Starting phenix.real_space_refine on Sun Mar 10 14:51:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmt_26002/03_2024/7tmt_26002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmt_26002/03_2024/7tmt_26002.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/7tmt_26002/03_2024/7tmt_26002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmt_26002/03_2024/7tmt_26002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmt_26002/03_2024/7tmt_26002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmt_26002/03_2024/7tmt_26002_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= 0.000 sd= 1.000 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 144 5.16 5 C 33489 2.51 5 N 9607 2.21 5 O 10191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 355": "OD1" <-> "OD2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 377": "OD1" <-> "OD2" Residue "E TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E GLU 494": "OE1" <-> "OE2" Residue "E GLU 496": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 341": "OD1" <-> "OD2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 221": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "a TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 372": "OD1" <-> "OD2" Residue "a ASP 395": "OD1" <-> "OD2" Residue "a PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 215": "OE1" <-> "OE2" Residue "d TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 285": "OE1" <-> "OE2" Residue "d PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 317": "OE1" <-> "OE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53433 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4545 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 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: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3688 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4541 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3690 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 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: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3712 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1202 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 562 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 283 Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 587 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "I" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1324 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 13, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 244 Chain: "J" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 584 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 24 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': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "K" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1332 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 6, 'TRANS': 217} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 235 Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 594 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 25 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': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "M" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1444 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 3, 'TRANS': 219} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Chain: "N" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 581 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 286 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': 7, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 207 Chain: "O" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 1792 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 337} Chain breaks: 1 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 888 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 20, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 590 Chain: "P" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2197 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 396} Link IDs: {'PTRANS': 9, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 1393 Unresolved non-hydrogen angles: 1777 Unresolved non-hydrogen dihedrals: 1129 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 721 Chain: "a" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 4317 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 492} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved non-hydrogen bonds: 1686 Unresolved non-hydrogen angles: 2146 Unresolved non-hydrogen dihedrals: 1346 Unresolved non-hydrogen chiralities: 201 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 8, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 1, 'ASP:plan': 35, 'PHE:plan': 23, 'GLU:plan': 38, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 837 Chain: "b" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 315 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "c" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1165 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'HIS:plan': 1, 'GLN%COO:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "d" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2209 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 333} Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 14, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'TYR%COO:plan': 1, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 311 Chain: "e" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 428 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "f" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 358 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "g" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 911 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "h" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 872 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "i" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 957 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "j" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 926 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "k" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 902 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "l" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 922 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "m" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 932 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "n" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 871 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "o" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 930 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 68 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: 21.65, per 1000 atoms: 0.41 Number of scatterers: 53433 At special positions: 0 Unit cell: (142.998, 187.46, 260.762, 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 144 16.00 P 2 15.00 O 10191 8.00 N 9607 7.00 C 33489 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: 16.55 Conformation dependent library (CDL) restraints added in 8.7 seconds 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 275 helices and 35 sheets defined 59.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.30 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 287 through 299 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 330 Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 382 through 393 removed outlier: 4.192A pdb=" N GLY A 385 " --> pdb=" O ALA A 382 " (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: 3.799A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A 472 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 501 removed outlier: 4.035A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.708A 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: 4.405A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.115A 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 615 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' 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 179 through 190 removed outlier: 4.330A pdb=" N ALA B 184 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.881A pdb=" N PHE B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.717A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 294 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 306 through 316 removed outlier: 4.382A pdb=" N TYR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 314 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.607A pdb=" N LYS B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 386 Processing helix chain 'B' and resid 396 through 418 removed outlier: 4.412A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 454 through 467 removed outlier: 4.964A pdb=" N ILE B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 removed outlier: 4.241A pdb=" N GLU B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 118 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 262 through 271 removed outlier: 3.570A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 326 through 345 removed outlier: 4.413A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.473A 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 392 removed outlier: 4.071A pdb=" N GLY C 385 " --> pdb=" O ALA C 382 " (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: 3.558A pdb=" N LYS C 469 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 499 Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' 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: 4.719A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.347A 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 615 removed outlier: 3.944A pdb=" N GLY C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' 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 190 Processing helix chain 'D' and resid 201 through 204 No H-bonds generated for 'chain 'D' and resid 201 through 204' Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 251 through 268 removed outlier: 4.011A pdb=" N THR D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Proline residue: D 256 - end of helix removed outlier: 3.974A 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 306 through 316 removed outlier: 4.314A pdb=" N TYR D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 312 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR D 314 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.725A pdb=" N TYR D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.980A 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 419 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.888A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) 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 removed outlier: 5.044A pdb=" N GLU E 292 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 293 " --> pdb=" O MET E 290 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE E 297 " --> pdb=" O LEU E 294 " (cutoff:3.500A) 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 345 removed outlier: 3.595A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 382 through 393 removed outlier: 4.022A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (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 431 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 468 through 474 Processing helix chain 'E' and resid 478 through 502 removed outlier: 4.014A pdb=" N LEU E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 563 Processing helix chain 'E' and resid 567 through 573 removed outlier: 4.487A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 removed outlier: 4.251A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 5.074A 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 14 through 17 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 232 removed outlier: 3.666A pdb=" N ASN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 267 removed outlier: 4.142A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix removed outlier: 4.491A pdb=" N LEU F 260 " --> pdb=" O ARG F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.532A pdb=" N ARG F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.222A pdb=" N TYR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 396 through 420 Processing helix chain 'F' and resid 427 through 442 Processing helix chain 'F' and resid 454 through 465 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 Processing helix chain 'G' and resid 9 through 112 removed outlier: 3.756A pdb=" N VAL G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS G 65 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 143 through 163 removed outlier: 3.554A pdb=" N VAL G 146 " --> pdb=" O GLU G 143 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP G 147 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 153 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP G 154 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS G 163 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 removed outlier: 3.640A pdb=" N GLU G 212 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'H' and resid 5 through 103 removed outlier: 3.770A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 112 Processing helix chain 'I' and resid 114 through 131 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 146 through 163 removed outlier: 5.623A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 removed outlier: 3.984A pdb=" N LYS I 208 " --> pdb=" O GLU I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 221 removed outlier: 3.726A pdb=" N GLU I 221 " --> pdb=" O ALA I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 103 removed outlier: 3.546A pdb=" N TYR J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL J 65 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 112 removed outlier: 3.907A pdb=" N GLY K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU K 105 " --> pdb=" O GLU K 101 " (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 145 through 163 removed outlier: 5.162A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 removed outlier: 4.006A pdb=" N LYS K 208 " --> pdb=" O GLU K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 223 Processing helix chain 'L' and resid 3 through 103 removed outlier: 3.668A pdb=" N VAL L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 75 removed outlier: 4.291A pdb=" N MET M 61 " --> pdb=" O MET M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 83 No H-bonds generated for 'chain 'M' and resid 80 through 83' Processing helix chain 'M' and resid 126 through 171 removed outlier: 3.560A pdb=" N GLY M 129 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA M 155 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN M 167 " --> pdb=" O LYS M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 186 Proline residue: M 179 - end of helix Processing helix chain 'M' and resid 188 through 217 Processing helix chain 'M' and resid 220 through 223 No H-bonds generated for 'chain 'M' and resid 220 through 223' Processing helix chain 'N' and resid 16 through 21 Processing helix chain 'N' and resid 47 through 59 Processing helix chain 'N' and resid 71 through 74 Processing helix chain 'N' and resid 77 through 85 removed outlier: 4.100A pdb=" N THR N 85 " --> pdb=" O VAL N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'O' and resid 30 through 40 Processing helix chain 'O' and resid 58 through 88 Processing helix chain 'O' and resid 107 through 110 No H-bonds generated for 'chain 'O' and resid 107 through 110' Processing helix chain 'O' and resid 127 through 165 Processing helix chain 'O' and resid 203 through 213 removed outlier: 3.884A pdb=" N THR O 212 " --> pdb=" O LYS O 208 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU O 213 " --> pdb=" O SER O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 230 No H-bonds generated for 'chain 'O' and resid 228 through 230' Processing helix chain 'O' and resid 240 through 251 removed outlier: 6.065A pdb=" N GLN O 244 " --> pdb=" O LYS O 241 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 251 " --> pdb=" O THR O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 319 removed outlier: 3.897A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 347 removed outlier: 4.536A pdb=" N SER O 338 " --> pdb=" O LYS O 335 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS O 340 " --> pdb=" O LEU O 337 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU O 344 " --> pdb=" O LYS O 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 20 removed outlier: 4.865A pdb=" N ILE P 16 " --> pdb=" O PHE P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 33 removed outlier: 4.023A pdb=" N ASP P 28 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA P 29 " --> pdb=" O ALA P 26 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER P 33 " --> pdb=" O LEU P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 76 through 86 Processing helix chain 'P' and resid 90 through 105 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 121 through 130 removed outlier: 3.675A pdb=" N GLU P 125 " --> pdb=" O LYS P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 150 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: 4.152A pdb=" N VAL P 195 " --> pdb=" O GLN P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 205 removed outlier: 3.657A pdb=" N VAL P 202 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU P 205 " --> pdb=" O ASP P 201 " (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 237 through 255 removed outlier: 4.307A pdb=" N SER P 246 " --> pdb=" O LEU P 242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU P 247 " --> pdb=" O GLN P 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 249 " --> pdb=" O HIS P 245 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE P 250 " --> pdb=" O SER P 246 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE P 255 " --> pdb=" O TRP P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 280 removed outlier: 3.697A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS P 266 " --> pdb=" O GLU P 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU P 268 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER P 269 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP P 270 " --> pdb=" O LYS P 266 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 298 Processing helix chain 'P' and resid 305 through 316 removed outlier: 4.132A pdb=" N LYS P 310 " --> pdb=" O LYS P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 333 through 354 removed outlier: 3.878A pdb=" N GLU P 347 " --> pdb=" O LYS P 343 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU P 349 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR P 350 " --> pdb=" O LEU P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 364 Processing helix chain 'P' and resid 372 through 379 removed outlier: 5.199A pdb=" N ASN P 377 " --> pdb=" O HIS P 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 387 Processing helix chain 'P' and resid 389 through 408 removed outlier: 5.231A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU P 398 " --> pdb=" O ILE P 394 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 433 Processing helix chain 'P' and resid 435 through 444 Processing helix chain 'P' and resid 446 through 454 Processing helix chain 'P' and resid 459 through 477 Processing helix chain 'a' and resid 26 through 36 Processing helix chain 'a' and resid 45 through 47 No H-bonds generated for 'chain 'a' and resid 45 through 47' Processing helix chain 'a' and resid 50 through 52 No H-bonds generated for 'chain 'a' and resid 50 through 52' Processing helix chain 'a' and resid 56 through 78 Processing helix chain 'a' and resid 84 through 98 Processing helix chain 'a' and resid 107 through 142 removed outlier: 3.805A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG a 142 " --> pdb=" O LEU a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 206 removed outlier: 3.546A pdb=" N VAL a 196 " --> pdb=" O ARG a 193 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ALA a 197 " --> pdb=" O ASP a 194 " (cutoff:3.500A) removed outlier: 3.692A 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 325 removed outlier: 4.019A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 388 through 397 removed outlier: 4.574A pdb=" N TYR a 397 " --> pdb=" O ILE a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 423 removed outlier: 4.058A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix removed outlier: 3.614A pdb=" N MET a 422 " --> pdb=" O MET a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 441 Processing helix chain 'a' and resid 443 through 448 Processing helix chain 'a' and resid 455 through 460 Processing helix chain 'a' and resid 464 through 478 Processing helix chain 'a' and resid 526 through 561 removed outlier: 4.777A pdb=" N LEU a 530 " --> pdb=" O GLU a 526 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS a 538 " --> pdb=" O SER a 534 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 595 removed outlier: 4.606A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix removed outlier: 4.961A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP a 594 " --> pdb=" O ILE a 590 " (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 608 through 617 Processing helix chain 'a' and resid 628 through 650 removed outlier: 3.973A pdb=" N LYS a 632 " --> pdb=" O PRO a 628 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 710 through 758 removed outlier: 3.627A pdb=" N ILE a 713 " --> pdb=" O ASP a 710 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR a 733 " --> pdb=" O THR a 730 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU a 734 " --> pdb=" O ALA a 731 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU a 741 " --> pdb=" O ALA a 738 " (cutoff:3.500A) Processing helix chain 'a' and resid 764 through 787 removed outlier: 3.592A pdb=" N ALA a 772 " --> pdb=" O PHE a 768 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA a 775 " --> pdb=" O VAL a 771 " (cutoff:3.500A) Processing helix chain 'a' and resid 789 through 809 removed outlier: 4.566A pdb=" N MET a 806 " --> pdb=" O TRP a 802 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER a 807 " --> pdb=" O VAL a 803 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 244 removed outlier: 4.073A pdb=" N CYS b 226 " --> pdb=" O GLY b 222 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 254 No H-bonds generated for 'chain 'b' and resid 251 through 254' Processing helix chain 'c' and resid 17 through 37 Processing helix chain 'c' and resid 40 through 50 removed outlier: 4.155A pdb=" N SER c 43 " --> pdb=" O GLY c 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE c 47 " --> pdb=" O ASP c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 91 removed outlier: 3.861A pdb=" N VAL c 91 " --> pdb=" O ILE c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 124 removed outlier: 4.263A pdb=" N LEU c 101 " --> pdb=" O THR c 97 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 174 removed outlier: 4.051A pdb=" N LEU c 139 " --> pdb=" O SER c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 208 removed outlier: 4.269A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 23 removed outlier: 3.959A pdb=" N ASN d 10 " --> pdb=" O ASN d 7 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY d 11 " --> pdb=" O ILE d 8 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE d 12 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 35 Processing helix chain 'd' and resid 39 through 48 Processing helix chain 'd' and resid 53 through 56 Processing helix chain 'd' and resid 65 through 85 Processing helix chain 'd' and resid 90 through 111 removed outlier: 3.784A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (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 136 through 141 Processing helix chain 'd' and resid 145 through 153 Processing helix chain 'd' and resid 157 through 164 Proline residue: d 160 - end of helix Processing helix chain 'd' and resid 180 through 199 Processing helix chain 'd' and resid 204 through 229 removed outlier: 4.238A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLN d 229 " --> pdb=" O LEU d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 241 removed outlier: 3.596A pdb=" N ASP d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 removed outlier: 3.945A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 271 removed outlier: 3.585A pdb=" N ARG d 266 " --> pdb=" O PHE d 262 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 269 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN d 271 " --> pdb=" O ALA d 267 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 302 removed outlier: 3.773A pdb=" N GLN d 302 " --> pdb=" O ASP d 298 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 331 removed outlier: 3.508A pdb=" N LYS d 316 " --> pdb=" O MET d 313 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE d 330 " --> pdb=" O ALA d 327 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA d 331 " --> pdb=" O GLU d 328 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 340 No H-bonds generated for 'chain 'd' and resid 338 through 340' Processing helix chain 'e' and resid 5 through 23 Processing helix chain 'e' and resid 30 through 56 Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.028A pdb=" N LEU f 16 " --> pdb=" O CYS f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 40 No H-bonds generated for 'chain 'f' and resid 38 through 40' Processing helix chain 'f' and resid 48 through 69 Processing helix chain 'g' and resid 7 through 45 removed outlier: 3.919A pdb=" N PHE g 11 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY g 38 " --> pdb=" O LYS g 34 " (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 Proline residue: g 56 - end of helix removed outlier: 3.776A pdb=" N TYR g 76 " --> pdb=" O LEU g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 121 Processing helix chain 'g' and resid 123 through 154 removed outlier: 3.566A pdb=" N PHE g 126 " --> pdb=" O PRO g 123 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL g 127 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE g 130 " --> pdb=" O VAL g 127 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL g 138 " --> pdb=" O PHE g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 7 through 43 Proline residue: h 10 - end of helix removed outlier: 4.797A pdb=" N PHE h 23 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR h 24 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS h 43 " --> pdb=" O CYS h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 47 through 50 No H-bonds generated for 'chain 'h' and resid 47 through 50' Processing helix chain 'h' and resid 52 through 77 removed outlier: 4.030A pdb=" N VAL h 55 " --> pdb=" O LYS h 52 " (cutoff:3.500A) Proline residue: h 56 - end of helix Processing helix chain 'h' and resid 84 through 121 Processing helix chain 'h' and resid 123 through 155 removed outlier: 4.413A pdb=" N VAL h 127 " --> pdb=" O ARG h 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 45 removed outlier: 4.388A pdb=" N ILE i 15 " --> pdb=" O PHE i 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA i 41 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL i 44 " --> pdb=" O CYS i 40 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU i 45 " --> pdb=" O ALA i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 53 removed outlier: 5.016A pdb=" N PHE i 51 " --> pdb=" O ASP i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 77 Processing helix chain 'i' and resid 84 through 121 Processing helix chain 'i' and resid 123 through 154 removed outlier: 3.561A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE i 130 " --> pdb=" O PHE i 126 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU i 131 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE i 132 " --> pdb=" O GLY i 128 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 43 removed outlier: 4.149A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER j 25 " --> pdb=" O ILE j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 77 removed outlier: 3.764A pdb=" N ILE j 54 " --> pdb=" O LEU j 50 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL j 55 " --> pdb=" O PHE j 51 " (cutoff:3.500A) Proline residue: j 56 - end of helix removed outlier: 3.671A pdb=" N ILE j 63 " --> pdb=" O MET j 59 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 121 removed outlier: 4.180A pdb=" N GLN j 121 " --> pdb=" O ARG j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 126 through 155 removed outlier: 3.858A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 3.784A pdb=" N SER k 25 " --> pdb=" O ILE k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 49 No H-bonds generated for 'chain 'k' and resid 47 through 49' Processing helix chain 'k' and resid 52 through 77 Proline residue: k 56 - end of helix Processing helix chain 'k' and resid 84 through 120 removed outlier: 3.683A pdb=" N SER k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 154 Processing helix chain 'l' and resid 9 through 45 removed outlier: 3.795A pdb=" N CYS l 17 " --> pdb=" O GLY l 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY l 38 " --> pdb=" O LYS l 34 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA l 41 " --> pdb=" O VAL l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 49 No H-bonds generated for 'chain 'l' and resid 47 through 49' Processing helix chain 'l' and resid 55 through 76 removed outlier: 3.589A pdb=" N ILE l 63 " --> pdb=" O MET l 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA l 64 " --> pdb=" O ALA l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 120 Processing helix chain 'l' and resid 123 through 155 removed outlier: 3.525A pdb=" N PHE l 126 " --> pdb=" O PRO l 123 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL l 127 " --> pdb=" O ARG l 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 42 Proline residue: m 10 - end of helix removed outlier: 4.263A pdb=" N PHE m 23 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR m 24 " --> pdb=" O ILE m 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER m 35 " --> pdb=" O THR m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 49 No H-bonds generated for 'chain 'm' and resid 47 through 49' Processing helix chain 'm' and resid 52 through 77 Proline residue: m 56 - end of helix Processing helix chain 'm' and resid 84 through 121 removed outlier: 3.684A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 123 through 154 removed outlier: 3.683A pdb=" N PHE m 126 " --> pdb=" O PRO m 123 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL m 127 " --> pdb=" O ARG m 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 45 Proline residue: n 10 - end of helix removed outlier: 4.420A pdb=" N PHE n 23 " --> pdb=" O ALA n 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR n 24 " --> pdb=" O ILE n 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR n 42 " --> pdb=" O ILE n 39 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS n 43 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL n 44 " --> pdb=" O ALA n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 76 removed outlier: 4.556A pdb=" N PHE n 51 " --> pdb=" O ASP n 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE n 54 " --> pdb=" O PHE n 51 " (cutoff:3.500A) Proline residue: n 56 - end of helix Processing helix chain 'n' and resid 85 through 121 removed outlier: 3.862A pdb=" N ALA n 114 " --> pdb=" O ILE n 110 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG n 117 " --> pdb=" O ASP n 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 157 removed outlier: 3.656A pdb=" N PHE n 135 " --> pdb=" O LEU n 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA n 136 " --> pdb=" O ILE n 132 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR n 155 " --> pdb=" O ASN n 151 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN n 156 " --> pdb=" O SER n 152 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP n 157 " --> pdb=" O ARG n 153 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 51 removed outlier: 3.846A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE o 51 " --> pdb=" O GLY o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 58 through 83 Proline residue: o 62 - end of helix removed outlier: 3.646A pdb=" N ASN o 83 " --> pdb=" O ILE o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 128 removed outlier: 3.650A pdb=" N MET o 128 " --> pdb=" O VAL o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 163 removed outlier: 4.563A pdb=" N VAL o 138 " --> pdb=" O VAL o 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.359A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.112A 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: 4.184A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.550A pdb=" N PHE A 202 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU A 201 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE A 182 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 251 through 255 removed outlier: 6.345A pdb=" N ILE A 412 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE A 254 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 414 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.592A pdb=" N GLU B 94 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 104 Processing sheet with id= H, first strand: chain 'B' and resid 172 through 174 Processing sheet with id= I, first strand: chain 'B' and resid 212 through 214 removed outlier: 7.488A pdb=" N ALA B 213 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 277 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 278 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.256A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 62 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'C' and resid 93 through 97 Processing sheet with id= M, first strand: chain 'C' and resid 139 through 141 Processing sheet with id= N, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.504A pdb=" N VAL C 281 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C 283 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 397 through 399 Processing sheet with id= P, first strand: chain 'C' and resid 181 through 185 removed outlier: 6.770A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 185 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE C 197 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE C 209 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.830A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN D 78 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL D 67 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 94 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.521A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 171 through 174 Processing sheet with id= T, first strand: chain 'D' and resid 273 through 276 removed outlier: 5.983A pdb=" N SER D 328 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 276 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D 330 " --> pdb=" O THR D 276 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 68 through 71 Processing sheet with id= V, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= W, first strand: chain 'E' and resid 189 through 191 removed outlier: 6.716A pdb=" N ILE E 172 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER E 160 " --> pdb=" O HIS E 170 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS E 170 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.674A pdb=" N TRP E 184 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU E 201 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE E 182 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 252 through 254 Processing sheet with id= Z, first strand: chain 'E' and resid 278 through 283 Processing sheet with id= AA, first strand: chain 'F' and resid 92 through 95 Processing sheet with id= AB, first strand: chain 'F' and resid 357 through 359 Processing sheet with id= AC, first strand: chain 'G' and resid 171 through 174 Processing sheet with id= AD, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.588A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.611A pdb=" N ALA K 137 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS K 140 " --> pdb=" O VAL K 189 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'O' and resid 14 through 16 removed outlier: 4.256A pdb=" N ILE O 14 " --> pdb=" O LYS O 328 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'a' and resid 367 through 370 removed outlier: 3.722A pdb=" N ILE a 367 " --> pdb=" O TYR a 20 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'a' and resid 259 through 261 removed outlier: 3.861A pdb=" N ASN a 259 " --> pdb=" O VAL a 190 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL a 190 " --> pdb=" O ASN a 259 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'a' and resid 212 through 214 removed outlier: 3.758A pdb=" N PHE a 212 " --> pdb=" O PHE a 239 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE a 239 " --> pdb=" O PHE a 212 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE a 237 " --> pdb=" O LYS a 214 " (cutoff:3.500A) 3744 hydrogen bonds defined for protein. 9222 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: 17.61 Time building geometry restraints manager: 18.13 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: 12915 1.33 - 1.45: 10543 1.45 - 1.57: 30613 1.57 - 1.69: 3 1.69 - 1.81: 247 Bond restraints: 54321 Sorted by residual: bond pdb=" CA THR C 130 " pdb=" C THR C 130 " ideal model delta sigma weight residual 1.524 1.554 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" CB MET A 607 " pdb=" CG MET A 607 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.39e+00 bond pdb=" N THR C 130 " pdb=" CA THR C 130 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.41e-02 5.03e+03 4.08e+00 bond pdb=" C ASP M 218 " pdb=" O ASP M 218 " ideal model delta sigma weight residual 1.234 1.209 0.025 1.40e-02 5.10e+03 3.19e+00 bond pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.17e+00 ... (remaining 54316 not shown) Histogram of bond angle deviations from ideal: 92.30 - 101.04: 79 101.04 - 109.78: 5374 109.78 - 118.51: 36623 118.51 - 127.25: 31835 127.25 - 135.99: 435 Bond angle restraints: 74346 Sorted by residual: angle pdb=" N VAL D 375 " pdb=" CA VAL D 375 " pdb=" C VAL D 375 " ideal model delta sigma weight residual 110.42 118.78 -8.36 9.60e-01 1.09e+00 7.58e+01 angle pdb=" N ASP C 129 " pdb=" CA ASP C 129 " pdb=" C ASP C 129 " ideal model delta sigma weight residual 111.28 118.95 -7.67 1.09e+00 8.42e-01 4.95e+01 angle pdb=" N THR M 214 " pdb=" CA THR M 214 " pdb=" C THR M 214 " ideal model delta sigma weight residual 111.36 104.71 6.65 1.09e+00 8.42e-01 3.73e+01 angle pdb=" C ASN O 95 " pdb=" CA ASN O 95 " pdb=" CB ASN O 95 " ideal model delta sigma weight residual 117.23 110.31 6.92 1.36e+00 5.41e-01 2.59e+01 angle pdb=" C GLU O 189 " pdb=" CA GLU O 189 " pdb=" CB GLU O 189 " ideal model delta sigma weight residual 116.54 110.73 5.81 1.15e+00 7.56e-01 2.55e+01 ... (remaining 74341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.82: 31398 28.82 - 57.64: 660 57.64 - 86.46: 58 86.46 - 115.28: 12 115.28 - 144.10: 2 Dihedral angle restraints: 32130 sinusoidal: 8526 harmonic: 23604 Sorted by residual: dihedral pdb=" O1B ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " pdb=" PA ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 155.90 144.10 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 66.21 -126.21 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" CA LEU M 217 " pdb=" C LEU M 217 " pdb=" N ASP M 218 " pdb=" CA ASP M 218 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 32127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6894 0.055 - 0.109: 1675 0.109 - 0.164: 175 0.164 - 0.219: 9 0.219 - 0.273: 2 Chirality restraints: 8755 Sorted by residual: chirality pdb=" CB ILE F 102 " pdb=" CA ILE F 102 " pdb=" CG1 ILE F 102 " pdb=" CG2 ILE F 102 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE M 185 " pdb=" CA ILE M 185 " pdb=" CG1 ILE M 185 " pdb=" CG2 ILE M 185 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 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 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 8752 not shown) Planarity restraints: 10052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 802 " -0.026 2.00e-02 2.50e+03 2.64e-02 1.74e+01 pdb=" CG TRP a 802 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP a 802 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP a 802 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 802 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 802 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 802 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 802 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 802 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 802 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 95 " 0.026 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE D 95 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 95 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 95 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 95 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 95 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 95 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL i 55 " -0.045 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO i 56 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO i 56 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO i 56 " -0.037 5.00e-02 4.00e+02 ... (remaining 10049 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 773 2.67 - 3.23: 57029 3.23 - 3.78: 88450 3.78 - 4.34: 108452 4.34 - 4.90: 179309 Nonbonded interactions: 434013 Sorted by model distance: nonbonded pdb=" OD1 ASP D 114 " pdb=" N GLY D 115 " model vdw 2.109 2.520 nonbonded pdb=" O GLY I 186 " pdb=" OG1 THR I 202 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR F 284 " pdb=" OD2 ASP F 311 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR c 57 " pdb=" O ALA c 128 " model vdw 2.206 2.440 nonbonded pdb=" OE2 GLU C 74 " pdb=" NH2 ARG C 110 " model vdw 2.208 2.520 ... (remaining 434008 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 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 261 or (resid 2 \ 62 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 n \ ame O or name CB )) or resid 278 through 615 or (resid 616 and (name N or name C \ A or name C or name O or name CB or name OXT)))) selection = (chain 'C' and (resid 24 through 284 or (resid 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 308 or (resid 309 and (name N o \ r name CA or name C or name O or name CB )) or resid 310 through 354 or (resid 3 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 356 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 589 or (resid 590 through 591 and (name N or name CA or name C \ or name O or name CB )) or resid 592 or (resid 593 through 595 and (name N or na \ me CA or name C or name O or name CB )) or resid 596 through 616)) selection = (chain 'E' and (resid 24 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 261 or (resid 2 \ 62 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 n \ ame O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name C \ A 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 resid 310 through 354 or \ (resid 355 and (name N or name CA or name C or name O or name CB )) or resid 356 \ 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 through 591 and (name N or name CA or \ name C or name O or name CB )) or resid 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 615 or (res \ id 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 192 or (resid 193 through 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 487)) selection = (chain 'D' and (resid 14 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB )) or resid 107 through 481 or (resid 482 and (name N o \ r name CA or name C or name O or name CB )) or resid 483 through 487)) selection = (chain 'F' and (resid 14 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB )) or resid 107 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 481 or (resid 4 \ 82 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 162 or (resid 163 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 or (resid 166 through 167 an \ d (name N or name CA or name C or name O or name CB )) or resid 168 through 198 \ or (resid 199 through 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 through 208 or (resid 209 through 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 through 222 or (resid 223 and (name \ N or name CA or name C or name O or name CB )) or resid 224 through 228)) selection = (chain 'I' and (resid 9 through 81 or (resid 82 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 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 \ through 134 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 35 or (resid 136 through 137 and (name N or name CA or name C or name O or name \ CB )) or resid 138 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 or (resid 154 through 156 and (na \ me N or name CA or name C or name O or name CB )) or resid 157 or (resid 158 thr \ ough 159 and (name N or name CA or name C or name O or name CB )) or resid 160 t \ hrough 162 or (resid 163 through 164 and (name N or name CA or name C or name O \ or name CB )) or resid 165 through 169 or (resid 170 through 177 and (name N or \ name CA or name C or name 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 \ 206 and (name N or name CA or name C or name O or name CB )) or resid 207 throug \ h 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 219 or (resid 220 and (name N or name CA or name C or name O o \ r name CB )) or resid 221 or (resid 222 through 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 through 228)) selection = (chain 'K' and (resid 9 through 61 or (resid 62 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 116 and (name N or n \ ame CA or name C or name O or name CB )) or resid 117 or (resid 118 and (name N \ or name CA or name C or name O or name CB )) or resid 119 through 120 or (resid \ 121 through 134 and (name N or name CA or name C or name O or name CB )) or resi \ d 135 or (resid 136 through 137 and (name N or name CA or name C or name O or na \ me CB )) or resid 138 through 141 or (resid 142 through 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 157 or (resid 158 thro \ ugh 159 and (name N or name CA or name C or name O or name CB )) or resid 160 th \ rough 165 or (resid 166 through 167 and (name N or name CA or name C or name O o \ r name CB )) or resid 168 through 171 or (resid 172 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 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 219 or (resid 220 and (name N or name CA or name C or name O or nam \ e CB )) or resid 221 through 228)) } ncs_group { reference = (chain 'H' and (resid 2 through 95 or (resid 96 through 103 and (name N or name \ CA or name C or name O or name CB )) or resid 104 through 109 or (resid 110 thro \ ugh 112 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 2 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB )) or resid 90 through 97 or (resid 98 through 103 and (na \ me N or name CA or name C or name O or name CB )) or resid 104 through 112)) selection = (chain 'L' and ((resid 2 through 83 and (name N or name CA or name C or name O o \ r name CB )) or resid 84 or (resid 85 through 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 97 or (resid 98 through 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 109 or ( \ resid 110 through 112 and (name N or name CA or name C or name O or name CB )))) \ } ncs_group { reference = (chain 'g' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 51 or (resid 52 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 or (resi \ d 57 through 60 and (name N or name CA or name C or name O or name CB )) or (res \ id 61 through 66 and (name N or name CA or name C or name O or name CB )) or (re \ sid 67 through 78 and (name N or name CA or name C or name O or name CB )) or re \ sid 79 or (resid 80 through 86 and (name N or name CA or name C or name O or nam \ e CB )) or resid 87 or (resid 88 through 91 and (name N or name CA or name C or \ name O or name CB )) or (resid 92 through 108 and (name N or name CA or name C o \ r name O or name CB )) or (resid 109 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 125 or (resid 126 through 127 and \ (name N or name CA or name C or name O or name CB )) or (resid 128 through 139 \ and (name N or name CA or name C or name O or name CB )) or (resid 140 through 1 \ 59 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'h' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 50 or (resid 51 through 55 and (nam \ e N or name CA or name C or name O or name CB )) or resid 56 through 77 or (resi \ d 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or (re \ sid 80 through 86 and (name N or name CA or name C or name O or name CB )) or re \ sid 87 or (resid 88 through 91 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 92 through 104 and (name N or name CA or name C or name O or n \ ame CB )) or resid 105 or (resid 106 through 108 and (name N or name CA or name \ C or name O or name CB )) or (resid 109 through 117 and (name N or name CA or na \ me C or name O or name CB )) or resid 118 through 125 or (resid 126 through 127 \ and (name N or name CA or name C or name O or name CB )) or (resid 128 through 1 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 140 or (res \ id 141 through 142 and (name N or name CA or name C or name O or name CB )) or r \ esid 143 or (resid 144 through 159 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'i' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 or (resid 32 through 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 or (resid 39 thr \ ough 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ ough 48 or (resid 49 through 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 through 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or (resid 61 through 66 and (name N or name CA \ or name C or name O or name CB )) or resid 67 or (resid 68 through 78 and (name \ N or name CA or name C or name O or name CB )) or resid 79 or (resid 80 through \ 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ d 88 through 91 and (name N or name CA or name C or name O or name CB )) or (res \ id 92 through 97 and (name N or name CA or name C or name O or name CB )) or res \ id 98 or (resid 99 through 100 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 101 through 108 and (name N or name CA or name C or name O or \ name CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 or (resid 113 through 114 and (name N or \ name CA or name C or name O or name CB )) or resid 115 or (resid 116 through 11 \ 7 and (name N or name CA or name C or name O or name CB )) or (resid 118 through \ 122 and (name N or name CA or name C or name O or name CB )) or resid 123 throu \ gh 129 or (resid 130 through 139 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 140 through 159 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'j' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 30 and (name N or name C \ A or name C or name O or name CB )) or (resid 31 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 throu \ gh 60 and (name N or name CA or name C or name O or name CB )) or (resid 61 thro \ ugh 66 and (name N or name CA or name C or name O or name CB )) or (resid 67 thr \ ough 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or \ (resid 80 through 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 or (resid 88 through 91 and (name N or name CA or name C or name O or \ name CB )) or (resid 92 through 100 and (name N or name CA or name C or name O o \ r name CB )) or (resid 101 through 108 and (name N or name CA or name C or name \ O or name CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or \ name C or name O or name CB )) or (resid 112 through 117 and (name N or name CA \ or name C or name O or name CB )) or resid 118 through 123 or (resid 124 throug \ h 127 and (name N or name CA or name C or name O or name CB )) or (resid 128 thr \ ough 139 and (name N or name CA or name C or name O or name CB )) or (resid 140 \ through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 39 or (resid 40 through 46 and (name N or name CA \ or name C or name O or name CB )) or resid 47 or (resid 48 through 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 58 or (resid \ 59 through 60 and (name N or name CA or name C or name O or name CB )) or (resi \ d 61 through 66 and (name N or name CA or name C or name O or name CB )) or (res \ id 67 through 78 and (name N or name CA or name C or name O or name CB )) or res \ id 79 or (resid 80 through 86 and (name N or name CA or name C or name O or name \ CB )) or resid 87 or (resid 88 through 91 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 92 through 100 and (name N or name CA or name C or \ name O or name CB )) or (resid 101 through 108 and (name N or name CA or name C \ or name O or name CB )) or (resid 109 through 114 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 115 through 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 or (resid 124 through 127 and (name \ N or name CA or name C or name O or name CB )) or (resid 128 through 139 and (na \ me N or name CA or name C or name O or name CB )) or (resid 140 through 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 or (resid 144 \ through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'l' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or (resid 31 through 35 and (name N or name \ CA or name C or name O or name CB )) or (resid 36 through 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 50 or (resid 51 throu \ gh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throu \ gh 58 or (resid 59 through 60 and (name N or name CA or name C or name O or name \ CB )) or (resid 61 through 66 and (name N or name CA or name C or name O or nam \ e CB )) or resid 67 or (resid 68 through 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 or (resid 80 through 86 and (name N or name CA \ or name C or name O or name CB )) or (resid 87 through 91 and (name N or name CA \ or name C or name O or name CB )) or (resid 92 through 111 and (name N or name \ CA or name C or name O or name CB )) or (resid 112 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 125 or (resid 126 t \ hrough 127 and (name N or name CA or name C or name O or name CB )) or (resid 12 \ 8 through 139 and (name N or name CA or name C or name O or name CB )) or (resid \ 140 through 142 and (name N or name CA or name C or name O or name CB )) or (re \ sid 143 through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'm' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 7 or (resid 8 through 9 and (name N or name CA or \ name C or name O or name CB )) or resid 10 or (resid 11 through 12 and (name N \ or name CA or name C or name O or name CB )) or (resid 13 through 15 and (name N \ or name CA or name C or name O or name CB )) or (resid 16 through 30 and (name \ N or name CA or name C or name O or name CB )) or (resid 31 through 35 and (name \ N or name CA or name C or name O or name CB )) or (resid 36 through 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 49 or (resi \ d 50 through 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 58 or (resid 59 through 60 and (name N or name CA or name C or name \ O or name CB )) or (resid 61 through 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 or (resid 68 through 78 and (name N or name CA or \ name C or name O or name CB )) or (resid 79 through 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 or (resid 88 through 91 and (name N \ or name CA or name C or name O or name CB )) or (resid 92 through 108 and (name \ N or name CA or name C or name O or name CB )) or (resid 109 through 117 and (na \ me N or name CA or name C or name O or name CB )) or (resid 118 through 122 and \ (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 124 \ through 127 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 28 through 139 and (name N or name CA or name C or name O or name CB )) or (resi \ d 140 through 142 and (name N or name CA or name C or name O or name CB )) or (r \ esid 143 through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'n' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 35 and (name N or name \ CA or name C or name O or name CB )) or (resid 36 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 56 or (resid 57 throug \ h 60 and (name N or name CA or name C or name O or name CB )) or (resid 61 throu \ gh 66 and (name N or name CA or name C or name O or name CB )) or (resid 67 thro \ ugh 78 and (name N or name CA or name C or name O or name CB )) or (resid 79 thr \ ough 86 and (name N or name CA or name C or name O or name CB )) or (resid 87 th \ rough 117 and (name N or name CA or name C or name O or name CB )) or (resid 118 \ through 122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 23 or (resid 124 through 127 and (name N or name CA or name C or name O or name \ CB )) or (resid 128 through 139 and (name N or name CA or name C or name O or na \ me CB )) or (resid 140 through 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 or (resid 144 through 159 and (name N or name CA or nam \ e C or name O or name CB )))) } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.390 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 113.100 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 54321 Z= 0.345 Angle : 0.652 10.721 74346 Z= 0.362 Chirality : 0.045 0.273 8755 Planarity : 0.005 0.066 10052 Dihedral : 12.453 144.097 16932 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 0.19 % Allowed : 0.60 % Favored : 99.21 % 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: 1.20 (0.10), residues: 8149 helix: 2.26 (0.08), residues: 4848 sheet: -2.68 (0.19), residues: 636 loop : -1.08 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP a 802 HIS 0.023 0.002 HIS F 344 PHE 0.054 0.002 PHE D 95 TYR 0.034 0.002 TYR k 66 ARG 0.011 0.001 ARG i 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 857 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8610 (p0) cc_final: 0.8162 (p0) REVERT: A 547 MET cc_start: 0.8833 (mtp) cc_final: 0.8276 (mtp) REVERT: B 363 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7943 (tp-100) REVERT: C 64 ASP cc_start: 0.7965 (m-30) cc_final: 0.7515 (t0) REVERT: C 359 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8495 (mmp80) REVERT: C 362 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 465 ASN cc_start: 0.8777 (p0) cc_final: 0.8542 (p0) REVERT: C 497 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 516 ASP cc_start: 0.8274 (t70) cc_final: 0.8059 (t0) REVERT: D 361 ASP cc_start: 0.7897 (t70) cc_final: 0.7109 (t0) REVERT: E 59 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 292 GLU cc_start: 0.8133 (pp20) cc_final: 0.7683 (pp20) REVERT: E 451 PHE cc_start: 0.8049 (m-10) cc_final: 0.7742 (m-10) REVERT: E 494 GLU cc_start: 0.8003 (pt0) cc_final: 0.7778 (pt0) REVERT: E 524 ASP cc_start: 0.8113 (m-30) cc_final: 0.7904 (m-30) REVERT: F 23 LYS cc_start: 0.8958 (mptt) cc_final: 0.8712 (mptt) REVERT: I 205 GLU cc_start: 0.8633 (pp20) cc_final: 0.8368 (tm-30) REVERT: L 82 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8815 (tm-30) REVERT: M 12 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7673 (tpp80) REVERT: M 182 GLU cc_start: 0.7809 (tp30) cc_final: 0.7258 (tp30) REVERT: a 536 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8738 (mtmm) REVERT: a 733 TYR cc_start: 0.8380 (m-80) cc_final: 0.7856 (m-80) REVERT: a 735 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8534 (ptm-80) REVERT: a 737 TRP cc_start: 0.8709 (t60) cc_final: 0.8483 (t60) REVERT: a 796 HIS cc_start: 0.8481 (m-70) cc_final: 0.8121 (m-70) REVERT: a 806 MET cc_start: 0.7970 (mpp) cc_final: 0.7685 (mpp) REVERT: d 314 LYS cc_start: 0.5586 (mmtp) cc_final: 0.4758 (tptt) REVERT: f 57 LEU cc_start: 0.7747 (tp) cc_final: 0.7519 (tp) REVERT: g 46 ARG cc_start: 0.8823 (tmm-80) cc_final: 0.8110 (tmm-80) REVERT: g 59 MET cc_start: 0.9088 (mmp) cc_final: 0.8846 (mtp) REVERT: g 84 LEU cc_start: 0.6363 (tp) cc_final: 0.6096 (tp) REVERT: i 99 LEU cc_start: 0.9118 (mt) cc_final: 0.8846 (mt) REVERT: m 66 TYR cc_start: 0.8329 (m-80) cc_final: 0.7896 (m-80) REVERT: o 118 MET cc_start: 0.8801 (tpp) cc_final: 0.8503 (tpp) outliers start: 7 outliers final: 1 residues processed: 861 average time/residue: 0.5280 time to fit residues: 748.9206 Evaluate side-chains 773 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 772 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 216 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 680 optimal weight: 20.0000 chunk 610 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 412 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 631 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 384 optimal weight: 0.2980 chunk 470 optimal weight: 50.0000 chunk 731 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 287 HIS d 334 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 54321 Z= 0.396 Angle : 0.628 11.396 74346 Z= 0.339 Chirality : 0.045 0.191 8755 Planarity : 0.006 0.058 10052 Dihedral : 5.251 137.745 8653 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 1.64 % Allowed : 10.76 % Favored : 87.61 % 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: 0.79 (0.10), residues: 8149 helix: 1.84 (0.07), residues: 4849 sheet: -2.62 (0.18), residues: 664 loop : -1.11 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 802 HIS 0.024 0.002 HIS F 344 PHE 0.061 0.002 PHE h 88 TYR 0.057 0.002 TYR j 66 ARG 0.007 0.001 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 813 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7832 (ttt90) cc_final: 0.7355 (ttt90) REVERT: A 547 MET cc_start: 0.8820 (mtp) cc_final: 0.8269 (mtp) REVERT: B 311 ASP cc_start: 0.8133 (m-30) cc_final: 0.7852 (t0) REVERT: B 363 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7942 (tp-100) REVERT: B 412 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7187 (p0) REVERT: C 64 ASP cc_start: 0.7933 (m-30) cc_final: 0.7549 (t0) REVERT: C 230 ASP cc_start: 0.8681 (p0) cc_final: 0.8476 (p0) REVERT: C 290 MET cc_start: 0.8835 (mmm) cc_final: 0.8516 (mmm) REVERT: C 304 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.2882 (ppp) REVERT: C 359 ARG cc_start: 0.8831 (mmp80) cc_final: 0.8486 (mmp80) REVERT: C 362 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 497 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8176 (tm-30) REVERT: D 387 ILE cc_start: 0.9105 (pt) cc_final: 0.8897 (pt) REVERT: E 59 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7378 (mt-10) REVERT: E 494 GLU cc_start: 0.8002 (pt0) cc_final: 0.7774 (pt0) REVERT: E 501 LEU cc_start: 0.9370 (mt) cc_final: 0.9115 (mt) REVERT: E 569 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7971 (tmmt) REVERT: F 23 LYS cc_start: 0.8963 (mptt) cc_final: 0.8618 (mptt) REVERT: I 152 MET cc_start: 0.6712 (ppp) cc_final: 0.6104 (ppp) REVERT: L 82 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8762 (tm-30) REVERT: M 12 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7639 (tpp80) REVERT: M 34 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7239 (mtp-110) REVERT: M 182 GLU cc_start: 0.7939 (tp30) cc_final: 0.7182 (tp30) REVERT: a 527 ASN cc_start: 0.7811 (t0) cc_final: 0.7389 (t0) REVERT: a 536 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8439 (mtmm) REVERT: a 594 TRP cc_start: 0.7608 (m-10) cc_final: 0.7310 (m100) REVERT: a 733 TYR cc_start: 0.8482 (m-80) cc_final: 0.7917 (m-80) REVERT: a 735 ARG cc_start: 0.8562 (ptm-80) cc_final: 0.8164 (ptm-80) REVERT: a 796 HIS cc_start: 0.8519 (m-70) cc_final: 0.8151 (m-70) REVERT: a 802 TRP cc_start: 0.8640 (m-90) cc_final: 0.8138 (m-90) REVERT: a 806 MET cc_start: 0.7696 (mpp) cc_final: 0.7464 (mpp) REVERT: d 271 ASN cc_start: 0.7536 (m110) cc_final: 0.7310 (m110) REVERT: d 314 LYS cc_start: 0.5349 (mmtp) cc_final: 0.4886 (tptt) REVERT: e 47 MET cc_start: 0.7806 (tpp) cc_final: 0.7548 (tpp) REVERT: f 57 LEU cc_start: 0.7755 (tp) cc_final: 0.7520 (tp) REVERT: g 59 MET cc_start: 0.8937 (mmp) cc_final: 0.8702 (mtp) REVERT: h 78 LEU cc_start: 0.6780 (pp) cc_final: 0.6362 (tp) REVERT: i 46 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7543 (ptp90) REVERT: i 99 LEU cc_start: 0.9134 (mt) cc_final: 0.8893 (mt) REVERT: k 135 PHE cc_start: 0.8816 (t80) cc_final: 0.8592 (t80) REVERT: m 66 TYR cc_start: 0.8514 (m-80) cc_final: 0.8252 (m-80) REVERT: m 82 GLN cc_start: 0.7553 (pt0) cc_final: 0.7213 (pt0) REVERT: n 142 TYR cc_start: 0.7997 (m-10) cc_final: 0.7716 (m-10) REVERT: o 118 MET cc_start: 0.8792 (tpp) cc_final: 0.8524 (tpp) outliers start: 60 outliers final: 44 residues processed: 836 average time/residue: 0.5282 time to fit residues: 730.4352 Evaluate side-chains 816 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 770 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 214 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 72 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 406 optimal weight: 50.0000 chunk 227 optimal weight: 0.0870 chunk 609 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 733 optimal weight: 20.0000 chunk 792 optimal weight: 9.9990 chunk 653 optimal weight: 6.9990 chunk 727 optimal weight: 0.0980 chunk 249 optimal weight: 4.9990 chunk 588 optimal weight: 5.9990 overall best weight: 2.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN M 183 ASN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 54321 Z= 0.355 Angle : 0.596 11.557 74346 Z= 0.317 Chirality : 0.044 0.214 8755 Planarity : 0.005 0.060 10052 Dihedral : 5.112 133.078 8649 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 2.57 % Allowed : 14.25 % Favored : 83.18 % 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: 0.69 (0.10), residues: 8149 helix: 1.73 (0.08), residues: 4798 sheet: -2.58 (0.18), residues: 671 loop : -1.03 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 567 HIS 0.023 0.001 HIS F 344 PHE 0.045 0.002 PHE h 88 TYR 0.049 0.002 TYR o 150 ARG 0.011 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 803 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7411 (ttt90) REVERT: A 123 TYR cc_start: 0.9251 (m-80) cc_final: 0.8953 (m-80) REVERT: B 337 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: B 363 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7762 (tp-100) REVERT: B 416 MET cc_start: 0.8026 (mmm) cc_final: 0.6926 (mmm) REVERT: C 40 MET cc_start: 0.8341 (mmm) cc_final: 0.8083 (mmm) REVERT: C 64 ASP cc_start: 0.7928 (m-30) cc_final: 0.7530 (t0) REVERT: C 230 ASP cc_start: 0.8642 (p0) cc_final: 0.8409 (p0) REVERT: C 279 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9172 (mm) REVERT: C 290 MET cc_start: 0.8733 (mmm) cc_final: 0.8504 (mmm) REVERT: C 304 MET cc_start: 0.3595 (OUTLIER) cc_final: 0.3000 (ppp) REVERT: C 362 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 465 ASN cc_start: 0.8734 (p0) cc_final: 0.8529 (p0) REVERT: C 496 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7109 (tm-30) REVERT: C 497 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8066 (tm-30) REVERT: C 538 CYS cc_start: 0.9009 (t) cc_final: 0.8436 (t) REVERT: D 311 ASP cc_start: 0.8126 (t0) cc_final: 0.7429 (t70) REVERT: E 59 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7199 (mt-10) REVERT: E 105 TYR cc_start: 0.9191 (m-80) cc_final: 0.8809 (m-10) REVERT: E 494 GLU cc_start: 0.7994 (pt0) cc_final: 0.7762 (pt0) REVERT: E 501 LEU cc_start: 0.9365 (mt) cc_final: 0.9113 (mt) REVERT: F 23 LYS cc_start: 0.8922 (mptt) cc_final: 0.8600 (mptt) REVERT: F 353 ILE cc_start: 0.9374 (mp) cc_final: 0.9066 (mp) REVERT: I 152 MET cc_start: 0.6486 (ppp) cc_final: 0.5993 (ppp) REVERT: L 82 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8714 (tm-30) REVERT: M 12 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7628 (tpp80) REVERT: M 182 GLU cc_start: 0.7888 (tp30) cc_final: 0.7173 (tp30) REVERT: a 478 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8488 (tp) REVERT: a 527 ASN cc_start: 0.7855 (t0) cc_final: 0.7369 (t0) REVERT: a 572 PHE cc_start: 0.7960 (t80) cc_final: 0.7635 (t80) REVERT: a 735 ARG cc_start: 0.8525 (ptm-80) cc_final: 0.8286 (ptm160) REVERT: a 737 TRP cc_start: 0.8808 (t60) cc_final: 0.8527 (t60) REVERT: a 802 TRP cc_start: 0.8630 (m-90) cc_final: 0.8129 (m-90) REVERT: a 806 MET cc_start: 0.7754 (mpp) cc_final: 0.7550 (mpp) REVERT: c 61 ASN cc_start: 0.9323 (m-40) cc_final: 0.8821 (t0) REVERT: c 124 LYS cc_start: 0.8671 (tptm) cc_final: 0.8430 (tptm) REVERT: d 191 ASP cc_start: 0.8304 (t0) cc_final: 0.8007 (t0) REVERT: d 271 ASN cc_start: 0.7585 (m110) cc_final: 0.7337 (m110) REVERT: d 314 LYS cc_start: 0.5368 (mmtp) cc_final: 0.4938 (tptt) REVERT: e 47 MET cc_start: 0.7928 (tpp) cc_final: 0.7676 (tpp) REVERT: f 57 LEU cc_start: 0.7737 (tp) cc_final: 0.7486 (tp) REVERT: g 59 MET cc_start: 0.8953 (mmp) cc_final: 0.8714 (mtp) REVERT: h 78 LEU cc_start: 0.6876 (pp) cc_final: 0.6279 (tp) REVERT: i 68 LEU cc_start: 0.8293 (mt) cc_final: 0.8080 (mp) REVERT: i 99 LEU cc_start: 0.9131 (mt) cc_final: 0.8893 (mt) REVERT: k 135 PHE cc_start: 0.8803 (t80) cc_final: 0.8563 (t80) REVERT: l 46 ARG cc_start: 0.8593 (tmm-80) cc_final: 0.8231 (tmm-80) REVERT: m 66 TYR cc_start: 0.8477 (m-80) cc_final: 0.8258 (m-80) REVERT: m 82 GLN cc_start: 0.7539 (pt0) cc_final: 0.7335 (pt0) REVERT: n 59 MET cc_start: 0.8613 (tmm) cc_final: 0.8204 (ttm) REVERT: n 142 TYR cc_start: 0.8012 (m-10) cc_final: 0.7706 (m-10) REVERT: o 118 MET cc_start: 0.8792 (tpp) cc_final: 0.8527 (tpp) REVERT: o 152 MET cc_start: 0.7650 (mmm) cc_final: 0.7264 (tpp) outliers start: 94 outliers final: 69 residues processed: 845 average time/residue: 0.5337 time to fit residues: 745.0226 Evaluate side-chains 845 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 772 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 190 PHE Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 76 TYR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 724 optimal weight: 10.0000 chunk 551 optimal weight: 6.9990 chunk 380 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 chunk 492 optimal weight: 6.9990 chunk 735 optimal weight: 0.8980 chunk 779 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 697 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 53 HIS ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 54321 Z= 0.411 Angle : 0.619 13.550 74346 Z= 0.328 Chirality : 0.045 0.281 8755 Planarity : 0.005 0.057 10052 Dihedral : 5.108 132.013 8649 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 16.63 % Favored : 79.99 % 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: 0.65 (0.10), residues: 8149 helix: 1.71 (0.08), residues: 4780 sheet: -2.62 (0.18), residues: 673 loop : -1.04 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 594 HIS 0.018 0.002 HIS F 344 PHE 0.045 0.002 PHE g 88 TYR 0.049 0.002 TYR j 66 ARG 0.007 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 792 time to evaluate : 4.562 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 62 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7594 (ttt90) REVERT: B 337 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7876 (mpp) REVERT: B 363 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7865 (tp-100) REVERT: B 412 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7414 (p0) REVERT: B 422 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 40 MET cc_start: 0.8394 (mmm) cc_final: 0.8193 (mmm) REVERT: C 64 ASP cc_start: 0.7948 (m-30) cc_final: 0.7553 (t0) REVERT: C 230 ASP cc_start: 0.8633 (p0) cc_final: 0.8414 (p0) REVERT: C 279 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9171 (mm) REVERT: C 496 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7162 (tm-30) REVERT: C 497 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 538 CYS cc_start: 0.9028 (t) cc_final: 0.8481 (t) REVERT: D 311 ASP cc_start: 0.8240 (t0) cc_final: 0.7581 (t70) REVERT: E 285 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7206 (mm-30) REVERT: E 494 GLU cc_start: 0.7988 (pt0) cc_final: 0.7759 (pt0) REVERT: E 501 LEU cc_start: 0.9401 (mt) cc_final: 0.9142 (mt) REVERT: E 569 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7909 (tmmt) REVERT: F 23 LYS cc_start: 0.8931 (mptt) cc_final: 0.8585 (mptt) REVERT: F 353 ILE cc_start: 0.9377 (mp) cc_final: 0.9044 (mp) REVERT: L 82 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8695 (tm-30) REVERT: M 12 ARG cc_start: 0.7989 (tpt-90) cc_final: 0.7624 (tpp80) REVERT: M 18 MET cc_start: 0.8836 (tpp) cc_final: 0.8615 (tpp) REVERT: M 57 MET cc_start: 0.6456 (mmt) cc_final: 0.4720 (tmm) REVERT: M 182 GLU cc_start: 0.7937 (tp30) cc_final: 0.7279 (tp30) REVERT: a 527 ASN cc_start: 0.7875 (t0) cc_final: 0.7375 (t0) REVERT: a 778 PHE cc_start: 0.7777 (t80) cc_final: 0.7522 (t80) REVERT: a 802 TRP cc_start: 0.8733 (m-10) cc_final: 0.8252 (m-90) REVERT: c 61 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.8864 (t0) REVERT: c 124 LYS cc_start: 0.8691 (tptm) cc_final: 0.8305 (tptm) REVERT: d 80 PHE cc_start: 0.8015 (t80) cc_final: 0.7690 (t80) REVERT: d 191 ASP cc_start: 0.8365 (t0) cc_final: 0.7880 (t0) REVERT: d 271 ASN cc_start: 0.7581 (m110) cc_final: 0.7330 (m110) REVERT: d 314 LYS cc_start: 0.5319 (mmtp) cc_final: 0.4898 (tptt) REVERT: e 47 MET cc_start: 0.8002 (tpp) cc_final: 0.7712 (tpp) REVERT: f 57 LEU cc_start: 0.7736 (tp) cc_final: 0.7480 (tp) REVERT: g 59 MET cc_start: 0.8978 (mmp) cc_final: 0.8729 (mtp) REVERT: h 78 LEU cc_start: 0.6956 (pp) cc_final: 0.6354 (tp) REVERT: i 68 LEU cc_start: 0.8290 (mt) cc_final: 0.8041 (mm) REVERT: i 99 LEU cc_start: 0.9153 (mt) cc_final: 0.8914 (mt) REVERT: k 135 PHE cc_start: 0.8801 (t80) cc_final: 0.8554 (t80) REVERT: l 46 ARG cc_start: 0.8573 (tmm-80) cc_final: 0.8070 (tmm-80) REVERT: m 66 TYR cc_start: 0.8472 (m-80) cc_final: 0.7965 (m-80) REVERT: n 59 MET cc_start: 0.8677 (tmm) cc_final: 0.8248 (ttm) REVERT: n 142 TYR cc_start: 0.8000 (m-10) cc_final: 0.7773 (m-10) REVERT: o 118 MET cc_start: 0.8776 (tpp) cc_final: 0.8515 (tpp) outliers start: 124 outliers final: 91 residues processed: 857 average time/residue: 0.5760 time to fit residues: 823.3774 Evaluate side-chains 866 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 771 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 190 PHE Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 144 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 76 TYR Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 72 TYR Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 648 optimal weight: 0.8980 chunk 442 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 580 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 664 optimal weight: 10.0000 chunk 538 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 397 optimal weight: 5.9990 chunk 699 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 135 ASN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 559 HIS d 182 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 54321 Z= 0.389 Angle : 0.609 12.728 74346 Z= 0.322 Chirality : 0.044 0.279 8755 Planarity : 0.005 0.058 10052 Dihedral : 5.053 129.102 8649 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 3.90 % Allowed : 18.40 % Favored : 77.70 % 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: 0.66 (0.10), residues: 8149 helix: 1.72 (0.08), residues: 4774 sheet: -2.63 (0.18), residues: 682 loop : -1.02 (0.12), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 567 HIS 0.018 0.001 HIS F 344 PHE 0.040 0.002 PHE h 88 TYR 0.057 0.002 TYR j 66 ARG 0.006 0.001 ARG d 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 794 time to evaluate : 4.519 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 62 ARG cc_start: 0.7860 (ttt90) cc_final: 0.7631 (ttt90) REVERT: A 362 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 337 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7884 (mpp) REVERT: B 363 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7892 (tp-100) REVERT: B 412 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7310 (p0) REVERT: B 422 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7280 (tm-30) REVERT: C 64 ASP cc_start: 0.7909 (m-30) cc_final: 0.7577 (t0) REVERT: C 230 ASP cc_start: 0.8620 (p0) cc_final: 0.8394 (p0) REVERT: C 279 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9158 (mm) REVERT: C 304 MET cc_start: 0.3794 (OUTLIER) cc_final: 0.3109 (ppp) REVERT: C 496 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7124 (tm-30) REVERT: C 497 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 538 CYS cc_start: 0.9045 (t) cc_final: 0.8490 (t) REVERT: D 260 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8650 (mm) REVERT: D 311 ASP cc_start: 0.8234 (t0) cc_final: 0.7872 (t70) REVERT: E 105 TYR cc_start: 0.9206 (m-80) cc_final: 0.8866 (m-10) REVERT: E 494 GLU cc_start: 0.8042 (pt0) cc_final: 0.7819 (pt0) REVERT: E 501 LEU cc_start: 0.9429 (mt) cc_final: 0.9158 (mt) REVERT: E 569 LYS cc_start: 0.8261 (tmmt) cc_final: 0.8019 (tmmt) REVERT: F 23 LYS cc_start: 0.8935 (mptt) cc_final: 0.8592 (mptt) REVERT: F 349 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8753 (mm) REVERT: F 353 ILE cc_start: 0.9338 (mp) cc_final: 0.9003 (mp) REVERT: I 171 GLU cc_start: 0.8792 (pm20) cc_final: 0.8155 (pm20) REVERT: L 82 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8697 (tm-30) REVERT: M 12 ARG cc_start: 0.7985 (tpt-90) cc_final: 0.7606 (tpp80) REVERT: M 18 MET cc_start: 0.8856 (tpp) cc_final: 0.8438 (tpp) REVERT: M 57 MET cc_start: 0.6390 (mmt) cc_final: 0.4786 (tmm) REVERT: M 182 GLU cc_start: 0.7923 (tp30) cc_final: 0.7287 (tp30) REVERT: a 478 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8286 (tp) REVERT: a 527 ASN cc_start: 0.7947 (t0) cc_final: 0.7461 (t0) REVERT: a 536 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8481 (mtmm) REVERT: a 778 PHE cc_start: 0.7818 (t80) cc_final: 0.7586 (t80) REVERT: c 61 ASN cc_start: 0.9345 (m-40) cc_final: 0.8859 (t0) REVERT: c 124 LYS cc_start: 0.8813 (tptm) cc_final: 0.8545 (tptm) REVERT: d 69 GLN cc_start: 0.5971 (tp40) cc_final: 0.5679 (tp40) REVERT: d 80 PHE cc_start: 0.8050 (t80) cc_final: 0.7704 (t80) REVERT: d 191 ASP cc_start: 0.8422 (t0) cc_final: 0.7885 (t0) REVERT: d 260 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6057 (tm-30) REVERT: d 271 ASN cc_start: 0.7592 (m110) cc_final: 0.7335 (m110) REVERT: d 314 LYS cc_start: 0.5411 (mmtp) cc_final: 0.4924 (tptt) REVERT: d 336 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7491 (tm-30) REVERT: e 47 MET cc_start: 0.8010 (tpp) cc_final: 0.7706 (tpp) REVERT: f 57 LEU cc_start: 0.7635 (tp) cc_final: 0.7360 (tp) REVERT: g 59 MET cc_start: 0.9005 (mmp) cc_final: 0.8750 (mtp) REVERT: h 78 LEU cc_start: 0.6886 (pp) cc_final: 0.6257 (tp) REVERT: i 46 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7871 (ptp90) REVERT: i 68 LEU cc_start: 0.8259 (mt) cc_final: 0.8037 (mm) REVERT: i 99 LEU cc_start: 0.9150 (mt) cc_final: 0.8923 (mt) REVERT: j 88 PHE cc_start: 0.7993 (t80) cc_final: 0.7758 (t80) REVERT: l 46 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: m 52 LYS cc_start: 0.8659 (pttt) cc_final: 0.8448 (pttt) REVERT: m 66 TYR cc_start: 0.8451 (m-80) cc_final: 0.8006 (m-80) REVERT: n 59 MET cc_start: 0.8673 (tmm) cc_final: 0.8242 (ttm) REVERT: o 90 TYR cc_start: 0.4820 (t80) cc_final: 0.4371 (t80) REVERT: o 118 MET cc_start: 0.8793 (tpp) cc_final: 0.8526 (tpp) outliers start: 143 outliers final: 106 residues processed: 875 average time/residue: 0.5262 time to fit residues: 766.0854 Evaluate side-chains 890 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 777 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 214 THR Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 194 ASN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 144 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 76 TYR Chi-restraints excluded: chain l residue 54 ILE Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain l residue 73 LEU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 262 optimal weight: 3.9990 chunk 701 optimal weight: 0.0370 chunk 154 optimal weight: 2.9990 chunk 457 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 779 optimal weight: 0.4980 chunk 647 optimal weight: 40.0000 chunk 361 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 409 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 54321 Z= 0.167 Angle : 0.534 13.558 74346 Z= 0.280 Chirality : 0.042 0.472 8755 Planarity : 0.004 0.061 10052 Dihedral : 4.687 122.066 8649 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.89 % Allowed : 20.17 % Favored : 76.93 % 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: 0.90 (0.10), residues: 8149 helix: 1.86 (0.08), residues: 4794 sheet: -2.47 (0.19), residues: 652 loop : -0.89 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 567 HIS 0.014 0.001 HIS F 344 PHE 0.032 0.001 PHE o 17 TYR 0.062 0.001 TYR j 66 ARG 0.007 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 830 time to evaluate : 4.516 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 62 ARG cc_start: 0.7788 (ttt90) cc_final: 0.7558 (ttt90) REVERT: A 362 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 494 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8952 (pp20) REVERT: B 337 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7588 (mpp) REVERT: B 363 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7653 (tp-100) REVERT: C 64 ASP cc_start: 0.7791 (m-30) cc_final: 0.7550 (t0) REVERT: C 230 ASP cc_start: 0.8459 (p0) cc_final: 0.8127 (p0) REVERT: C 279 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9082 (mm) REVERT: C 290 MET cc_start: 0.8377 (mmm) cc_final: 0.8083 (mmm) REVERT: C 304 MET cc_start: 0.3812 (ppp) cc_final: 0.3201 (ppp) REVERT: C 312 MET cc_start: 0.9036 (tpt) cc_final: 0.8764 (tpp) REVERT: C 362 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7112 (tm-30) REVERT: C 495 LEU cc_start: 0.8744 (tp) cc_final: 0.8443 (tp) REVERT: C 496 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6978 (tm-30) REVERT: C 497 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 538 CYS cc_start: 0.9073 (t) cc_final: 0.8781 (t) REVERT: C 547 MET cc_start: 0.9075 (ttm) cc_final: 0.8846 (mtm) REVERT: D 68 LEU cc_start: 0.9132 (tp) cc_final: 0.8835 (tp) REVERT: D 244 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8986 (mt) REVERT: D 260 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8583 (mm) REVERT: D 311 ASP cc_start: 0.8123 (t0) cc_final: 0.7542 (t70) REVERT: E 105 TYR cc_start: 0.9014 (m-80) cc_final: 0.8725 (m-10) REVERT: E 494 GLU cc_start: 0.8030 (pt0) cc_final: 0.7798 (pt0) REVERT: E 501 LEU cc_start: 0.9382 (mt) cc_final: 0.9111 (mt) REVERT: F 23 LYS cc_start: 0.8940 (mptt) cc_final: 0.8629 (mptt) REVERT: F 353 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8947 (mp) REVERT: I 171 GLU cc_start: 0.8701 (pm20) cc_final: 0.8111 (pm20) REVERT: L 82 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8782 (tm-30) REVERT: M 12 ARG cc_start: 0.7961 (tpt-90) cc_final: 0.7645 (tpp80) REVERT: M 34 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7923 (ttp-110) REVERT: M 49 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7200 (mtm110) REVERT: M 56 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7824 (mmtp) REVERT: M 57 MET cc_start: 0.6234 (mmt) cc_final: 0.4635 (tmm) REVERT: M 182 GLU cc_start: 0.7821 (tp30) cc_final: 0.7215 (tp30) REVERT: a 200 GLU cc_start: 0.9264 (tp30) cc_final: 0.8694 (tp30) REVERT: a 422 MET cc_start: 0.8090 (ptp) cc_final: 0.7655 (mtm) REVERT: a 478 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8134 (tt) REVERT: a 527 ASN cc_start: 0.7881 (t0) cc_final: 0.7511 (t0) REVERT: a 536 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8488 (mtmm) REVERT: a 554 PHE cc_start: 0.7260 (t80) cc_final: 0.6870 (t80) REVERT: a 778 PHE cc_start: 0.7660 (t80) cc_final: 0.7444 (t80) REVERT: c 61 ASN cc_start: 0.9336 (m-40) cc_final: 0.8837 (t0) REVERT: c 124 LYS cc_start: 0.8834 (tptm) cc_final: 0.8539 (tptm) REVERT: d 69 GLN cc_start: 0.6108 (tp40) cc_final: 0.5720 (tp40) REVERT: d 80 PHE cc_start: 0.7989 (t80) cc_final: 0.7671 (t80) REVERT: d 260 GLN cc_start: 0.6801 (tm-30) cc_final: 0.6078 (tm-30) REVERT: d 314 LYS cc_start: 0.5380 (mmtp) cc_final: 0.4923 (tptt) REVERT: d 332 GLN cc_start: 0.5684 (mm110) cc_final: 0.5384 (mm110) REVERT: d 336 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7461 (tm-30) REVERT: e 47 MET cc_start: 0.7937 (tpp) cc_final: 0.7690 (tpp) REVERT: f 57 LEU cc_start: 0.7555 (tp) cc_final: 0.7308 (tp) REVERT: g 59 MET cc_start: 0.8932 (mmp) cc_final: 0.8707 (mtp) REVERT: h 78 LEU cc_start: 0.6655 (pp) cc_final: 0.5992 (tp) REVERT: i 46 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7712 (ptp90) REVERT: i 68 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8072 (mm) REVERT: i 99 LEU cc_start: 0.9105 (mt) cc_final: 0.8870 (mt) REVERT: j 88 PHE cc_start: 0.7879 (t80) cc_final: 0.7584 (t80) REVERT: l 46 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8068 (tmm-80) REVERT: m 66 TYR cc_start: 0.8434 (m-80) cc_final: 0.7982 (m-80) REVERT: n 59 MET cc_start: 0.8649 (tmm) cc_final: 0.8405 (ttm) REVERT: o 90 TYR cc_start: 0.4714 (t80) cc_final: 0.4391 (t80) REVERT: o 118 MET cc_start: 0.8722 (tpp) cc_final: 0.8453 (tpp) REVERT: o 152 MET cc_start: 0.7640 (mmm) cc_final: 0.7338 (tpp) outliers start: 106 outliers final: 65 residues processed: 883 average time/residue: 0.5273 time to fit residues: 768.4754 Evaluate side-chains 847 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 774 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 144 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 54 ILE Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 20 PHE Chi-restraints excluded: chain o residue 141 LEU Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 751 optimal weight: 10.0000 chunk 87 optimal weight: 0.0970 chunk 444 optimal weight: 9.9990 chunk 569 optimal weight: 10.0000 chunk 441 optimal weight: 4.9990 chunk 656 optimal weight: 9.9990 chunk 435 optimal weight: 5.9990 chunk 776 optimal weight: 0.0070 chunk 486 optimal weight: 9.9990 chunk 473 optimal weight: 50.0000 chunk 358 optimal weight: 9.9990 overall best weight: 4.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN M 55 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 54321 Z= 0.493 Angle : 0.669 12.776 74346 Z= 0.352 Chirality : 0.046 0.522 8755 Planarity : 0.005 0.061 10052 Dihedral : 4.954 130.686 8649 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 3.82 % Allowed : 20.58 % Favored : 75.59 % 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 (0.10), residues: 8149 helix: 1.77 (0.08), residues: 4763 sheet: -2.68 (0.18), residues: 674 loop : -0.96 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 48 HIS 0.016 0.002 HIS F 344 PHE 0.035 0.002 PHE A 244 TYR 0.061 0.002 TYR j 66 ARG 0.011 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 781 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7761 (ttt90) cc_final: 0.7544 (ttt90) REVERT: A 362 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 311 ASP cc_start: 0.7967 (t0) cc_final: 0.7458 (t70) REVERT: B 337 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8030 (mpp) REVERT: B 412 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 422 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7201 (tm-30) REVERT: C 230 ASP cc_start: 0.8631 (p0) cc_final: 0.8410 (p0) REVERT: C 279 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9149 (mm) REVERT: C 496 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 497 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 538 CYS cc_start: 0.9006 (t) cc_final: 0.8541 (t) REVERT: D 244 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9108 (mt) REVERT: D 260 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8696 (mm) REVERT: D 311 ASP cc_start: 0.8323 (t0) cc_final: 0.7729 (t70) REVERT: E 105 TYR cc_start: 0.9185 (m-80) cc_final: 0.8815 (m-10) REVERT: E 501 LEU cc_start: 0.9431 (mt) cc_final: 0.9151 (mt) REVERT: E 569 LYS cc_start: 0.8229 (tmmt) cc_final: 0.7982 (tmmt) REVERT: F 23 LYS cc_start: 0.8914 (mptt) cc_final: 0.8592 (mptt) REVERT: I 171 GLU cc_start: 0.8823 (pm20) cc_final: 0.8170 (pm20) REVERT: M 12 ARG cc_start: 0.8072 (tpt-90) cc_final: 0.7730 (tpp80) REVERT: M 34 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.8057 (ttp-110) REVERT: M 49 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7351 (mtm110) REVERT: M 55 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6653 (pp30) REVERT: M 182 GLU cc_start: 0.7930 (tp30) cc_final: 0.7334 (tp30) REVERT: a 478 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8337 (tp) REVERT: a 527 ASN cc_start: 0.8045 (t0) cc_final: 0.7693 (t0) REVERT: a 536 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8564 (mtmm) REVERT: c 61 ASN cc_start: 0.9319 (m-40) cc_final: 0.8851 (t0) REVERT: c 108 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: c 124 LYS cc_start: 0.8845 (tptm) cc_final: 0.8566 (tptm) REVERT: d 69 GLN cc_start: 0.6136 (tp40) cc_final: 0.5734 (tp40) REVERT: d 80 PHE cc_start: 0.7920 (t80) cc_final: 0.7700 (t80) REVERT: d 191 ASP cc_start: 0.8366 (t0) cc_final: 0.7923 (t0) REVERT: d 260 GLN cc_start: 0.6820 (tm-30) cc_final: 0.6105 (tm-30) REVERT: d 271 ASN cc_start: 0.7678 (m110) cc_final: 0.7446 (p0) REVERT: d 314 LYS cc_start: 0.5377 (mmtp) cc_final: 0.4854 (tptt) REVERT: e 47 MET cc_start: 0.7976 (tpp) cc_final: 0.7647 (tpp) REVERT: f 57 LEU cc_start: 0.7594 (tp) cc_final: 0.7347 (tp) REVERT: g 59 MET cc_start: 0.9025 (mmp) cc_final: 0.8737 (mtp) REVERT: h 78 LEU cc_start: 0.6885 (pp) cc_final: 0.6541 (pp) REVERT: i 68 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8020 (mm) REVERT: i 99 LEU cc_start: 0.9186 (mt) cc_final: 0.8955 (mt) REVERT: j 11 PHE cc_start: 0.8844 (t80) cc_final: 0.8539 (t80) REVERT: j 88 PHE cc_start: 0.8223 (t80) cc_final: 0.7964 (t80) REVERT: l 46 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.8235 (tmm-80) REVERT: m 66 TYR cc_start: 0.8442 (m-80) cc_final: 0.8000 (m-80) REVERT: n 59 MET cc_start: 0.8660 (tmm) cc_final: 0.8391 (ttm) REVERT: o 52 LYS cc_start: 0.7169 (pptt) cc_final: 0.6550 (pptt) REVERT: o 72 TYR cc_start: 0.8554 (m-80) cc_final: 0.8160 (t80) REVERT: o 90 TYR cc_start: 0.4895 (t80) cc_final: 0.4467 (t80) REVERT: o 118 MET cc_start: 0.8778 (tpp) cc_final: 0.8550 (tpp) REVERT: o 152 MET cc_start: 0.7908 (mmm) cc_final: 0.6993 (tpp) outliers start: 140 outliers final: 104 residues processed: 864 average time/residue: 0.5430 time to fit residues: 782.9754 Evaluate side-chains 881 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 766 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 55 GLN Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 536 LYS Chi-restraints excluded: chain a residue 587 SER Chi-restraints excluded: chain a residue 737 TRP Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 54 ILE Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 480 optimal weight: 20.0000 chunk 310 optimal weight: 0.6980 chunk 463 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 493 optimal weight: 40.0000 chunk 529 optimal weight: 20.0000 chunk 384 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 610 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN d 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54321 Z= 0.190 Angle : 0.554 13.128 74346 Z= 0.290 Chirality : 0.042 0.348 8755 Planarity : 0.004 0.064 10052 Dihedral : 4.652 122.071 8649 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 3.08 % Allowed : 21.57 % Favored : 75.35 % 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: 0.89 (0.10), residues: 8149 helix: 1.87 (0.08), residues: 4777 sheet: -2.49 (0.18), residues: 666 loop : -0.88 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 567 HIS 0.013 0.001 HIS F 344 PHE 0.034 0.001 PHE e 45 TYR 0.059 0.001 TYR j 66 ARG 0.013 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 800 time to evaluate : 4.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7571 (ttt90) REVERT: A 362 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 546 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7006 (mtm) REVERT: B 337 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7701 (mpp) REVERT: B 412 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7173 (p0) REVERT: C 230 ASP cc_start: 0.8462 (p0) cc_final: 0.8137 (p0) REVERT: C 279 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9013 (mm) REVERT: C 290 MET cc_start: 0.8380 (mmm) cc_final: 0.8099 (mmm) REVERT: C 304 MET cc_start: 0.3876 (ppp) cc_final: 0.3230 (ppp) REVERT: C 362 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6982 (tm-30) REVERT: C 366 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: C 495 LEU cc_start: 0.8788 (tp) cc_final: 0.8555 (tp) REVERT: C 496 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6974 (tm-30) REVERT: C 497 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 538 CYS cc_start: 0.9054 (t) cc_final: 0.8745 (t) REVERT: D 260 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8512 (mm) REVERT: D 311 ASP cc_start: 0.8177 (t0) cc_final: 0.7678 (t70) REVERT: E 105 TYR cc_start: 0.9032 (m-80) cc_final: 0.8700 (m-10) REVERT: E 494 GLU cc_start: 0.7966 (pt0) cc_final: 0.7761 (pt0) REVERT: E 501 LEU cc_start: 0.9396 (mt) cc_final: 0.9141 (mt) REVERT: E 569 LYS cc_start: 0.8165 (tmmt) cc_final: 0.7887 (tmmt) REVERT: F 23 LYS cc_start: 0.8919 (mptt) cc_final: 0.8609 (mptt) REVERT: F 337 MET cc_start: 0.8517 (mtm) cc_final: 0.8285 (mpp) REVERT: F 382 LEU cc_start: 0.8955 (mt) cc_final: 0.8681 (mp) REVERT: I 171 GLU cc_start: 0.8744 (pm20) cc_final: 0.8121 (pm20) REVERT: L 82 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8835 (tm-30) REVERT: M 12 ARG cc_start: 0.8050 (tpt-90) cc_final: 0.7765 (tpp80) REVERT: M 49 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7108 (mtm110) REVERT: M 182 GLU cc_start: 0.7813 (tp30) cc_final: 0.7207 (tp30) REVERT: a 200 GLU cc_start: 0.9260 (tp30) cc_final: 0.8734 (tp30) REVERT: a 478 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8187 (tt) REVERT: a 527 ASN cc_start: 0.7908 (t0) cc_final: 0.7591 (t0) REVERT: a 536 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8452 (mtmm) REVERT: a 735 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.7821 (ptm160) REVERT: a 799 ARG cc_start: 0.9097 (tmt170) cc_final: 0.8850 (tmt-80) REVERT: c 61 ASN cc_start: 0.9323 (m-40) cc_final: 0.8839 (t0) REVERT: c 108 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: c 124 LYS cc_start: 0.8855 (tptm) cc_final: 0.8562 (tptm) REVERT: d 69 GLN cc_start: 0.6061 (tp40) cc_final: 0.5614 (tp40) REVERT: d 80 PHE cc_start: 0.7893 (t80) cc_final: 0.7635 (t80) REVERT: d 191 ASP cc_start: 0.8366 (t0) cc_final: 0.7880 (t0) REVERT: d 260 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6147 (tm-30) REVERT: d 287 HIS cc_start: 0.8075 (m-70) cc_final: 0.7856 (m-70) REVERT: d 314 LYS cc_start: 0.5273 (mmtp) cc_final: 0.4746 (tptt) REVERT: d 332 GLN cc_start: 0.6013 (mm110) cc_final: 0.5544 (mm110) REVERT: d 334 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6434 (mp10) REVERT: e 47 MET cc_start: 0.7994 (tpp) cc_final: 0.7647 (tpp) REVERT: f 57 LEU cc_start: 0.7512 (tp) cc_final: 0.7305 (tp) REVERT: g 46 ARG cc_start: 0.8331 (tmm-80) cc_final: 0.7434 (tmm-80) REVERT: g 59 MET cc_start: 0.8986 (mmp) cc_final: 0.8728 (mtp) REVERT: h 78 LEU cc_start: 0.6506 (pp) cc_final: 0.5774 (tp) REVERT: i 46 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7748 (ptt180) REVERT: i 68 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8062 (mm) REVERT: j 88 PHE cc_start: 0.7966 (t80) cc_final: 0.7755 (t80) REVERT: l 46 ARG cc_start: 0.8451 (tmm-80) cc_final: 0.8203 (tmm-80) REVERT: m 66 TYR cc_start: 0.8400 (m-80) cc_final: 0.7947 (m-80) REVERT: n 59 MET cc_start: 0.8667 (tmm) cc_final: 0.8375 (ttm) REVERT: o 72 TYR cc_start: 0.8526 (m-80) cc_final: 0.8130 (t80) REVERT: o 90 TYR cc_start: 0.4731 (t80) cc_final: 0.4294 (t80) REVERT: o 118 MET cc_start: 0.8749 (tpp) cc_final: 0.8484 (tpp) REVERT: o 152 MET cc_start: 0.7826 (mmm) cc_final: 0.6933 (tpp) outliers start: 113 outliers final: 75 residues processed: 861 average time/residue: 0.5524 time to fit residues: 776.9389 Evaluate side-chains 877 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 790 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 536 LYS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain d residue 334 GLN Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 76 TYR Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 54 ILE Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 20 PHE Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 706 optimal weight: 0.0040 chunk 744 optimal weight: 10.0000 chunk 679 optimal weight: 10.0000 chunk 723 optimal weight: 20.0000 chunk 435 optimal weight: 7.9990 chunk 315 optimal weight: 0.7980 chunk 568 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 654 optimal weight: 7.9990 chunk 684 optimal weight: 7.9990 chunk 721 optimal weight: 9.9990 overall best weight: 3.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN ** i 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 GLN ** l 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 54321 Z= 0.466 Angle : 0.651 12.270 74346 Z= 0.343 Chirality : 0.046 0.333 8755 Planarity : 0.005 0.065 10052 Dihedral : 4.845 132.127 8649 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 3.28 % Allowed : 21.70 % Favored : 75.02 % 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: 8149 helix: 1.78 (0.08), residues: 4767 sheet: -2.65 (0.18), residues: 677 loop : -0.95 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 567 HIS 0.016 0.001 HIS F 344 PHE 0.032 0.002 PHE o 17 TYR 0.060 0.002 TYR j 66 ARG 0.011 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 785 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7751 (ttt90) cc_final: 0.7536 (ttt90) REVERT: A 362 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 311 ASP cc_start: 0.8100 (t0) cc_final: 0.7634 (t70) REVERT: B 337 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7994 (mpp) REVERT: B 412 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7414 (p0) REVERT: C 230 ASP cc_start: 0.8586 (p0) cc_final: 0.8376 (p0) REVERT: C 279 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9090 (mm) REVERT: C 495 LEU cc_start: 0.8928 (tp) cc_final: 0.8701 (tp) REVERT: C 496 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 497 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 538 CYS cc_start: 0.9035 (t) cc_final: 0.8509 (t) REVERT: D 260 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8641 (mm) REVERT: D 311 ASP cc_start: 0.8284 (t0) cc_final: 0.7770 (t70) REVERT: D 339 ASN cc_start: 0.8233 (t0) cc_final: 0.8029 (t0) REVERT: E 105 TYR cc_start: 0.9161 (m-80) cc_final: 0.8788 (m-10) REVERT: E 494 GLU cc_start: 0.8015 (pt0) cc_final: 0.7794 (pt0) REVERT: E 501 LEU cc_start: 0.9427 (mt) cc_final: 0.9163 (mt) REVERT: E 569 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7994 (tmmt) REVERT: F 23 LYS cc_start: 0.8909 (mptt) cc_final: 0.8600 (mptt) REVERT: I 171 GLU cc_start: 0.8797 (pm20) cc_final: 0.8136 (pm20) REVERT: L 82 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8801 (tm-30) REVERT: M 12 ARG cc_start: 0.8126 (tpt-90) cc_final: 0.7803 (tpp80) REVERT: M 49 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7184 (mtm110) REVERT: M 57 MET cc_start: 0.6326 (mmt) cc_final: 0.4759 (tmm) REVERT: M 182 GLU cc_start: 0.7913 (tp30) cc_final: 0.7321 (tp30) REVERT: a 200 GLU cc_start: 0.9243 (tp30) cc_final: 0.8671 (tp30) REVERT: a 478 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8368 (tp) REVERT: a 527 ASN cc_start: 0.7998 (t0) cc_final: 0.7727 (t0) REVERT: a 536 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8485 (mtmm) REVERT: a 735 ARG cc_start: 0.8650 (ptm-80) cc_final: 0.8018 (ptt90) REVERT: a 796 HIS cc_start: 0.8545 (m-70) cc_final: 0.7938 (m-70) REVERT: c 61 ASN cc_start: 0.9294 (m-40) cc_final: 0.8857 (t0) REVERT: c 108 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: c 124 LYS cc_start: 0.8834 (tptm) cc_final: 0.8519 (tptm) REVERT: d 69 GLN cc_start: 0.6091 (tp40) cc_final: 0.5639 (tp40) REVERT: d 80 PHE cc_start: 0.7836 (t80) cc_final: 0.7604 (t80) REVERT: d 191 ASP cc_start: 0.8413 (t0) cc_final: 0.7840 (t0) REVERT: d 260 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6290 (tm-30) REVERT: d 314 LYS cc_start: 0.5338 (mmtp) cc_final: 0.4770 (tptt) REVERT: e 45 PHE cc_start: 0.8775 (t80) cc_final: 0.8481 (t80) REVERT: e 47 MET cc_start: 0.8031 (tpp) cc_final: 0.7629 (tpp) REVERT: g 46 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.7607 (tmm-80) REVERT: g 59 MET cc_start: 0.9057 (mmp) cc_final: 0.8800 (mtp) REVERT: i 68 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8010 (mm) REVERT: j 88 PHE cc_start: 0.8165 (t80) cc_final: 0.7949 (t80) REVERT: m 66 TYR cc_start: 0.8439 (m-80) cc_final: 0.8017 (m-80) REVERT: m 135 PHE cc_start: 0.8346 (m-80) cc_final: 0.8000 (t80) REVERT: n 59 MET cc_start: 0.8633 (tmm) cc_final: 0.8415 (ttm) REVERT: o 52 LYS cc_start: 0.7131 (pptt) cc_final: 0.6520 (pptt) REVERT: o 72 TYR cc_start: 0.8559 (m-80) cc_final: 0.8149 (t80) REVERT: o 90 TYR cc_start: 0.4871 (t80) cc_final: 0.4423 (t80) REVERT: o 118 MET cc_start: 0.8764 (tpp) cc_final: 0.8538 (tpp) REVERT: o 152 MET cc_start: 0.7947 (mmm) cc_final: 0.7144 (tpp) outliers start: 120 outliers final: 90 residues processed: 856 average time/residue: 0.5469 time to fit residues: 777.9701 Evaluate side-chains 875 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 776 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 536 LYS Chi-restraints excluded: chain a residue 737 TRP Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 475 optimal weight: 20.0000 chunk 765 optimal weight: 0.0270 chunk 467 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 532 optimal weight: 50.0000 chunk 802 optimal weight: 5.9990 chunk 739 optimal weight: 10.0000 chunk 639 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 493 optimal weight: 40.0000 chunk 392 optimal weight: 0.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 349 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN l 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54321 Z= 0.231 Angle : 0.580 13.359 74346 Z= 0.301 Chirality : 0.043 0.680 8755 Planarity : 0.005 0.066 10052 Dihedral : 4.659 121.349 8649 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.62 % Allowed : 22.41 % Favored : 74.97 % 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: 0.88 (0.10), residues: 8149 helix: 1.86 (0.08), residues: 4778 sheet: -2.48 (0.18), residues: 666 loop : -0.88 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 567 HIS 0.012 0.001 HIS F 344 PHE 0.042 0.002 PHE k 88 TYR 0.058 0.001 TYR j 66 ARG 0.010 0.001 ARG d 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 795 time to evaluate : 4.543 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 62 ARG cc_start: 0.7766 (ttt90) cc_final: 0.7510 (ttt90) REVERT: A 362 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 337 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7678 (mpp) REVERT: C 105 TYR cc_start: 0.8454 (m-80) cc_final: 0.8203 (m-80) REVERT: C 230 ASP cc_start: 0.8455 (p0) cc_final: 0.8134 (p0) REVERT: C 290 MET cc_start: 0.8379 (mmm) cc_final: 0.8147 (mmm) REVERT: C 304 MET cc_start: 0.3932 (ppp) cc_final: 0.3246 (ppp) REVERT: C 362 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7053 (tm-30) REVERT: C 495 LEU cc_start: 0.8740 (tp) cc_final: 0.8459 (tp) REVERT: C 496 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6981 (tm-30) REVERT: C 497 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 523 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7982 (mt-10) REVERT: C 538 CYS cc_start: 0.9055 (t) cc_final: 0.8497 (t) REVERT: C 547 MET cc_start: 0.8921 (mtm) cc_final: 0.8659 (mtm) REVERT: D 68 LEU cc_start: 0.9150 (tp) cc_final: 0.8853 (tp) REVERT: D 71 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7539 (ttm-80) REVERT: D 260 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8519 (mm) REVERT: D 311 ASP cc_start: 0.8276 (t0) cc_final: 0.7942 (t70) REVERT: D 339 ASN cc_start: 0.8097 (t0) cc_final: 0.7894 (t0) REVERT: E 105 TYR cc_start: 0.9048 (m-80) cc_final: 0.8723 (m-10) REVERT: E 494 GLU cc_start: 0.8000 (pt0) cc_final: 0.7800 (pt0) REVERT: E 501 LEU cc_start: 0.9409 (mt) cc_final: 0.9146 (mt) REVERT: F 23 LYS cc_start: 0.8906 (mptt) cc_final: 0.8591 (mptt) REVERT: F 83 THR cc_start: 0.9318 (p) cc_final: 0.9037 (p) REVERT: F 382 LEU cc_start: 0.8983 (mt) cc_final: 0.8467 (mt) REVERT: I 171 GLU cc_start: 0.8762 (pm20) cc_final: 0.8193 (pm20) REVERT: L 82 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8766 (tm-30) REVERT: M 12 ARG cc_start: 0.8064 (tpt-90) cc_final: 0.7787 (tpp80) REVERT: M 49 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7170 (mtm110) REVERT: M 55 GLN cc_start: 0.7120 (pp30) cc_final: 0.6867 (pp30) REVERT: M 57 MET cc_start: 0.6166 (mmt) cc_final: 0.4716 (tmm) REVERT: M 182 GLU cc_start: 0.7833 (tp30) cc_final: 0.7211 (tp30) REVERT: a 200 GLU cc_start: 0.9239 (tp30) cc_final: 0.8659 (tp30) REVERT: a 478 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8210 (tt) REVERT: a 527 ASN cc_start: 0.7895 (t0) cc_final: 0.7604 (t0) REVERT: a 536 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8447 (mtmm) REVERT: a 735 ARG cc_start: 0.8646 (ptm-80) cc_final: 0.7962 (ptt90) REVERT: a 796 HIS cc_start: 0.8454 (m-70) cc_final: 0.7921 (m-70) REVERT: c 61 ASN cc_start: 0.9297 (m-40) cc_final: 0.8847 (t0) REVERT: c 108 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: c 124 LYS cc_start: 0.8850 (tptm) cc_final: 0.8540 (tptm) REVERT: d 69 GLN cc_start: 0.6082 (tp40) cc_final: 0.5608 (tp40) REVERT: d 80 PHE cc_start: 0.7822 (t80) cc_final: 0.7552 (t80) REVERT: d 191 ASP cc_start: 0.8351 (t0) cc_final: 0.7815 (t0) REVERT: d 260 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6309 (tm-30) REVERT: d 271 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7042 (p0) REVERT: d 314 LYS cc_start: 0.5283 (mmtp) cc_final: 0.4716 (tptt) REVERT: d 332 GLN cc_start: 0.6102 (mm110) cc_final: 0.5484 (mm110) REVERT: e 45 PHE cc_start: 0.8791 (t80) cc_final: 0.8481 (t80) REVERT: e 47 MET cc_start: 0.7913 (tpp) cc_final: 0.7534 (tpp) REVERT: g 46 ARG cc_start: 0.8549 (tmm-80) cc_final: 0.7667 (tmm-80) REVERT: g 59 MET cc_start: 0.9040 (mmp) cc_final: 0.8797 (mtp) REVERT: i 68 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8053 (mm) REVERT: i 99 LEU cc_start: 0.9119 (mt) cc_final: 0.8848 (mt) REVERT: l 4 LEU cc_start: 0.2072 (mt) cc_final: 0.0746 (tt) REVERT: m 66 TYR cc_start: 0.8384 (m-80) cc_final: 0.7945 (m-80) REVERT: m 135 PHE cc_start: 0.8325 (m-80) cc_final: 0.8114 (t80) REVERT: n 59 MET cc_start: 0.8656 (tmm) cc_final: 0.8322 (ttm) REVERT: o 72 TYR cc_start: 0.8540 (m-80) cc_final: 0.8119 (t80) REVERT: o 90 TYR cc_start: 0.4783 (t80) cc_final: 0.4362 (t80) REVERT: o 118 MET cc_start: 0.8729 (tpp) cc_final: 0.8512 (tpp) REVERT: o 152 MET cc_start: 0.7894 (mmm) cc_final: 0.7078 (tpp) outliers start: 96 outliers final: 75 residues processed: 849 average time/residue: 0.5477 time to fit residues: 772.0239 Evaluate side-chains 867 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 784 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 536 LYS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 235 PHE Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 181 PHE Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 271 ASN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 144 LEU Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 150 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 507 optimal weight: 20.0000 chunk 681 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 589 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 640 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 657 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN l 82 GLN l 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094899 restraints weight = 97687.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093729 restraints weight = 66462.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093851 restraints weight = 46751.972| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 54321 Z= 0.335 Angle : 0.615 13.724 74346 Z= 0.320 Chirality : 0.045 0.990 8755 Planarity : 0.005 0.066 10052 Dihedral : 4.706 126.082 8649 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 22.33 % Favored : 74.69 % 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: 0.82 (0.10), residues: 8149 helix: 1.82 (0.08), residues: 4775 sheet: -2.53 (0.18), residues: 681 loop : -0.90 (0.12), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP d 312 HIS 0.014 0.001 HIS F 344 PHE 0.082 0.002 PHE h 88 TYR 0.060 0.002 TYR j 66 ARG 0.009 0.001 ARG d 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11648.11 seconds wall clock time: 204 minutes 34.89 seconds (12274.89 seconds total)