.6438 (pp30) REVERT: h 99 LEU cc_start: 0.8911 (mt) cc_final: 0.8709 (mm) REVERT: j 73 LEU cc_start: 0.8393 (tp) cc_final: 0.8121 (tp) REVERT: j 117 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7794 (mmm-85) REVERT: k 49 LEU cc_start: 0.8274 (tp) cc_final: 0.7946 (tp) REVERT: k 73 LEU cc_start: 0.8465 (tp) cc_final: 0.8201 (tp) REVERT: k 157 ASP cc_start: 0.7765 (p0) cc_final: 0.7343 (p0) REVERT: l 34 LYS cc_start: 0.8763 (tptt) cc_final: 0.8437 (mptt) REVERT: l 95 LEU cc_start: 0.8859 (mm) cc_final: 0.8464 (mm) REVERT: l 144 LEU cc_start: 0.8924 (tp) cc_final: 0.8640 (tp) REVERT: m 39 ILE cc_start: 0.8362 (mm) cc_final: 0.8129 (mm) REVERT: m 90 GLN cc_start: 0.8128 (mt0) cc_final: 0.7724 (mt0) REVERT: m 121 GLN cc_start: 0.7997 (mp10) cc_final: 0.7658 (mp10) REVERT: m 129 MET cc_start: 0.8035 (tmm) cc_final: 0.7142 (tmm) REVERT: m 133 LEU cc_start: 0.8521 (mt) cc_final: 0.7700 (mt) REVERT: m 152 SER cc_start: 0.8810 (p) cc_final: 0.8586 (p) REVERT: m 156 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7757 (tm-30) REVERT: n 59 MET cc_start: 0.8692 (tpp) cc_final: 0.8297 (mmm) REVERT: n 72 VAL cc_start: 0.8934 (m) cc_final: 0.8620 (p) REVERT: n 122 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8395 (tm-30) REVERT: o 51 PHE cc_start: 0.8554 (m-80) cc_final: 0.8188 (m-80) REVERT: o 83 ASN cc_start: 0.8003 (p0) cc_final: 0.7704 (p0) REVERT: o 141 LEU cc_start: 0.7719 (tp) cc_final: 0.7487 (tp) REVERT: o 149 LEU cc_start: 0.8843 (tp) cc_final: 0.8549 (tp) REVERT: o 152 MET cc_start: 0.7986 (tmm) cc_final: 0.7745 (tmm) outliers start: 128 outliers final: 106 residues processed: 1656 average time/residue: 0.6144 time to fit residues: 1717.0482 Evaluate side-chains 1716 residues out of total 6935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1598 time to evaluate : 5.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 497 GLN Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain a residue 8 ILE Chi-restraints excluded: chain a residue 14 MET Chi-restraints excluded: chain a residue 19 PHE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 441 LEU Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 535 TYR Chi-restraints excluded: chain a residue 601 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 243 TRP Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 147 TRP Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain d residue 29 GLN Chi-restraints excluded: chain d residue 93 LYS Chi-restraints excluded: chain d residue 175 MET Chi-restraints excluded: chain d residue 176 ASN Chi-restraints excluded: chain d residue 198 GLU Chi-restraints excluded: chain d residue 199 GLU Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 295 LEU Chi-restraints excluded: chain d residue 304 PHE Chi-restraints excluded: chain d residue 307 SER Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 113 ASP Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 130 ILE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 99 LEU Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 72 VAL Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 132 ILE Chi-restraints excluded: chain k residue 148 LEU Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain l residue 51 PHE Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 74 VAL Chi-restraints excluded: chain m residue 62 ILE Chi-restraints excluded: chain m residue 73 LEU Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 125 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 153 ARG Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain o residue 128 MET Chi-restraints excluded: chain o residue 140 ILE Chi-restraints excluded: chain o residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 9.9990 chunk 508 optimal weight: 0.9990 chunk 681 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 590 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 177 optimal weight: 0.4980 chunk 641 optimal weight: 0.5980 chunk 268 optimal weight: 5.9990 chunk 658 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 122 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 ASN ** a 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097768 restraints weight = 136465.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099366 restraints weight = 69231.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100465 restraints weight = 42480.305| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 58646 Z= 0.205 Angle : 0.653 21.930 80001 Z= 0.329 Chirality : 0.044 0.448 9567 Planarity : 0.005 0.083 10420 Dihedral : 4.627 162.431 8735 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 2.94 % Allowed : 25.14 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 8154 helix: 1.28 (0.08), residues: 4761 sheet: -1.25 (0.20), residues: 612 loop : -0.26 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP a 737 HIS 0.006 0.001 HIS o 98 PHE 0.079 0.002 PHE l 88 TYR 0.038 0.001 TYR l 142 ARG 0.016 0.001 ARG a 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20922.60 seconds wall clock time: 363 minutes 8.28 seconds (21788.28 seconds total)