Starting phenix.real_space_refine on Sat Jan 20 07:07:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esw_28581/01_2024/8esw_28581_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 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: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 52 5.49 5 S 475 5.16 5 C 43201 2.51 5 N 10853 2.21 5 O 11945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AN TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN GLU 66": "OE1" <-> "OE2" Residue "AN GLU 83": "OE1" <-> "OE2" Residue "AN GLU 136": "OE1" <-> "OE2" Residue "S6 ASP 35": "OD1" <-> "OD2" Residue "S6 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 GLU 82": "OE1" <-> "OE2" Residue "S6 ASP 88": "OD1" <-> "OD2" Residue "S1 ASP 159": "OD1" <-> "OD2" Residue "S1 ASP 176": "OD1" <-> "OD2" Residue "S1 GLU 225": "OE1" <-> "OE2" Residue "S1 GLU 258": "OE1" <-> "OE2" Residue "S1 GLU 382": "OE1" <-> "OE2" Residue "S1 TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 448": "OD1" <-> "OD2" Residue "S1 TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 452": "OD1" <-> "OD2" Residue "S1 TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 653": "OE1" <-> "OE2" Residue "S1 GLU 722": "OE1" <-> "OE2" Residue "S3 ASP 53": "OD1" <-> "OD2" Residue "S3 GLU 85": "OE1" <-> "OE2" Residue "S3 ASP 104": "OD1" <-> "OD2" Residue "S3 ASP 185": "OD1" <-> "OD2" Residue "S3 GLU 217": "OE1" <-> "OE2" Residue "V2 ASP 77": "OD1" <-> "OD2" Residue "V2 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 GLU 143": "OE1" <-> "OE2" Residue "V2 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 ASP 183": "OD1" <-> "OD2" Residue "V2 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 GLU 85": "OE1" <-> "OE2" Residue "S8 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 GLU 139": "OE1" <-> "OE2" Residue "S8 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 221": "OE1" <-> "OE2" Residue "1 PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 117": "OE1" <-> "OE2" Residue "4 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 51": "OD1" <-> "OD2" Residue "A1 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO GLU 86": "OE1" <-> "OE2" Residue "S5 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S5 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S5 ASP 25": "OD1" <-> "OD2" Residue "S5 GLU 39": "OE1" <-> "OE2" Residue "S5 GLU 49": "OE1" <-> "OE2" Residue "S5 GLU 85": "OE1" <-> "OE2" Residue "AM TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM GLU 133": "OE1" <-> "OE2" Residue "AM GLU 166": "OE1" <-> "OE2" Residue "BL GLU 32": "OE1" <-> "OE2" Residue "BL TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL ASP 58": "OD1" <-> "OD2" Residue "BL TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 162": "OE1" <-> "OE2" Residue "B4 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 ASP 70": "OD1" <-> "OD2" Residue "B5 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 94": "OE1" <-> "OE2" Residue "B5 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 175": "OE1" <-> "OE2" Residue "B9 GLU 27": "OE1" <-> "OE2" Residue "BM ASP 64": "OD1" <-> "OD2" Residue "BM TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ASP 140": "OD1" <-> "OD2" Residue "BM GLU 147": "OE1" <-> "OE2" Residue "B8 GLU 60": "OE1" <-> "OE2" Residue "B8 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 45": "OE1" <-> "OE2" Residue "AC ASP 149": "OD1" <-> "OD2" Residue "B1 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 GLU 77": "OE1" <-> "OE2" Residue "S4 GLU 112": "OE1" <-> "OE2" Residue "S4 GLU 146": "OE1" <-> "OE2" Residue "A9 ASP 97": "OD1" <-> "OD2" Residue "A9 ASP 98": "OD1" <-> "OD2" Residue "A9 ASP 222": "OD1" <-> "OD2" Residue "A9 GLU 227": "OE1" <-> "OE2" Residue "A9 GLU 294": "OE1" <-> "OE2" Residue "A9 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ASP 320": "OD1" <-> "OD2" Residue "A9 GLU 350": "OE1" <-> "OE2" Residue "A9 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 GLU 47": "OE1" <-> "OE2" Residue "S2 GLU 109": "OE1" <-> "OE2" Residue "S2 ASP 306": "OD1" <-> "OD2" Residue "S2 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 GLU 134": "OE1" <-> "OE2" Residue "V1 GLU 136": "OE1" <-> "OE2" Residue "V1 TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 GLU 304": "OE1" <-> "OE2" Residue "V1 GLU 305": "OE1" <-> "OE2" Residue "V1 ASP 327": "OD1" <-> "OD2" Residue "2 GLU 194": "OE1" <-> "OE2" Residue "2 GLU 303": "OE1" <-> "OE2" Residue "2 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 115": "OD1" <-> "OD2" Residue "A7 GLU 43": "OE1" <-> "OE2" Residue "A3 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ASP 48": "OD1" <-> "OD2" Residue "AL TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ASP 143": "OD1" <-> "OD2" Residue "AL GLU 199": "OE1" <-> "OE2" Residue "AL GLU 225": "OE1" <-> "OE2" Residue "AL ASP 279": "OD1" <-> "OD2" Residue "AL GLU 296": "OE1" <-> "OE2" Residue "AL TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ASP 90": "OD1" <-> "OD2" Residue "AB ASP 128": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66555 Number of models: 1 Model: "" Number of chains: 64 Chain: "AN" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1150 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "S6" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "S1" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5168 Classifications: {'peptide': 680} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 646} Chain breaks: 1 Chain: "S3" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1719 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 14, 'TRANS': 193} Chain: "V2" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1680 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "S7" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 168} Chain: "S8" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1485 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} Chain: "3" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 855 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2571 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "4" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3604 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 434} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4605 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 12, 'TRANS': 564} Chain: "A8" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1384 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "A1" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 581 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "AO" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1188 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "S5" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "AM" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1251 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain: "BL" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1252 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B6" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1302 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 11, 'TRANS': 149} Chain: "B4" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 907 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "B7" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 925 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "B5" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1221 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "B9" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1143 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "BM" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 871 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B8" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 14, 'TRANS': 129} Chain: "B3" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AC" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "C2" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 904 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B1" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "S4" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1023 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 116} Chain: "A9" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2972 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B2" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 485 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "S2" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3349 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 394} Chain breaks: 1 Chain: "V3" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 136 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "V1" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3368 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain: "2" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2797 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain: "4L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "6" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1331 Classifications: {'peptide': 165} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 162} Chain: "A7" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A5" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A3" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 528 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A6" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 968 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "AL" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3008 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 348} Chain: "AB" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "AN" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S7" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'CDL': 1, 'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "5" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 391 Unusual residues: {'3PE': 6, 'CDL': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 115 Chain: "AM" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 177 Unusual residues: {'3PE': 3, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 84 Chain: "B6" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "B4" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B5" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 74 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "B9" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "C2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "A9" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'CDL': 2, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 99 Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "6" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "AL" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1615 SG CYSS6 87 66.326 86.353 243.577 1.00 11.35 S ATOM 1791 SG CYSS6 111 67.788 83.533 241.834 1.00 11.94 S ATOM 1813 SG CYSS6 114 68.866 87.008 241.525 1.00 11.20 S ATOM 2705 SG CYSS1 147 61.641 67.631 232.531 1.00 10.49 S ATOM 2644 SG CYSS1 138 60.988 73.821 232.804 1.00 8.17 S ATOM 2665 SG CYSS1 141 66.289 71.314 234.708 1.00 10.80 S ATOM 3067 SG CYSS1 193 61.484 58.814 239.171 1.00 7.44 S ATOM 3043 SG CYSS1 190 62.968 63.728 243.437 1.00 8.22 S ATOM 3091 SG CYSS1 196 66.880 58.506 242.695 1.00 8.27 S ATOM 3420 SG CYSS1 240 66.201 62.962 237.913 1.00 9.26 S ATOM 2144 SG CYSS1 74 55.919 54.982 239.367 1.00 9.97 S ATOM 2229 SG CYSS1 85 54.174 57.888 237.658 1.00 9.23 S ATOM 2254 SG CYSS1 88 52.181 54.137 234.088 1.00 11.76 S ATOM 2355 SG CYSS1 102 53.747 51.461 236.375 1.00 12.79 S ATOM 9581 SG CYSV2 128 45.778 64.811 269.875 1.00 36.15 S ATOM 9615 SG CYSV2 133 42.814 64.277 271.861 1.00 37.13 S ATOM 9896 SG CYSV2 169 44.329 59.445 267.626 1.00 36.61 S ATOM 9919 SG CYSV2 173 41.467 59.813 270.009 1.00 46.57 S ATOM 10888 SG CYSS7 97 65.400 96.398 202.330 1.00 8.96 S ATOM 11389 SG CYSS7 161 66.246 89.858 201.856 1.00 13.31 S ATOM 11620 SG CYSS7 191 63.690 92.379 206.665 1.00 20.06 S ATOM 10882 SG CYSS7 96 60.999 93.044 201.502 1.00 9.09 S ATOM 12900 SG CYSS8 160 62.014 87.884 214.340 1.00 21.95 S ATOM 12874 SG CYSS8 157 67.922 91.150 213.953 1.00 25.50 S ATOM 12921 SG CYSS8 163 65.442 88.928 219.633 1.00 15.57 S ATOM 12646 SG CYSS8 128 67.446 84.801 214.780 1.00 19.96 S ATOM 12595 SG CYSS8 121 66.598 81.074 227.886 1.00 19.24 S ATOM 12950 SG CYSS8 167 65.664 87.178 227.029 1.00 10.69 S ATOM 12576 SG CYSS8 118 71.934 85.219 227.451 1.00 7.97 S ATOM 12618 SG CYSS8 124 68.535 83.863 222.288 1.00 16.26 S ATOM 52422 SG CYSV1 397 49.851 58.563 247.751 1.00 10.52 S ATOM 52422 SG CYSV1 397 49.851 58.563 247.751 1.00 10.52 S ATOM 52442 SG CYSV1 400 48.809 60.547 250.359 1.00 8.76 S ATOM 52764 SG CYSV1 440 47.105 54.345 252.003 1.00 15.42 S ATOM 52403 SG CYSV1 394 53.265 56.076 251.976 1.00 15.53 S Time building chain proxies: 26.12, per 1000 atoms: 0.39 Number of scatterers: 66555 At special positions: 0 Unit cell: (134.64, 194.48, 300.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 475 16.00 P 52 15.00 O 11945 8.00 N 10853 7.00 C 43201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYSA8 38 " - pdb=" SG CYSA8 68 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 48 " - pdb=" SG CYSA8 58 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 80 " - pdb=" SG CYSA8 113 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 90 " - pdb=" SG CYSA8 103 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 27 " - pdb=" SG CYSS5 60 " distance=2.02 Simple disulfide: pdb=" SG CYSS5 37 " - pdb=" SG CYSS5 50 " distance=2.03 Simple disulfide: pdb=" SG CYSBL 54 " - pdb=" SG CYSBL 61 " distance=2.03 Simple disulfide: pdb=" SG CYSBL 90 " - pdb=" SG CYSBL 102 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 57 " - pdb=" SG CYSB7 88 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 67 " - pdb=" SG CYSB7 78 " distance=2.03 Simple disulfide: pdb=" SG CYSV1 301 " - pdb=" SG CYSV1 319 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.29 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 85 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 88 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 74 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 102 " pdb=" FESV2 301 " pdb="FE1 FESV2 301 " - pdb=" SG CYSV2 133 " pdb="FE2 FESV2 301 " - pdb=" SG CYSV2 173 " pdb="FE1 FESV2 301 " - pdb=" SG CYSV2 128 " pdb="FE2 FESV2 301 " - pdb=" SG CYSV2 169 " pdb=" SF4S1 801 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 138 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 141 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 147 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 134 " pdb=" SF4S1 802 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 190 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 193 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 196 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 240 " pdb=" SF4S7 301 " pdb="FE3 SF4S7 301 " - pdb=" SG CYSS7 191 " pdb="FE4 SF4S7 301 " - pdb=" SG CYSS7 96 " pdb="FE1 SF4S7 301 " - pdb=" SG CYSS7 97 " pdb="FE2 SF4S7 301 " - pdb=" SG CYSS7 161 " pdb=" SF4S8 301 " pdb="FE2 SF4S8 301 " - pdb=" NE2 HISS8 106 " pdb="FE3 SF4S8 301 " - pdb=" SG CYSS8 163 " pdb="FE2 SF4S8 301 " - pdb=" SG CYSS8 157 " pdb="FE4 SF4S8 301 " - pdb=" SG CYSS8 128 " pdb="FE1 SF4S8 301 " - pdb=" SG CYSS8 160 " pdb=" SF4S8 302 " pdb="FE4 SF4S8 302 " - pdb=" SG CYSS8 124 " pdb="FE2 SF4S8 302 " - pdb=" SG CYSS8 167 " pdb="FE1 SF4S8 302 " - pdb=" SG CYSS8 121 " pdb="FE3 SF4S8 302 " - pdb=" SG CYSS8 118 " pdb=" SF4V1 502 " pdb="FE1 SF4V1 502 " - pdb=" SG CYSV1 397 " pdb="FE2 SF4V1 502 " - pdb=" SG CYSV1 400 " pdb="FE3 SF4V1 502 " - pdb=" SG CYSV1 440 " pdb="FE4 SF4V1 502 " - pdb=" SG CYSV1 394 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZNS6 201 " pdb="ZN ZNS6 201 " - pdb=" NE2 HISS6 96 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 114 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 111 " Number of angles added : 3 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 325 helices and 27 sheets defined 50.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 118.56 Creating SS restraints... Processing helix chain 'AN' and resid 7 through 20 removed outlier: 3.940A pdb=" N THRAN 11 " --> pdb=" O ASNAN 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARGAN 18 " --> pdb=" O GLNAN 15 " (cutoff:3.500A) Processing helix chain 'AN' and resid 23 through 32 Processing helix chain 'AN' and resid 85 through 88 No H-bonds generated for 'chain 'AN' and resid 85 through 88' Processing helix chain 'S6' and resid 51 through 56 removed outlier: 3.785A pdb=" N ARGS6 55 " --> pdb=" O ARGS6 52 " (cutoff:3.500A) Processing helix chain 'S6' and resid 68 through 73 Processing helix chain 'S1' and resid 59 through 64 Processing helix chain 'S1' and resid 117 through 130 Processing helix chain 'S1' and resid 138 through 140 No H-bonds generated for 'chain 'S1' and resid 138 through 140' Processing helix chain 'S1' and resid 148 through 155 Processing helix chain 'S1' and resid 195 through 202 Processing helix chain 'S1' and resid 215 through 217 No H-bonds generated for 'chain 'S1' and resid 215 through 217' Processing helix chain 'S1' and resid 234 through 239 Processing helix chain 'S1' and resid 256 through 258 No H-bonds generated for 'chain 'S1' and resid 256 through 258' Processing helix chain 'S1' and resid 302 through 305 No H-bonds generated for 'chain 'S1' and resid 302 through 305' Processing helix chain 'S1' and resid 308 through 311 removed outlier: 3.532A pdb=" N LEUS1 311 " --> pdb=" O CYSS1 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 308 through 311' Processing helix chain 'S1' and resid 333 through 347 Processing helix chain 'S1' and resid 361 through 373 Processing helix chain 'S1' and resid 393 through 395 No H-bonds generated for 'chain 'S1' and resid 393 through 395' Processing helix chain 'S1' and resid 405 through 407 No H-bonds generated for 'chain 'S1' and resid 405 through 407' Processing helix chain 'S1' and resid 418 through 421 No H-bonds generated for 'chain 'S1' and resid 418 through 421' Processing helix chain 'S1' and resid 423 through 435 Processing helix chain 'S1' and resid 461 through 466 Processing helix chain 'S1' and resid 472 through 478 removed outlier: 3.714A pdb=" N VALS1 476 " --> pdb=" O ALAS1 472 " (cutoff:3.500A) Processing helix chain 'S1' and resid 489 through 493 Processing helix chain 'S1' and resid 498 through 510 removed outlier: 4.070A pdb=" N VALS1 504 " --> pdb=" O ILES1 500 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALAS1 505 " --> pdb=" O HISS1 501 " (cutoff:3.500A) Processing helix chain 'S1' and resid 526 through 534 removed outlier: 4.565A pdb=" N GLYS1 530 " --> pdb=" O ALAS1 526 " (cutoff:3.500A) Processing helix chain 'S1' and resid 540 through 544 Processing helix chain 'S1' and resid 625 through 636 Processing helix chain 'S1' and resid 645 through 655 Processing helix chain 'S1' and resid 693 through 697 Processing helix chain 'S1' and resid 701 through 705 Processing helix chain 'S1' and resid 707 through 730 removed outlier: 4.020A pdb=" N ALAS1 730 " --> pdb=" O LYSS1 726 " (cutoff:3.500A) Processing helix chain 'S3' and resid 55 through 70 removed outlier: 3.901A pdb=" N HISS3 59 " --> pdb=" O VALS3 55 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEUS3 60 " --> pdb=" O ALAS3 56 " (cutoff:3.500A) Processing helix chain 'S3' and resid 92 through 104 removed outlier: 4.019A pdb=" N VALS3 95 " --> pdb=" O PROS3 92 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VALS3 96 " --> pdb=" O GLUS3 93 " (cutoff:3.500A) Proline residue: S3 97 - end of helix removed outlier: 4.273A pdb=" N GLNS3 100 " --> pdb=" O PROS3 97 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEUS3 102 " --> pdb=" O LEUS3 99 " (cutoff:3.500A) Processing helix chain 'S3' and resid 163 through 175 removed outlier: 4.249A pdb=" N TYRS3 168 " --> pdb=" O ALAS3 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLUS3 169 " --> pdb=" O ASNS3 166 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILES3 172 " --> pdb=" O GLUS3 169 " (cutoff:3.500A) Processing helix chain 'S3' and resid 245 through 247 No H-bonds generated for 'chain 'S3' and resid 245 through 247' Processing helix chain 'V2' and resid 50 through 62 removed outlier: 4.103A pdb=" N LYSV2 54 " --> pdb=" O ALAV2 50 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARGV2 55 " --> pdb=" O GLUV2 51 " (cutoff:3.500A) Processing helix chain 'V2' and resid 68 through 71 Processing helix chain 'V2' and resid 73 through 80 removed outlier: 3.799A pdb=" N LEUV2 78 " --> pdb=" O PROV2 74 " (cutoff:3.500A) Processing helix chain 'V2' and resid 88 through 97 Processing helix chain 'V2' and resid 102 through 111 Processing helix chain 'V2' and resid 131 through 134 No H-bonds generated for 'chain 'V2' and resid 131 through 134' Processing helix chain 'V2' and resid 138 through 149 Processing helix chain 'V2' and resid 191 through 202 Processing helix chain 'S7' and resid 46 through 51 removed outlier: 4.021A pdb=" N ASNS7 51 " --> pdb=" O GLUS7 47 " (cutoff:3.500A) Processing helix chain 'S7' and resid 67 through 85 Processing helix chain 'S7' and resid 96 through 105 removed outlier: 3.708A pdb=" N METS7 102 " --> pdb=" O VALS7 99 " (cutoff:3.500A) Processing helix chain 'S7' and resid 111 through 114 Processing helix chain 'S7' and resid 139 through 148 Processing helix chain 'S7' and resid 166 through 168 No H-bonds generated for 'chain 'S7' and resid 166 through 168' Processing helix chain 'S7' and resid 178 through 180 No H-bonds generated for 'chain 'S7' and resid 178 through 180' Processing helix chain 'S7' and resid 195 through 210 Processing helix chain 'S7' and resid 215 through 219 Processing helix chain 'S8' and resid 55 through 66 Processing helix chain 'S8' and resid 69 through 81 removed outlier: 3.677A pdb=" N HISS8 81 " --> pdb=" O VALS8 77 " (cutoff:3.500A) Processing helix chain 'S8' and resid 123 through 127 Processing helix chain 'S8' and resid 162 through 165 No H-bonds generated for 'chain 'S8' and resid 162 through 165' Processing helix chain 'S8' and resid 185 through 188 Processing helix chain 'S8' and resid 192 through 201 Processing helix chain 'S8' and resid 203 through 211 Processing helix chain '3' and resid 2 through 25 Processing helix chain '3' and resid 55 through 82 removed outlier: 3.576A pdb=" N LEU 3 73 " --> pdb=" O VAL 3 69 " (cutoff:3.500A) Proline residue: 3 76 - end of helix removed outlier: 5.560A pdb=" N ILE 3 79 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 3 80 " --> pdb=" O PRO 3 76 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS 3 82 " --> pdb=" O ILE 3 78 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 109 Processing helix chain '1' and resid 3 through 38 Processing helix chain '1' and resid 52 through 62 Proline residue: 1 55 - end of helix removed outlier: 3.827A pdb=" N ILE 1 60 " --> pdb=" O CYS 1 57 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 1 62 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) Processing helix chain '1' and resid 76 through 95 removed outlier: 3.643A pdb=" N ILE 1 80 " --> pdb=" O LEU 1 76 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER 1 81 " --> pdb=" O SER 1 77 " (cutoff:3.500A) Proline residue: 1 82 - end of helix removed outlier: 4.467A pdb=" N TRP 1 93 " --> pdb=" O SER 1 89 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET 1 94 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS 1 95 " --> pdb=" O PHE 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 108 through 128 removed outlier: 3.749A pdb=" N VAL 1 120 " --> pdb=" O THR 1 116 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR 1 121 " --> pdb=" O SER 1 117 " (cutoff:3.500A) Processing helix chain '1' and resid 133 through 164 removed outlier: 4.024A pdb=" N VAL 1 151 " --> pdb=" O ILE 1 147 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER 1 152 " --> pdb=" O SER 1 148 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE 1 162 " --> pdb=" O LEU 1 158 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU 1 163 " --> pdb=" O SER 1 159 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 1 164 " --> pdb=" O PHE 1 160 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 176 removed outlier: 3.770A pdb=" N PHE 1 174 " --> pdb=" O TYR 1 171 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR 1 175 " --> pdb=" O PHE 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 181 through 184 No H-bonds generated for 'chain '1' and resid 181 through 184' Processing helix chain '1' and resid 186 through 199 removed outlier: 3.703A pdb=" N ALA 1 198 " --> pdb=" O SER 1 194 " (cutoff:3.500A) Processing helix chain '1' and resid 226 through 248 Processing helix chain '1' and resid 257 through 276 removed outlier: 3.521A pdb=" N THR 1 276 " --> pdb=" O TRP 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 290 Processing helix chain '1' and resid 292 through 314 Processing helix chain '4' and resid 3 through 14 Proline residue: 4 13 - end of helix Processing helix chain '4' and resid 21 through 37 removed outlier: 4.169A pdb=" N GLN 4 25 " --> pdb=" O TYR 4 21 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 4 26 " --> pdb=" O TRP 4 22 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 75 Processing helix chain '4' and resid 78 through 81 No H-bonds generated for 'chain '4' and resid 78 through 81' Processing helix chain '4' and resid 86 through 104 Processing helix chain '4' and resid 109 through 130 removed outlier: 4.209A pdb=" N LEU 4 120 " --> pdb=" O PHE 4 116 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE 4 121 " --> pdb=" O GLU 4 117 " (cutoff:3.500A) Proline residue: 4 122 - end of helix Processing helix chain '4' and resid 134 through 165 removed outlier: 4.493A pdb=" N LEU 4 137 " --> pdb=" O PRO 4 134 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY 4 140 " --> pdb=" O LEU 4 137 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU 4 141 " --> pdb=" O GLN 4 138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 4 142 " --> pdb=" O ALA 4 139 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU 4 144 " --> pdb=" O LEU 4 141 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE 4 145 " --> pdb=" O TYR 4 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR 4 146 " --> pdb=" O LEU 4 143 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR 4 147 " --> pdb=" O LEU 4 144 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 4 148 " --> pdb=" O PHE 4 145 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL 4 150 " --> pdb=" O THR 4 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU 4 152 " --> pdb=" O LEU 4 149 " (cutoff:3.500A) Proline residue: 4 153 - end of helix removed outlier: 3.523A pdb=" N PHE 4 159 " --> pdb=" O ILE 4 156 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE 4 165 " --> pdb=" O MET 4 162 " (cutoff:3.500A) Processing helix chain '4' and resid 170 through 175 removed outlier: 3.584A pdb=" N ASN 4 175 " --> pdb=" O TYR 4 171 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 194 removed outlier: 4.260A pdb=" N ALA 4 190 " --> pdb=" O CYS 4 186 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE 4 191 " --> pdb=" O LEU 4 187 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 207 Proline residue: 4 205 - end of helix Processing helix chain '4' and resid 213 through 221 Processing helix chain '4' and resid 226 through 237 removed outlier: 4.946A pdb=" N SER 4 236 " --> pdb=" O LEU 4 232 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE 4 237 " --> pdb=" O ARG 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 239 through 266 removed outlier: 5.556A pdb=" N PHE 4 247 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL 4 248 " --> pdb=" O LYS 4 244 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP 4 249 " --> pdb=" O TYR 4 245 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU 4 265 " --> pdb=" O SER 4 261 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG 4 266 " --> pdb=" O LEU 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 289 removed outlier: 3.822A pdb=" N VAL 4 279 " --> pdb=" O ALA 4 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS 4 281 " --> pdb=" O SER 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 325 removed outlier: 3.703A pdb=" N LEU 4 309 " --> pdb=" O ILE 4 305 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS 4 310 " --> pdb=" O ALA 4 306 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER 4 312 " --> pdb=" O GLY 4 308 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER 4 321 " --> pdb=" O LEU 4 317 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG 4 324 " --> pdb=" O VAL 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 336 through 339 No H-bonds generated for 'chain '4' and resid 336 through 339' Processing helix chain '4' and resid 341 through 354 removed outlier: 4.061A pdb=" N LEU 4 345 " --> pdb=" O PRO 4 341 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP 4 346 " --> pdb=" O SER 4 342 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 4 353 " --> pdb=" O LEU 4 349 " (cutoff:3.500A) Processing helix chain '4' and resid 361 through 376 removed outlier: 3.595A pdb=" N SER 4 368 " --> pdb=" O LEU 4 364 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) Processing helix chain '4' and resid 379 through 403 removed outlier: 4.074A pdb=" N LEU 4 384 " --> pdb=" O MET 4 381 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER 4 385 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE 4 386 " --> pdb=" O LEU 4 383 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER 4 388 " --> pdb=" O SER 4 385 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER 4 391 " --> pdb=" O SER 4 388 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 4 394 " --> pdb=" O SER 4 391 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR 4 395 " --> pdb=" O ALA 4 392 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU 4 396 " --> pdb=" O ALA 4 393 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 4 398 " --> pdb=" O THR 4 395 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR 4 399 " --> pdb=" O LEU 4 396 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE 4 401 " --> pdb=" O LEU 4 398 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER 4 402 " --> pdb=" O TYR 4 399 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 4 403 " --> pdb=" O SER 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 419 through 426 Processing helix chain '4' and resid 430 through 434 Processing helix chain '5' and resid 6 through 30 removed outlier: 3.539A pdb=" N TYR 5 27 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 57 through 80 removed outlier: 4.338A pdb=" N GLU 5 79 " --> pdb=" O PHE 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 105 removed outlier: 4.411A pdb=" N MET 5 92 " --> pdb=" O ASN 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 110 through 128 Processing helix chain '5' and resid 134 through 161 removed outlier: 3.858A pdb=" N ASN 5 147 " --> pdb=" O THR 5 143 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY 5 150 " --> pdb=" O SER 5 146 " (cutoff:3.500A) Processing helix chain '5' and resid 169 through 171 No H-bonds generated for 'chain '5' and resid 169 through 171' Processing helix chain '5' and resid 180 through 196 Processing helix chain '5' and resid 204 through 210 removed outlier: 3.682A pdb=" N ALA 5 208 " --> pdb=" O SER 5 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA 5 209 " --> pdb=" O TRP 5 205 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET 5 210 " --> pdb=" O LEU 5 206 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 204 through 210' Processing helix chain '5' and resid 214 through 221 Processing helix chain '5' and resid 226 through 235 removed outlier: 4.426A pdb=" N VAL 5 230 " --> pdb=" O VAL 5 226 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 240 No H-bonds generated for 'chain '5' and resid 237 through 240' Processing helix chain '5' and resid 244 through 266 Processing helix chain '5' and resid 270 through 291 Processing helix chain '5' and resid 294 through 321 Processing helix chain '5' and resid 334 through 337 No H-bonds generated for 'chain '5' and resid 334 through 337' Processing helix chain '5' and resid 339 through 353 Processing helix chain '5' and resid 359 through 373 removed outlier: 3.821A pdb=" N MET 5 366 " --> pdb=" O TYR 5 362 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE 5 370 " --> pdb=" O MET 5 366 " (cutoff:3.500A) Processing helix chain '5' and resid 378 through 402 removed outlier: 3.736A pdb=" N TYR 5 385 " --> pdb=" O PHE 5 381 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER 5 387 " --> pdb=" O LEU 5 383 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER 5 402 " --> pdb=" O LEU 5 398 " (cutoff:3.500A) Processing helix chain '5' and resid 420 through 435 Processing helix chain '5' and resid 438 through 441 No H-bonds generated for 'chain '5' and resid 438 through 441' Processing helix chain '5' and resid 455 through 458 No H-bonds generated for 'chain '5' and resid 455 through 458' Processing helix chain '5' and resid 460 through 474 removed outlier: 3.607A pdb=" N TYR 5 473 " --> pdb=" O GLY 5 469 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU 5 474 " --> pdb=" O LEU 5 470 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 497 Processing helix chain '5' and resid 502 through 506 Processing helix chain '5' and resid 512 through 524 removed outlier: 3.904A pdb=" N TYR 5 517 " --> pdb=" O TYR 5 513 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN 5 519 " --> pdb=" O LEU 5 515 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL 5 522 " --> pdb=" O GLY 5 518 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 550 Processing helix chain '5' and resid 557 through 576 removed outlier: 3.996A pdb=" N LEU 5 575 " --> pdb=" O LEU 5 571 " (cutoff:3.500A) Processing helix chain 'A8' and resid 24 through 28 Processing helix chain 'A8' and resid 31 through 37 removed outlier: 3.819A pdb=" N LYSA8 36 " --> pdb=" O PHEA8 32 " (cutoff:3.500A) Processing helix chain 'A8' and resid 39 through 51 removed outlier: 3.787A pdb=" N ASNA8 43 " --> pdb=" O GLUA8 39 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLUA8 44 " --> pdb=" O GLNA8 40 " (cutoff:3.500A) Processing helix chain 'A8' and resid 59 through 79 removed outlier: 3.511A pdb=" N THRA8 79 " --> pdb=" O LYSA8 75 " (cutoff:3.500A) Processing helix chain 'A8' and resid 82 through 94 Processing helix chain 'A8' and resid 105 through 117 removed outlier: 3.804A pdb=" N VALA8 109 " --> pdb=" O LYSA8 105 " (cutoff:3.500A) Processing helix chain 'A1' and resid 5 through 26 removed outlier: 4.241A pdb=" N ILEA1 11 " --> pdb=" O PROA1 7 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILEA1 12 " --> pdb=" O GLYA1 8 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SERA1 17 " --> pdb=" O THRA1 13 " (cutoff:3.500A) Proline residue: A1 19 - end of helix removed outlier: 4.529A pdb=" N META1 23 " --> pdb=" O PROA1 19 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 54 Processing helix chain 'A1' and resid 64 through 66 No H-bonds generated for 'chain 'A1' and resid 64 through 66' Processing helix chain 'AO' and resid 36 through 101 removed outlier: 3.648A pdb=" N GLYAO 52 " --> pdb=" O ALAAO 48 " (cutoff:3.500A) Proline residue: AO 77 - end of helix Processing helix chain 'AO' and resid 132 through 135 No H-bonds generated for 'chain 'AO' and resid 132 through 135' Processing helix chain 'AO' and resid 141 through 148 removed outlier: 3.692A pdb=" N ARGAO 147 " --> pdb=" O SERAO 143 " (cutoff:3.500A) Processing helix chain 'S5' and resid 10 through 17 removed outlier: 4.447A pdb=" N LEUS5 14 " --> pdb=" O LEUS5 11 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THRS5 15 " --> pdb=" O THRS5 12 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLYS5 16 " --> pdb=" O ASPS5 13 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYSS5 17 " --> pdb=" O LEUS5 14 " (cutoff:3.500A) Processing helix chain 'S5' and resid 28 through 40 removed outlier: 3.563A pdb=" N LYSS5 33 " --> pdb=" O LYSS5 29 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYSS5 37 " --> pdb=" O LYSS5 33 " (cutoff:3.500A) Processing helix chain 'S5' and resid 42 through 45 No H-bonds generated for 'chain 'S5' and resid 42 through 45' Processing helix chain 'S5' and resid 51 through 62 removed outlier: 3.651A pdb=" N ASPS5 56 " --> pdb=" O ASPS5 52 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHES5 57 " --> pdb=" O LEUS5 53 " (cutoff:3.500A) Processing helix chain 'S5' and resid 64 through 82 removed outlier: 3.589A pdb=" N ARGS5 77 " --> pdb=" O METS5 73 " (cutoff:3.500A) Processing helix chain 'S5' and resid 88 through 90 No H-bonds generated for 'chain 'S5' and resid 88 through 90' Processing helix chain 'AM' and resid 18 through 40 removed outlier: 3.794A pdb=" N PHEAM 38 " --> pdb=" O ALAAM 34 " (cutoff:3.500A) Processing helix chain 'AM' and resid 49 through 79 Proline residue: AM 62 - end of helix Processing helix chain 'AM' and resid 86 through 104 Processing helix chain 'AM' and resid 107 through 130 removed outlier: 3.878A pdb=" N PHEAM 116 " --> pdb=" O CYSAM 112 " (cutoff:3.500A) Processing helix chain 'BL' and resid 7 through 29 Proline residue: BL 22 - end of helix Processing helix chain 'BL' and resid 60 through 93 removed outlier: 3.561A pdb=" N PHEBL 87 " --> pdb=" O LEUBL 83 " (cutoff:3.500A) Processing helix chain 'BL' and resid 98 through 101 No H-bonds generated for 'chain 'BL' and resid 98 through 101' Processing helix chain 'BL' and resid 103 through 119 Processing helix chain 'BL' and resid 129 through 146 Processing helix chain 'B6' and resid 19 through 22 removed outlier: 3.961A pdb=" N VALB6 22 " --> pdb=" O GLYB6 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B6' and resid 19 through 22' Processing helix chain 'B6' and resid 24 through 28 Processing helix chain 'B6' and resid 33 through 46 Processing helix chain 'B6' and resid 56 through 61 Processing helix chain 'B6' and resid 65 through 80 Proline residue: B6 73 - end of helix Processing helix chain 'B6' and resid 82 through 116 removed outlier: 7.507A pdb=" N PHEB6 87 " --> pdb=" O PROB6 83 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N GLNB6 88 " --> pdb=" O VALB6 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARGB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAB6 90 " --> pdb=" O GLYB6 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THRB6 92 " --> pdb=" O GLNB6 88 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VALB6 93 " --> pdb=" O ARGB6 89 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALAB6 100 " --> pdb=" O TRPB6 96 " (cutoff:3.500A) Processing helix chain 'B6' and resid 160 through 162 No H-bonds generated for 'chain 'B6' and resid 160 through 162' Processing helix chain 'B4' and resid 5 through 29 removed outlier: 3.744A pdb=" N GLUB4 9 " --> pdb=" O ASNB4 5 " (cutoff:3.500A) Processing helix chain 'B4' and resid 32 through 36 Processing helix chain 'B4' and resid 46 through 56 Processing helix chain 'B4' and resid 66 through 75 Processing helix chain 'B4' and resid 77 through 100 removed outlier: 3.647A pdb=" N LYSB4 97 " --> pdb=" O GLYB4 93 " (cutoff:3.500A) Processing helix chain 'B7' and resid 3 through 9 removed outlier: 3.702A pdb=" N HISB7 7 " --> pdb=" O ASNB7 3 " (cutoff:3.500A) Processing helix chain 'B7' and resid 41 through 46 Processing helix chain 'B7' and resid 59 through 70 Processing helix chain 'B7' and resid 75 through 99 removed outlier: 4.119A pdb=" N CYSB7 78 " --> pdb=" O VALB7 75 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HISB7 80 " --> pdb=" O LYSB7 77 " (cutoff:3.500A) Processing helix chain 'B7' and resid 101 through 109 Processing helix chain 'B5' and resid 53 through 82 removed outlier: 3.954A pdb=" N GLYB5 69 " --> pdb=" O TYRB5 65 " (cutoff:3.500A) Proline residue: B5 72 - end of helix Processing helix chain 'B5' and resid 101 through 103 No H-bonds generated for 'chain 'B5' and resid 101 through 103' Processing helix chain 'B5' and resid 107 through 115 Processing helix chain 'B5' and resid 120 through 154 removed outlier: 3.588A pdb=" N ARGB5 154 " --> pdb=" O LYSB5 150 " (cutoff:3.500A) Processing helix chain 'B5' and resid 168 through 183 removed outlier: 3.602A pdb=" N GLUB5 181 " --> pdb=" O ALAB5 177 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALAB5 182 " --> pdb=" O ASPB5 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEUB5 183 " --> pdb=" O GLUB5 179 " (cutoff:3.500A) Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 33 through 48 Processing helix chain 'B9' and resid 55 through 71 Processing helix chain 'B9' and resid 97 through 102 Processing helix chain 'B9' and resid 105 through 132 removed outlier: 4.057A pdb=" N GLNB9 110 " --> pdb=" O LEUB9 106 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYRB9 111 " --> pdb=" O GLUB9 107 " (cutoff:3.500A) Proline residue: B9 112 - end of helix removed outlier: 4.006A pdb=" N LYSB9 123 " --> pdb=" O GLUB9 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLUB9 124 " --> pdb=" O GLNB9 120 " (cutoff:3.500A) Processing helix chain 'BM' and resid 47 through 51 Processing helix chain 'BM' and resid 68 through 82 Processing helix chain 'BM' and resid 89 through 95 Processing helix chain 'BM' and resid 103 through 120 removed outlier: 3.802A pdb=" N GLUBM 118 " --> pdb=" O LEUBM 114 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEUBM 119 " --> pdb=" O ARGBM 115 " (cutoff:3.500A) Processing helix chain 'BM' and resid 140 through 143 No H-bonds generated for 'chain 'BM' and resid 140 through 143' Processing helix chain 'B8' and resid 45 through 54 Processing helix chain 'B8' and resid 84 through 86 No H-bonds generated for 'chain 'B8' and resid 84 through 86' Processing helix chain 'B8' and resid 128 through 151 removed outlier: 4.007A pdb=" N PHEB8 132 " --> pdb=" O ASNB8 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEUB8 149 " --> pdb=" O LEUB8 145 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASPB8 151 " --> pdb=" O TYRB8 147 " (cutoff:3.500A) Processing helix chain 'B3' and resid 19 through 21 No H-bonds generated for 'chain 'B3' and resid 19 through 21' Processing helix chain 'B3' and resid 23 through 35 removed outlier: 4.114A pdb=" N VALB3 28 " --> pdb=" O GLNB3 24 " (cutoff:3.500A) Processing helix chain 'B3' and resid 57 through 65 Processing helix chain 'B3' and resid 69 through 86 removed outlier: 3.651A pdb=" N ALAB3 85 " --> pdb=" O ALAB3 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUB3 86 " --> pdb=" O VALB3 82 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 84 Processing helix chain 'AC' and resid 108 through 122 removed outlier: 3.866A pdb=" N VALAC 112 " --> pdb=" O SERAC 108 " (cutoff:3.500A) Processing helix chain 'AC' and resid 128 through 132 Processing helix chain 'AC' and resid 137 through 147 Processing helix chain 'C2' and resid 7 through 11 removed outlier: 3.943A pdb=" N LEUC2 11 " --> pdb=" O PROC2 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 7 through 11' Processing helix chain 'C2' and resid 26 through 45 Processing helix chain 'C2' and resid 54 through 92 Processing helix chain 'B1' and resid 7 through 32 removed outlier: 3.683A pdb=" N ALAB1 13 " --> pdb=" O LEUB1 10 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUB1 14 " --> pdb=" O TRPB1 11 " (cutoff:3.500A) Proline residue: B1 15 - end of helix removed outlier: 3.509A pdb=" N THRB1 30 " --> pdb=" O LYSB1 27 " (cutoff:3.500A) Processing helix chain 'S4' and resid 76 through 79 No H-bonds generated for 'chain 'S4' and resid 76 through 79' Processing helix chain 'S4' and resid 138 through 147 Processing helix chain 'S4' and resid 169 through 171 No H-bonds generated for 'chain 'S4' and resid 169 through 171' Processing helix chain 'A9' and resid 74 through 84 removed outlier: 4.032A pdb=" N TYRA9 78 " --> pdb=" O PHEA9 74 " (cutoff:3.500A) Processing helix chain 'A9' and resid 102 through 106 removed outlier: 3.605A pdb=" N LYSA9 105 " --> pdb=" O ILEA9 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VALA9 106 " --> pdb=" O ARGA9 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A9' and resid 102 through 106' Processing helix chain 'A9' and resid 123 through 129 Processing helix chain 'A9' and resid 151 through 154 No H-bonds generated for 'chain 'A9' and resid 151 through 154' Processing helix chain 'A9' and resid 157 through 168 Processing helix chain 'A9' and resid 196 through 211 Processing helix chain 'A9' and resid 248 through 251 Processing helix chain 'A9' and resid 261 through 273 Processing helix chain 'A9' and resid 292 through 302 Processing helix chain 'A9' and resid 321 through 333 Processing helix chain 'A9' and resid 339 through 341 No H-bonds generated for 'chain 'A9' and resid 339 through 341' Processing helix chain 'A9' and resid 344 through 351 Processing helix chain 'A9' and resid 363 through 366 Processing helix chain 'A9' and resid 373 through 381 Proline residue: A9 378 - end of helix Processing helix chain 'A9' and resid 408 through 414 Processing helix chain 'B2' and resid 42 through 65 Processing helix chain 'S2' and resid 46 through 50 Processing helix chain 'S2' and resid 63 through 65 No H-bonds generated for 'chain 'S2' and resid 63 through 65' Processing helix chain 'S2' and resid 125 through 129 Processing helix chain 'S2' and resid 134 through 144 Proline residue: S2 139 - end of helix removed outlier: 4.082A pdb=" N ASPS2 142 " --> pdb=" O LEUS2 138 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARGS2 143 " --> pdb=" O PROS2 139 " (cutoff:3.500A) Processing helix chain 'S2' and resid 149 through 164 Processing helix chain 'S2' and resid 170 through 199 Processing helix chain 'S2' and resid 203 through 222 removed outlier: 4.367A pdb=" N GLUS2 211 " --> pdb=" O TRPS2 207 " (cutoff:3.500A) Processing helix chain 'S2' and resid 246 through 264 removed outlier: 4.140A pdb=" N GLUS2 251 " --> pdb=" O ASPS2 247 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALAS2 257 " --> pdb=" O ALAS2 253 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLUS2 258 " --> pdb=" O SERS2 254 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARGS2 259 " --> pdb=" O LYSS2 255 " (cutoff:3.500A) Processing helix chain 'S2' and resid 271 through 277 Processing helix chain 'S2' and resid 285 through 290 Processing helix chain 'S2' and resid 295 through 300 removed outlier: 4.189A pdb=" N GLYS2 300 " --> pdb=" O METS2 297 " (cutoff:3.500A) Processing helix chain 'S2' and resid 307 through 310 No H-bonds generated for 'chain 'S2' and resid 307 through 310' Processing helix chain 'S2' and resid 331 through 354 removed outlier: 3.657A pdb=" N LEUS2 346 " --> pdb=" O METS2 342 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARGS2 347 " --> pdb=" O ARGS2 343 " (cutoff:3.500A) Processing helix chain 'S2' and resid 373 through 378 Processing helix chain 'S2' and resid 380 through 391 Processing helix chain 'S2' and resid 432 through 443 removed outlier: 4.102A pdb=" N ALAS2 439 " --> pdb=" O ALAS2 435 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEUS2 440 " --> pdb=" O HISS2 436 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLUS2 441 " --> pdb=" O LEUS2 437 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYSS2 442 " --> pdb=" O ALAS2 438 " (cutoff:3.500A) Processing helix chain 'S2' and resid 449 through 459 Processing helix chain 'S2' and resid 463 through 467 Processing helix chain 'V3' and resid 91 through 97 Processing helix chain 'V1' and resid 52 through 54 No H-bonds generated for 'chain 'V1' and resid 52 through 54' Processing helix chain 'V1' and resid 68 through 73 Processing helix chain 'V1' and resid 80 through 85 Processing helix chain 'V1' and resid 88 through 98 Processing helix chain 'V1' and resid 110 through 117 removed outlier: 3.697A pdb=" N PHEV1 116 " --> pdb=" O METV1 112 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N METV1 117 " --> pdb=" O LYSV1 113 " (cutoff:3.500A) Processing helix chain 'V1' and resid 141 through 148 Processing helix chain 'V1' and resid 150 through 164 Processing helix chain 'V1' and resid 178 through 194 Processing helix chain 'V1' and resid 201 through 203 No H-bonds generated for 'chain 'V1' and resid 201 through 203' Processing helix chain 'V1' and resid 224 through 231 Processing helix chain 'V1' and resid 250 through 252 No H-bonds generated for 'chain 'V1' and resid 250 through 252' Processing helix chain 'V1' and resid 260 through 272 Proline residue: V1 267 - end of helix Processing helix chain 'V1' and resid 311 through 317 Processing helix chain 'V1' and resid 326 through 328 No H-bonds generated for 'chain 'V1' and resid 326 through 328' Processing helix chain 'V1' and resid 344 through 349 removed outlier: 4.872A pdb=" N ASPV1 349 " --> pdb=" O ASNV1 345 " (cutoff:3.500A) Processing helix chain 'V1' and resid 354 through 359 Processing helix chain 'V1' and resid 378 through 391 Processing helix chain 'V1' and resid 398 through 416 removed outlier: 4.074A pdb=" N ILEV1 404 " --> pdb=" O CYSV1 400 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLYV1 405 " --> pdb=" O ARGV1 401 " (cutoff:3.500A) Processing helix chain 'V1' and resid 421 through 433 removed outlier: 4.574A pdb=" N ASPV1 425 " --> pdb=" O PROV1 421 " (cutoff:3.500A) Processing helix chain 'V1' and resid 442 through 456 Proline residue: V1 449 - end of helix Processing helix chain 'V1' and resid 458 through 473 Processing helix chain '2' and resid 5 through 22 Processing helix chain '2' and resid 29 through 43 Proline residue: 2 43 - end of helix Processing helix chain '2' and resid 52 through 81 Processing helix chain '2' and resid 92 through 105 Processing helix chain '2' and resid 108 through 110 No H-bonds generated for 'chain '2' and resid 108 through 110' Processing helix chain '2' and resid 112 through 120 removed outlier: 4.150A pdb=" N ASN 2 116 " --> pdb=" O PHE 2 112 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY 2 120 " --> pdb=" O ASN 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 131 removed outlier: 3.588A pdb=" N THR 2 131 " --> pdb=" O LEU 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 133 through 143 Proline residue: 2 137 - end of helix removed outlier: 4.078A pdb=" N LEU 2 140 " --> pdb=" O ALA 2 136 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 2 142 " --> pdb=" O LEU 2 138 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR 2 143 " --> pdb=" O MET 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 163 removed outlier: 3.769A pdb=" N ALA 2 162 " --> pdb=" O VAL 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 190 removed outlier: 3.554A pdb=" N MET 2 186 " --> pdb=" O HIS 2 182 " (cutoff:3.500A) Processing helix chain '2' and resid 196 through 217 removed outlier: 3.843A pdb=" N MET 2 214 " --> pdb=" O VAL 2 210 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE 2 215 " --> pdb=" O LEU 2 211 " (cutoff:3.500A) Processing helix chain '2' and resid 223 through 227 removed outlier: 3.856A pdb=" N PHE 2 227 " --> pdb=" O LEU 2 223 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 223 through 227' Processing helix chain '2' and resid 234 through 247 removed outlier: 3.915A pdb=" N MET 2 242 " --> pdb=" O PHE 2 238 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN 2 243 " --> pdb=" O THR 2 239 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE 2 244 " --> pdb=" O LEU 2 240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU 2 245 " --> pdb=" O PHE 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 256 through 268 Processing helix chain '2' and resid 273 through 279 Processing helix chain '2' and resid 283 through 297 removed outlier: 3.708A pdb=" N ILE 2 292 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER 2 295 " --> pdb=" O ARG 2 291 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA 2 296 " --> pdb=" O ILE 2 292 " (cutoff:3.500A) Processing helix chain '2' and resid 315 through 328 removed outlier: 3.810A pdb=" N ILE 2 322 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET 2 323 " --> pdb=" O MET 2 319 " (cutoff:3.500A) Processing helix chain '2' and resid 330 through 334 removed outlier: 3.616A pdb=" N ILE 2 334 " --> pdb=" O LEU 2 331 " (cutoff:3.500A) Processing helix chain '4L' and resid 2 through 5 No H-bonds generated for 'chain '4L' and resid 2 through 5' Processing helix chain '4L' and resid 8 through 22 Processing helix chain '4L' and resid 28 through 50 Processing helix chain '4L' and resid 57 through 85 removed outlier: 3.637A pdb=" N MET4L 61 " --> pdb=" O TYR4L 58 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE4L 63 " --> pdb=" O SER4L 60 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU4L 64 " --> pdb=" O MET4L 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER4L 67 " --> pdb=" O LEU4L 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL4L 68 " --> pdb=" O THR4L 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA4L 72 " --> pdb=" O CYS4L 69 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL4L 79 " --> pdb=" O SER4L 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET4L 81 " --> pdb=" O LEU4L 78 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG4L 83 " --> pdb=" O SER4L 80 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS4L 85 " --> pdb=" O ILE4L 82 " (cutoff:3.500A) Processing helix chain '4L' and resid 87 through 91 removed outlier: 4.232A pdb=" N PHE4L 90 " --> pdb=" O ASN4L 87 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN4L 91 " --> pdb=" O ASP4L 88 " (cutoff:3.500A) No H-bonds generated for 'chain '4L' and resid 87 through 91' Processing helix chain '6' and resid 2 through 19 Processing helix chain '6' and resid 23 through 43 removed outlier: 3.826A pdb=" N ILE 6 35 " --> pdb=" O LEU 6 31 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE 6 36 " --> pdb=" O ILE 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 49 through 58 Processing helix chain '6' and resid 63 through 73 Processing helix chain '6' and resid 82 through 100 Processing helix chain '6' and resid 104 through 107 No H-bonds generated for 'chain '6' and resid 104 through 107' Processing helix chain '6' and resid 123 through 125 No H-bonds generated for 'chain '6' and resid 123 through 125' Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 142 through 163 Processing helix chain 'A7' and resid 10 through 20 Processing helix chain 'A7' and resid 58 through 60 No H-bonds generated for 'chain 'A7' and resid 58 through 60' Processing helix chain 'A7' and resid 72 through 79 removed outlier: 3.665A pdb=" N GLNA7 76 " --> pdb=" O LEUA7 72 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSA7 77 " --> pdb=" O VALA7 73 " (cutoff:3.500A) Processing helix chain 'A5' and resid 20 through 37 removed outlier: 4.393A pdb=" N LYSA5 37 " --> pdb=" O ARGA5 33 " (cutoff:3.500A) Processing helix chain 'A5' and resid 43 through 61 Processing helix chain 'A5' and resid 65 through 72 Processing helix chain 'A5' and resid 77 through 97 removed outlier: 4.023A pdb=" N GLYA5 96 " --> pdb=" O ARGA5 92 " (cutoff:3.500A) Processing helix chain 'A3' and resid 13 through 19 Processing helix chain 'A3' and resid 21 through 46 Processing helix chain 'A3' and resid 66 through 70 removed outlier: 3.526A pdb=" N LEUA3 69 " --> pdb=" O PROA3 66 " (cutoff:3.500A) Processing helix chain 'A6' and resid 22 through 46 Proline residue: A6 41 - end of helix Processing helix chain 'A6' and resid 53 through 69 removed outlier: 3.630A pdb=" N HISA6 67 " --> pdb=" O GLUA6 63 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASNA6 69 " --> pdb=" O VALA6 65 " (cutoff:3.500A) Processing helix chain 'A6' and resid 73 through 91 Processing helix chain 'A6' and resid 97 through 102 Processing helix chain 'A6' and resid 115 through 121 Processing helix chain 'AL' and resid 43 through 46 No H-bonds generated for 'chain 'AL' and resid 43 through 46' Processing helix chain 'AL' and resid 66 through 69 No H-bonds generated for 'chain 'AL' and resid 66 through 69' Processing helix chain 'AL' and resid 96 through 105 Processing helix chain 'AL' and resid 117 through 120 No H-bonds generated for 'chain 'AL' and resid 117 through 120' Processing helix chain 'AL' and resid 128 through 131 removed outlier: 3.609A pdb=" N LEUAL 131 " --> pdb=" O METAL 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'AL' and resid 128 through 131' Processing helix chain 'AL' and resid 137 through 139 No H-bonds generated for 'chain 'AL' and resid 137 through 139' Processing helix chain 'AL' and resid 144 through 149 Processing helix chain 'AL' and resid 156 through 181 removed outlier: 4.116A pdb=" N ILEAL 161 " --> pdb=" O ALAAL 157 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SERAL 169 " --> pdb=" O METAL 165 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILEAL 172 " --> pdb=" O TYRAL 168 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASPAL 173 " --> pdb=" O SERAL 169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HISAL 177 " --> pdb=" O ASPAL 173 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SERAL 180 " --> pdb=" O GLNAL 176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRAL 181 " --> pdb=" O HISAL 177 " (cutoff:3.500A) Processing helix chain 'AL' and resid 191 through 204 removed outlier: 3.617A pdb=" N ASPAL 194 " --> pdb=" O PROAL 191 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHEAL 195 " --> pdb=" O TYRAL 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAL 196 " --> pdb=" O SERAL 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUAL 199 " --> pdb=" O VALAL 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARGAL 203 " --> pdb=" O ALAAL 200 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLNAL 204 " --> pdb=" O METAL 201 " (cutoff:3.500A) Processing helix chain 'AL' and resid 209 through 225 removed outlier: 5.341A pdb=" N GLYAL 224 " --> pdb=" O GLNAL 220 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLUAL 225 " --> pdb=" O ASNAL 221 " (cutoff:3.500A) Processing helix chain 'AL' and resid 239 through 249 Processing helix chain 'AL' and resid 264 through 282 removed outlier: 3.560A pdb=" N LYSAL 273 " --> pdb=" O GLUAL 269 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEUAL 277 " --> pdb=" O LYSAL 273 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYSAL 278 " --> pdb=" O GLNAL 274 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THRAL 282 " --> pdb=" O LYSAL 278 " (cutoff:3.500A) Processing helix chain 'AL' and resid 298 through 305 Processing helix chain 'AL' and resid 329 through 340 removed outlier: 3.650A pdb=" N TYRAL 339 " --> pdb=" O ALAAL 335 " (cutoff:3.500A) Processing helix chain 'AL' and resid 343 through 350 removed outlier: 4.492A pdb=" N PHEAL 350 " --> pdb=" O LEUAL 346 " (cutoff:3.500A) Processing helix chain 'AL' and resid 364 through 374 Processing helix chain 'AL' and resid 388 through 390 No H-bonds generated for 'chain 'AL' and resid 388 through 390' Processing helix chain 'AL' and resid 395 through 397 No H-bonds generated for 'chain 'AL' and resid 395 through 397' Processing helix chain 'AB' and resid 72 through 84 Processing helix chain 'AB' and resid 108 through 122 removed outlier: 3.543A pdb=" N VALAB 112 " --> pdb=" O SERAB 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLUAB 113 " --> pdb=" O LEUAB 109 " (cutoff:3.500A) Processing helix chain 'AB' and resid 128 through 131 No H-bonds generated for 'chain 'AB' and resid 128 through 131' Processing helix chain 'AB' and resid 137 through 147 removed outlier: 4.385A pdb=" N ASPAB 146 " --> pdb=" O LYSAB 142 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'AN' and resid 63 through 66 removed outlier: 6.544A pdb=" N GLUAN 53 " --> pdb=" O LEUAN 41 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEUAN 41 " --> pdb=" O GLUAN 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S6' and resid 78 through 80 Processing sheet with id= C, first strand: chain 'S6' and resid 84 through 87 Processing sheet with id= D, first strand: chain 'S1' and resid 42 through 46 Processing sheet with id= E, first strand: chain 'S1' and resid 183 through 185 Processing sheet with id= F, first strand: chain 'S1' and resid 260 through 265 removed outlier: 3.861A pdb=" N ARGS1 286 " --> pdb=" O SERS1 278 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S1' and resid 320 through 322 Processing sheet with id= H, first strand: chain 'S1' and resid 352 through 354 removed outlier: 6.373A pdb=" N PHES1 571 " --> pdb=" O LEUS1 551 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEUS1 553 " --> pdb=" O PHES1 571 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VALS1 573 " --> pdb=" O LEUS1 553 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALAS1 588 " --> pdb=" O TYRS1 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S1' and resid 519 through 522 removed outlier: 7.948A pdb=" N ASNS1 520 " --> pdb=" O PROS1 483 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILES1 485 " --> pdb=" O ASNS1 520 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEUS1 522 " --> pdb=" O ILES1 485 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILES1 487 " --> pdb=" O LEUS1 522 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALAS1 410 " --> pdb=" O ALAS1 484 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILES1 486 " --> pdb=" O ALAS1 410 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEUS1 412 " --> pdb=" O ILES1 486 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLYS1 488 " --> pdb=" O LEUS1 412 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VALS1 414 " --> pdb=" O GLYS1 488 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLNS1 439 " --> pdb=" O VALS1 411 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEUS1 413 " --> pdb=" O GLNS1 439 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALAS1 441 " --> pdb=" O LEUS1 413 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLUS1 454 " --> pdb=" O SERS1 442 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'S1' and resid 600 through 603 removed outlier: 3.667A pdb=" N GLYS1 600 " --> pdb=" O THRS1 612 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S3' and resid 112 through 120 removed outlier: 7.045A pdb=" N ASNS3 133 " --> pdb=" O VALS3 114 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILES3 116 " --> pdb=" O VALS3 131 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VALS3 131 " --> pdb=" O ILES3 116 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLYS3 118 " --> pdb=" O GLUS3 129 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLUS3 129 " --> pdb=" O GLYS3 118 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEUS3 86 " --> pdb=" O ARGS3 142 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYRS3 148 " --> pdb=" O ILES3 90 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLUS3 85 " --> pdb=" O THRS3 81 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYSS3 77 " --> pdb=" O LEUS3 89 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S3' and resid 210 through 215 Processing sheet with id= M, first strand: chain 'V2' and resid 162 through 167 removed outlier: 6.508A pdb=" N TYRV2 123 " --> pdb=" O THRV2 163 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SERV2 165 " --> pdb=" O TYRV2 123 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILEV2 125 " --> pdb=" O SERV2 165 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VALV2 167 " --> pdb=" O ILEV2 125 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VALV2 127 " --> pdb=" O VALV2 167 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S7' and resid 127 through 131 removed outlier: 6.753A pdb=" N TRPS7 154 " --> pdb=" O ILES7 128 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VALS7 130 " --> pdb=" O TRPS7 154 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILES7 156 " --> pdb=" O VALS7 130 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILES7 186 " --> pdb=" O SERS7 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'S8' and resid 106 through 108 Processing sheet with id= P, first strand: chain 'S8' and resid 133 through 137 Processing sheet with id= Q, first strand: chain '5' and resid 35 through 44 removed outlier: 7.032A pdb=" N ILE 5 49 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER 5 43 " --> pdb=" O MET 5 47 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S4' and resid 151 through 154 Processing sheet with id= S, first strand: chain 'S4' and resid 113 through 115 Processing sheet with id= T, first strand: chain 'A9' and resid 66 through 69 removed outlier: 7.379A pdb=" N VALA9 135 " --> pdb=" O THRA9 67 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHEA9 69 " --> pdb=" O VALA9 135 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILEA9 137 " --> pdb=" O PHEA9 69 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARGA9 173 " --> pdb=" O VALA9 136 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASNA9 138 " --> pdb=" O ARGA9 173 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEA9 175 " --> pdb=" O ASNA9 138 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A9' and resid 244 through 247 removed outlier: 6.709A pdb=" N META9 313 " --> pdb=" O META9 245 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEUA9 247 " --> pdb=" O META9 313 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYRA9 315 " --> pdb=" O LEUA9 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'S2' and resid 85 through 89 removed outlier: 6.515A pdb=" N ASPS2 107 " --> pdb=" O VALS2 111 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VALS2 111 " --> pdb=" O ASPS2 107 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S2' and resid 399 through 406 Processing sheet with id= X, first strand: chain 'V1' and resid 255 through 259 removed outlier: 7.074A pdb=" N TYRV1 127 " --> pdb=" O THRV1 256 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THRV1 258 " --> pdb=" O TYRV1 127 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VALV1 129 " --> pdb=" O THRV1 258 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALAV1 132 " --> pdb=" O TYRV1 172 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARGV1 174 " --> pdb=" O ALAV1 132 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASPV1 209 " --> pdb=" O ALAV1 169 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILEV1 171 " --> pdb=" O ASPV1 209 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHEV1 211 " --> pdb=" O ILEV1 171 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILEV1 173 " --> pdb=" O PHEV1 211 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HISV1 213 " --> pdb=" O ILEV1 173 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'V1' and resid 288 through 293 Processing sheet with id= Z, first strand: chain 'V1' and resid 341 through 343 removed outlier: 7.017A pdb=" N METV1 372 " --> pdb=" O LEUV1 330 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VALV1 332 " --> pdb=" O ILEV1 370 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILEV1 370 " --> pdb=" O VALV1 332 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'AL' and resid 285 through 290 removed outlier: 6.512A pdb=" N VALAL 185 " --> pdb=" O ILEAL 85 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VALAL 87 " --> pdb=" O VALAL 185 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEUAL 187 " --> pdb=" O VALAL 87 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLYAL 89 " --> pdb=" O LEUAL 187 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLUAL 109 " --> pdb=" O VALAL 186 " (cutoff:3.500A) 2615 hydrogen bonds defined for protein. 7386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.85 Time building geometry restraints manager: 23.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 28189 1.42 - 1.64: 39164 1.64 - 1.87: 754 1.87 - 2.09: 0 2.09 - 2.32: 80 Bond restraints: 68187 Sorted by residual: bond pdb=" C3' DGTAL 501 " pdb=" C4' DGTAL 501 " ideal model delta sigma weight residual 1.324 1.520 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C1' DGTAL 501 " pdb=" C2' DGTAL 501 " ideal model delta sigma weight residual 1.362 1.522 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C4' DGTAL 501 " pdb=" O4' DGTAL 501 " ideal model delta sigma weight residual 1.595 1.440 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C4 DGTAL 501 " pdb=" N3 DGTAL 501 " ideal model delta sigma weight residual 1.497 1.353 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C PRO 4 358 " pdb=" N PRO 4 359 " ideal model delta sigma weight residual 1.332 1.390 -0.058 8.20e-03 1.49e+04 4.94e+01 ... (remaining 68182 not shown) Histogram of bond angle deviations from ideal: 65.03 - 79.24: 74 79.24 - 93.45: 7 93.45 - 107.66: 3348 107.66 - 121.87: 75125 121.87 - 136.07: 13541 Bond angle restraints: 92095 Sorted by residual: angle pdb=" N PROS7 192 " pdb=" CA PROS7 192 " pdb=" C PROS7 192 " ideal model delta sigma weight residual 110.70 92.32 18.38 1.22e+00 6.72e-01 2.27e+02 angle pdb=" PA NDPA9 501 " pdb=" O3 NDPA9 501 " pdb=" PN NDPA9 501 " ideal model delta sigma weight residual 107.74 132.17 -24.43 1.95e+00 2.62e-01 1.56e+02 angle pdb=" N SERC2 111 " pdb=" CA SERC2 111 " pdb=" C SERC2 111 " ideal model delta sigma weight residual 111.39 125.82 -14.43 1.38e+00 5.25e-01 1.09e+02 angle pdb=" N PROS7 189 " pdb=" CA PROS7 189 " pdb=" C PROS7 189 " ideal model delta sigma weight residual 113.53 127.50 -13.97 1.39e+00 5.18e-01 1.01e+02 angle pdb=" S2 SF4V1 502 " pdb="FE1 SF4V1 502 " pdb=" S3 SF4V1 502 " ideal model delta sigma weight residual 104.10 89.47 14.63 1.50e+00 4.44e-01 9.52e+01 ... (remaining 92090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 39735 34.82 - 69.65: 1254 69.65 - 104.47: 96 104.47 - 139.30: 10 139.30 - 174.12: 4 Dihedral angle restraints: 41099 sinusoidal: 17636 harmonic: 23463 Sorted by residual: dihedral pdb=" CB CYSA8 90 " pdb=" SG CYSA8 90 " pdb=" SG CYSA8 103 " pdb=" CB CYSA8 103 " ideal model delta sinusoidal sigma weight residual -86.00 -161.50 75.50 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYSA8 38 " pdb=" SG CYSA8 38 " pdb=" SG CYSA8 68 " pdb=" CB CYSA8 68 " ideal model delta sinusoidal sigma weight residual 93.00 167.99 -74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" C10 FMNV1 501 " pdb=" C1' FMNV1 501 " pdb=" N10 FMNV1 501 " pdb=" C2' FMNV1 501 " ideal model delta sinusoidal sigma weight residual 257.59 86.60 170.99 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.258: 9808 4.258 - 8.516: 0 8.516 - 12.773: 0 12.773 - 17.031: 0 17.031 - 21.289: 24 Chirality restraints: 9832 Sorted by residual: chirality pdb="FE3 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4S8 301 " pdb=" S1 SF4S8 301 " pdb=" S3 SF4S8 301 " pdb=" S4 SF4S8 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.71 21.26 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4S8 301 " pdb=" S2 SF4S8 301 " pdb=" S3 SF4S8 301 " pdb=" S4 SF4S8 301 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.21 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9829 not shown) Planarity restraints: 11493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGTAL 501 " -0.252 2.00e-02 2.50e+03 5.76e-01 6.64e+03 pdb=" C2' DGTAL 501 " 0.924 2.00e-02 2.50e+03 pdb=" C3' DGTAL 501 " 0.439 2.00e-02 2.50e+03 pdb=" C4' DGTAL 501 " -0.337 2.00e-02 2.50e+03 pdb=" C5' DGTAL 501 " 0.513 2.00e-02 2.50e+03 pdb=" N9 DGTAL 501 " 0.131 2.00e-02 2.50e+03 pdb=" O3' DGTAL 501 " -0.436 2.00e-02 2.50e+03 pdb=" O4' DGTAL 501 " -0.981 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 ZMPB9 201 " 0.277 2.00e-02 2.50e+03 2.32e-01 6.73e+02 pdb=" C13 ZMPB9 201 " -0.077 2.00e-02 2.50e+03 pdb=" C14 ZMPB9 201 " 0.182 2.00e-02 2.50e+03 pdb=" N1 ZMPB9 201 " -0.391 2.00e-02 2.50e+03 pdb=" O2 ZMPB9 201 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 ZMPB9 201 " -0.267 2.00e-02 2.50e+03 2.29e-01 6.56e+02 pdb=" C16 ZMPB9 201 " 0.063 2.00e-02 2.50e+03 pdb=" C17 ZMPB9 201 " 0.021 2.00e-02 2.50e+03 pdb=" N2 ZMPB9 201 " 0.383 2.00e-02 2.50e+03 pdb=" O3 ZMPB9 201 " -0.200 2.00e-02 2.50e+03 ... (remaining 11490 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 355 2.53 - 3.12: 44777 3.12 - 3.71: 106551 3.71 - 4.31: 153629 4.31 - 4.90: 256029 Nonbonded interactions: 561341 Sorted by model distance: nonbonded pdb=" NH2 ARGV1 413 " pdb=" OE2 GLUV1 423 " model vdw 1.932 2.520 nonbonded pdb=" OG SER 5 253 " pdb=" O GLY 5 283 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THRS2 183 " pdb=" OH TYRS2 219 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASPS8 153 " pdb=" OG1 THRS8 155 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THRS2 177 " pdb=" O ASPS2 314 " model vdw 2.280 2.440 ... (remaining 561336 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 'AB' and resid 71 through 151) selection = (chain 'AC' and resid 71 through 151) } 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 individual isotropic 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 28.060 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 155.290 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 68187 Z= 0.381 Angle : 1.009 28.618 92095 Z= 0.543 Chirality : 1.045 21.289 9832 Planarity : 0.010 0.576 11493 Dihedral : 16.615 174.120 25996 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 0.63 % Allowed : 0.85 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.08), residues: 7942 helix: -1.69 (0.06), residues: 4180 sheet: -0.65 (0.25), residues: 437 loop : -1.32 (0.09), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 4 347 HIS 0.022 0.001 HISS8 106 PHE 0.065 0.002 PHE 2 209 TYR 0.061 0.002 TYRS7 167 ARG 0.021 0.001 ARGAL 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1089 time to evaluate : 5.742 Fit side-chains REVERT: S1 323 MET cc_start: 0.6854 (mmt) cc_final: 0.6615 (mmt) REVERT: S3 90 ILE cc_start: 0.8858 (pt) cc_final: 0.8645 (pt) REVERT: S3 166 ASN cc_start: 0.7705 (t0) cc_final: 0.7426 (t0) REVERT: S3 175 MET cc_start: 0.7960 (mmt) cc_final: 0.7712 (mmt) REVERT: 4 70 SER cc_start: 0.7808 (m) cc_final: 0.7469 (m) REVERT: 4 168 MET cc_start: 0.7473 (mmt) cc_final: 0.7162 (mmt) REVERT: 5 403 MET cc_start: 0.7435 (mpp) cc_final: 0.7193 (mtt) REVERT: S5 29 LYS cc_start: 0.8402 (ptpp) cc_final: 0.7881 (pttm) REVERT: S5 39 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B6 45 ASP cc_start: 0.6950 (t0) cc_final: 0.6677 (t0) REVERT: B4 54 MET cc_start: 0.7131 (tmm) cc_final: 0.6625 (tmm) REVERT: AC 101 ILE cc_start: 0.8730 (mm) cc_final: 0.8512 (mm) REVERT: AC 120 ASP cc_start: 0.7663 (m-30) cc_final: 0.7456 (m-30) REVERT: S2 190 MET cc_start: 0.8236 (tpt) cc_final: 0.7962 (tpt) REVERT: S2 356 MET cc_start: 0.8102 (ttm) cc_final: 0.7869 (ttt) REVERT: 2 267 THR cc_start: 0.8838 (m) cc_final: 0.8635 (m) REVERT: 4L 81 MET cc_start: 0.8276 (mtt) cc_final: 0.8002 (mtt) REVERT: 6 62 MET cc_start: 0.7890 (tmm) cc_final: 0.7445 (ttt) REVERT: 6 161 LYS cc_start: 0.7874 (mptt) cc_final: 0.7655 (mptt) REVERT: AL 386 TYR cc_start: 0.8244 (m-80) cc_final: 0.7814 (m-80) outliers start: 44 outliers final: 16 residues processed: 1123 average time/residue: 0.6508 time to fit residues: 1242.5966 Evaluate side-chains 932 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 916 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V2 residue 77 ASP Chi-restraints excluded: chain 1 residue 252 CYS Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain S5 residue 14 LEU Chi-restraints excluded: chain S5 residue 15 THR Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain AM residue 106 ASN Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 46 MET Chi-restraints excluded: chain C2 residue 104 THR Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 115 VAL Chi-restraints excluded: chain C2 residue 116 ARG Chi-restraints excluded: chain 6 residue 31 LEU Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AB residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 666 optimal weight: 1.9990 chunk 598 optimal weight: 1.9990 chunk 331 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 618 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 376 optimal weight: 2.9990 chunk 460 optimal weight: 0.9990 chunk 716 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 528 GLN S3 107 GLN 1 54 GLN ** 4 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 403 GLN 5 31 ASN ** 5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 349 ASN A8 86 GLN A8 117 ASN ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B8 110 HIS A9 116 HIS A9 291 GLN V1 151 HIS V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 181 ASN 4L 51 ASN ** AL 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.270 68187 Z= 0.557 Angle : 1.578 50.941 92095 Z= 1.017 Chirality : 0.314 6.633 9832 Planarity : 0.004 0.071 11493 Dihedral : 13.174 168.938 10395 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.20 % Favored : 97.78 % Rotamer: Outliers : 1.14 % Allowed : 7.03 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 7942 helix: -0.16 (0.08), residues: 4178 sheet: -0.59 (0.26), residues: 424 loop : -0.91 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPS4 152 HIS 0.023 0.001 HISS8 106 PHE 0.042 0.001 PHE 5 307 TYR 0.022 0.001 TYRS8 159 ARG 0.008 0.000 ARGAL 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 989 time to evaluate : 5.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S6 60 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8085 (ttpp) REVERT: S1 323 MET cc_start: 0.6797 (mmt) cc_final: 0.6581 (mmt) REVERT: S3 166 ASN cc_start: 0.7900 (t0) cc_final: 0.7610 (t0) REVERT: S8 213 ASP cc_start: 0.7949 (t70) cc_final: 0.7733 (t70) REVERT: 4 403 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7280 (mm-40) REVERT: 5 517 TYR cc_start: 0.7649 (t80) cc_final: 0.6994 (t80) REVERT: 5 576 PHE cc_start: 0.5258 (m-10) cc_final: 0.3983 (m-80) REVERT: B6 45 ASP cc_start: 0.7066 (t0) cc_final: 0.6819 (t0) REVERT: B6 144 PRO cc_start: 0.6896 (Cg_exo) cc_final: 0.6659 (Cg_endo) REVERT: B4 108 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6772 (ttm170) REVERT: B8 130 TYR cc_start: 0.8128 (t80) cc_final: 0.7782 (t80) REVERT: AC 101 ILE cc_start: 0.8818 (mm) cc_final: 0.8579 (mm) REVERT: C2 116 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6937 (ptp90) REVERT: S2 149 MET cc_start: 0.6813 (mpp) cc_final: 0.6604 (mtm) REVERT: V1 78 TYR cc_start: 0.8083 (t80) cc_final: 0.7784 (t80) REVERT: 2 159 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (mt) REVERT: 2 297 PHE cc_start: 0.8155 (m-10) cc_final: 0.7666 (m-10) REVERT: A5 94 MET cc_start: 0.7957 (mmp) cc_final: 0.7369 (mmt) REVERT: AL 386 TYR cc_start: 0.8267 (m-80) cc_final: 0.7843 (m-80) outliers start: 79 outliers final: 56 residues processed: 1035 average time/residue: 0.6326 time to fit residues: 1115.2199 Evaluate side-chains 986 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 928 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 184 THR Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 4 residue 195 MET Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 166 SER Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain 5 residue 502 MET Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 15 THR Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 99 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain AM residue 106 ASN Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain B9 residue 132 GLN Chi-restraints excluded: chain BM residue 69 VAL Chi-restraints excluded: chain BM residue 119 LEU Chi-restraints excluded: chain B3 residue 61 LEU Chi-restraints excluded: chain C2 residue 104 THR Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 116 ARG Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain S4 residue 103 THR Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain S2 residue 227 MET Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 286 SER Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 420 GLN Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 159 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 115 ILE Chi-restraints excluded: chain AB residue 139 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 398 optimal weight: 4.9990 chunk 222 optimal weight: 0.3980 chunk 596 optimal weight: 3.9990 chunk 487 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 717 optimal weight: 0.0050 chunk 775 optimal weight: 3.9990 chunk 639 optimal weight: 8.9990 chunk 711 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 575 optimal weight: 0.7980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S1 133 ASN ** S1 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 107 GLN 4 82 HIS ** 5 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 519 GLN ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 50 ASN BM 68 GLN C2 27 ASN ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 291 GLN ** S2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN 6 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.277 68187 Z= 0.561 Angle : 1.571 50.809 92095 Z= 1.013 Chirality : 0.315 6.581 9832 Planarity : 0.004 0.066 11493 Dihedral : 12.530 177.405 10384 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.54 % Allowed : 9.68 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7942 helix: 0.51 (0.08), residues: 4170 sheet: -0.57 (0.26), residues: 419 loop : -0.66 (0.10), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPS4 152 HIS 0.031 0.001 HISS8 106 PHE 0.033 0.001 PHE 5 307 TYR 0.020 0.001 TYR 5 394 ARG 0.008 0.000 ARGAL 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 944 time to evaluate : 5.636 Fit side-chains revert: symmetry clash REVERT: S6 60 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8148 (ttpp) REVERT: S1 323 MET cc_start: 0.6849 (mmt) cc_final: 0.6579 (mmt) REVERT: S1 409 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: S3 90 ILE cc_start: 0.9048 (pt) cc_final: 0.8784 (pt) REVERT: S3 166 ASN cc_start: 0.7892 (t0) cc_final: 0.7616 (t0) REVERT: S8 213 ASP cc_start: 0.8006 (t70) cc_final: 0.7716 (t70) REVERT: 5 102 MET cc_start: 0.6983 (mpp) cc_final: 0.6616 (mpp) REVERT: 5 517 TYR cc_start: 0.7776 (t80) cc_final: 0.7157 (t80) REVERT: 5 576 PHE cc_start: 0.5583 (m-10) cc_final: 0.4602 (m-80) REVERT: B6 144 PRO cc_start: 0.7074 (Cg_exo) cc_final: 0.6844 (Cg_endo) REVERT: B4 108 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6973 (ttm170) REVERT: AC 101 ILE cc_start: 0.8853 (mm) cc_final: 0.8610 (mm) REVERT: S2 190 MET cc_start: 0.8257 (tpt) cc_final: 0.7910 (tpt) REVERT: S2 376 MET cc_start: 0.8562 (tmm) cc_final: 0.8251 (ttp) REVERT: V1 212 MET cc_start: 0.7994 (tpt) cc_final: 0.7461 (tpt) REVERT: 2 159 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8528 (mt) REVERT: 2 297 PHE cc_start: 0.8151 (m-10) cc_final: 0.7668 (m-10) REVERT: A5 94 MET cc_start: 0.7934 (mmp) cc_final: 0.7567 (mmt) outliers start: 107 outliers final: 73 residues processed: 1003 average time/residue: 0.6634 time to fit residues: 1149.7417 Evaluate side-chains 990 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 915 time to evaluate : 5.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 187 MET Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 287 SER Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 47 MET Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain 5 residue 502 MET Chi-restraints excluded: chain A8 residue 94 SER Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 22 VAL Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain BM residue 119 LEU Chi-restraints excluded: chain B8 residue 172 THR Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain S2 residue 227 MET Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 286 SER Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 84 MET Chi-restraints excluded: chain 2 residue 117 MET Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 159 ILE Chi-restraints excluded: chain 2 residue 193 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 158 GLN Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 709 optimal weight: 2.9990 chunk 539 optimal weight: 3.9990 chunk 372 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 342 optimal weight: 0.8980 chunk 481 optimal weight: 2.9990 chunk 720 optimal weight: 7.9990 chunk 762 optimal weight: 0.6980 chunk 376 optimal weight: 7.9990 chunk 682 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 282 ASN ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 82 HIS 5 237 ASN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 42 GLN BM 68 GLN S4 175 ASN ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 132 HIS ** S2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 193 GLN V1 396 GLN 2 300 ASN 4L 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 68187 Z= 0.570 Angle : 1.577 50.716 92095 Z= 1.017 Chirality : 0.314 6.362 9832 Planarity : 0.004 0.063 11493 Dihedral : 12.091 176.852 10375 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.84 % Allowed : 11.19 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 7942 helix: 0.82 (0.08), residues: 4159 sheet: -0.49 (0.26), residues: 411 loop : -0.53 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRPS4 152 HIS 0.020 0.001 HISS8 106 PHE 0.030 0.001 PHE 5 307 TYR 0.021 0.001 TYRB2 33 ARG 0.007 0.000 ARGA9 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 961 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S6 60 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8158 (ttpp) REVERT: S1 323 MET cc_start: 0.6856 (mmt) cc_final: 0.6548 (mmt) REVERT: S1 409 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: S3 90 ILE cc_start: 0.9121 (pt) cc_final: 0.8816 (pt) REVERT: S3 166 ASN cc_start: 0.8023 (t0) cc_final: 0.7792 (t0) REVERT: S8 213 ASP cc_start: 0.8061 (t70) cc_final: 0.7745 (t70) REVERT: 4 111 MET cc_start: 0.6714 (mpp) cc_final: 0.6374 (mpp) REVERT: 5 102 MET cc_start: 0.6918 (mpp) cc_final: 0.6695 (mpp) REVERT: 5 487 LEU cc_start: 0.7711 (tp) cc_final: 0.7508 (mt) REVERT: AO 86 GLU cc_start: 0.7519 (tp30) cc_final: 0.7316 (tp30) REVERT: BL 97 ASP cc_start: 0.8199 (p0) cc_final: 0.7941 (p0) REVERT: B6 144 PRO cc_start: 0.7218 (Cg_exo) cc_final: 0.6989 (Cg_endo) REVERT: B8 143 LEU cc_start: 0.8762 (mm) cc_final: 0.8285 (mm) REVERT: AC 101 ILE cc_start: 0.8872 (mm) cc_final: 0.8637 (mm) REVERT: A9 332 PHE cc_start: 0.8159 (t80) cc_final: 0.7785 (t80) REVERT: S2 376 MET cc_start: 0.8570 (tmm) cc_final: 0.8263 (ttp) REVERT: S2 392 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: V1 134 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: 4L 81 MET cc_start: 0.8516 (mtt) cc_final: 0.8143 (mtt) REVERT: A5 94 MET cc_start: 0.7935 (mmp) cc_final: 0.7523 (mmt) outliers start: 128 outliers final: 84 residues processed: 1034 average time/residue: 0.6386 time to fit residues: 1141.0605 Evaluate side-chains 996 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 909 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 65 ILE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 46 VAL Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 169 THR Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 287 SER Chi-restraints excluded: chain 4 residue 383 LEU Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 4 residue 437 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 33 MET Chi-restraints excluded: chain 5 residue 47 MET Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 106 ILE Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain BM residue 69 VAL Chi-restraints excluded: chain B8 residue 151 ASP Chi-restraints excluded: chain B3 residue 19 VAL Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain S2 residue 86 THR Chi-restraints excluded: chain S2 residue 227 MET Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 134 GLU Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 193 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 635 optimal weight: 9.9990 chunk 432 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 567 optimal weight: 0.7980 chunk 314 optimal weight: 0.7980 chunk 650 optimal weight: 0.9980 chunk 527 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 389 optimal weight: 5.9990 chunk 684 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 82 HIS A8 86 GLN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 42 GLN B9 50 ASN BM 68 GLN ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN 6 113 ASN ** AL 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 274 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 68187 Z= 0.553 Angle : 1.568 50.662 92095 Z= 1.012 Chirality : 0.314 6.432 9832 Planarity : 0.004 0.061 11493 Dihedral : 11.791 177.095 10375 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.90 % Allowed : 12.80 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 7942 helix: 1.07 (0.08), residues: 4164 sheet: -0.48 (0.27), residues: 407 loop : -0.44 (0.11), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPS4 152 HIS 0.015 0.001 HISS8 106 PHE 0.029 0.001 PHE 5 307 TYR 0.026 0.001 TYRV1 78 ARG 0.006 0.000 ARGA9 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 951 time to evaluate : 5.659 Fit side-chains revert: symmetry clash REVERT: S6 60 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8169 (ttpp) REVERT: S1 70 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7629 (mp) REVERT: S1 323 MET cc_start: 0.6888 (mmt) cc_final: 0.6602 (mmt) REVERT: S1 409 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: S3 90 ILE cc_start: 0.9081 (pt) cc_final: 0.8787 (pt) REVERT: S3 166 ASN cc_start: 0.8016 (t0) cc_final: 0.7768 (t0) REVERT: S8 213 ASP cc_start: 0.8051 (t70) cc_final: 0.7709 (t70) REVERT: 3 35 LYS cc_start: 0.7577 (tttm) cc_final: 0.7298 (tttt) REVERT: 1 66 GLU cc_start: 0.7896 (tt0) cc_final: 0.7511 (tt0) REVERT: B6 144 PRO cc_start: 0.7262 (Cg_exo) cc_final: 0.7031 (Cg_endo) REVERT: B8 143 LEU cc_start: 0.8879 (mm) cc_final: 0.8598 (mm) REVERT: AC 101 ILE cc_start: 0.8890 (mm) cc_final: 0.8626 (mm) REVERT: S4 147 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8407 (mtm180) REVERT: A9 332 PHE cc_start: 0.8148 (t80) cc_final: 0.7801 (t80) REVERT: S2 376 MET cc_start: 0.8536 (tmm) cc_final: 0.8252 (ttp) REVERT: S2 392 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: V1 134 GLU cc_start: 0.7018 (mp0) cc_final: 0.6756 (mt-10) REVERT: V1 174 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6987 (mtp180) REVERT: 2 199 ILE cc_start: 0.8474 (mm) cc_final: 0.8240 (mt) REVERT: 4L 81 MET cc_start: 0.8529 (mtt) cc_final: 0.8188 (mtt) REVERT: A5 94 MET cc_start: 0.7934 (mmp) cc_final: 0.7538 (mmt) REVERT: AL 194 ASP cc_start: 0.8523 (t70) cc_final: 0.8010 (t0) outliers start: 132 outliers final: 87 residues processed: 1033 average time/residue: 0.6240 time to fit residues: 1104.1390 Evaluate side-chains 1003 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 912 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 70 ILE Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 211 THR Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 217 GLU Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 66 MET Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 184 THR Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 287 SER Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 9 THR Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 144 GLU Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 90 GLU Chi-restraints excluded: chain B8 residue 74 ASP Chi-restraints excluded: chain B8 residue 172 THR Chi-restraints excluded: chain C2 residue 50 VAL Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain S2 residue 202 LEU Chi-restraints excluded: chain S2 residue 227 MET Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 174 ARG Chi-restraints excluded: chain V1 residue 247 ASP Chi-restraints excluded: chain V1 residue 285 ASN Chi-restraints excluded: chain V1 residue 301 CYS Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 122 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 193 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 74 THR Chi-restraints excluded: chain AL residue 158 GLN Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 115 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 256 optimal weight: 0.9990 chunk 686 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 447 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 763 optimal weight: 4.9990 chunk 633 optimal weight: 0.7980 chunk 353 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 209 ASN 4 82 HIS A8 86 GLN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 50 ASN BM 68 GLN ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 65 HIS S2 92 GLN ** S2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 68187 Z= 0.562 Angle : 1.571 50.738 92095 Z= 1.014 Chirality : 0.314 6.437 9832 Planarity : 0.004 0.060 11493 Dihedral : 11.599 177.717 10375 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.03 % Allowed : 13.60 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 7942 helix: 1.13 (0.08), residues: 4168 sheet: -0.56 (0.26), residues: 414 loop : -0.40 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPS4 152 HIS 0.014 0.001 HISS8 106 PHE 0.027 0.001 PHE 2 288 TYR 0.020 0.001 TYR 5 394 ARG 0.007 0.000 ARGS8 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 943 time to evaluate : 5.672 Fit side-chains revert: symmetry clash REVERT: S6 60 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8205 (ttpp) REVERT: S1 70 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 68187 Z= 0.552 Angle : 1.568 50.691 92095 Z= 1.012 Chirality : 0.314 6.407 9832 Planarity : 0.004 0.059 11493 Dihedral : 11.397 177.849 10375 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.93 % Allowed : 14.10 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7942 helix: 1.25 (0.08), residues: 4166 sheet: -0.56 (0.26), residues: 415 loop : -0.37 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPS4 152 HIS 0.011 0.001 HISS8 106 PHE 0.027 0.001 PHE 2 288 TYR 0.021 0.001 TYR 5 394 ARG 0.006 0.000 ARGA9 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 928 time to evaluate : 5.488 Fit side-chains revert: symmetry clash REVERT: S1 70 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7658 (mp) REVERT: S1 127 MET cc_start: 0.7470 (tpp) cc_final: 0.7231 (tpp) REVERT: S1 409 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: S1 726 LYS cc_start: 0.7521 (mmmt) cc_final: 0.6978 (mmmt) REVERT: S3 90 ILE cc_start: 0.9095 (pt) cc_final: 0.8780 (pt) REVERT: S3 166 ASN cc_start: 0.8093 (t0) cc_final: 0.7830 (t0) REVERT: S8 213 ASP cc_start: 0.8062 (t70) cc_final: 0.7720 (t70) REVERT: 3 81 MET cc_start: 0.8289 (tmm) cc_final: 0.7926 (ttt) REVERT: 5 102 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6761 (mpp) REVERT: S5 38 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: B8 143 LEU cc_start: 0.8845 (mm) cc_final: 0.8532 (mm) REVERT: AC 101 ILE cc_start: 0.8896 (mm) cc_final: 0.8644 (mm) REVERT: S4 147 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8439 (mtm180) REVERT: A9 332 PHE cc_start: 0.8232 (t80) cc_final: 0.8003 (t80) REVERT: S2 376 MET cc_start: 0.8538 (tmm) cc_final: 0.8266 (ttp) REVERT: S2 392 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: V1 173 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8183 (mm) REVERT: V1 174 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7029 (mtp180) REVERT: 4L 81 MET cc_start: 0.8553 (mtt) cc_final: 0.8228 (mtt) REVERT: A5 94 MET cc_start: 0.7923 (mmp) cc_final: 0.7505 (mmt) REVERT: AL 194 ASP cc_start: 0.8535 (t70) cc_final: 0.8027 (t0) REVERT: AB 116 MET cc_start: 0.8306 (ptp) cc_final: 0.7932 (mtm) REVERT: AB 120 ASP cc_start: 0.5810 (m-30) cc_final: 0.5392 (m-30) outliers start: 134 outliers final: 104 residues processed: 1008 average time/residue: 0.6158 time to fit residues: 1071.8606 Evaluate side-chains 1022 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 911 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 65 ILE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 70 ILE Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 211 THR Chi-restraints excluded: chain S1 residue 320 MET Chi-restraints excluded: chain S1 residue 325 ASN Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 217 GLU Chi-restraints excluded: chain V2 residue 190 THR Chi-restraints excluded: chain S8 residue 66 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 184 THR Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 235 ILE Chi-restraints excluded: chain 4 residue 287 SER Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 194 MET Chi-restraints excluded: chain 5 residue 226 VAL Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 134 ILE Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 14 LEU Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 38 PHE Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 9 THR Chi-restraints excluded: chain B6 residue 22 VAL Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B6 residue 80 VAL Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 144 GLU Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain B9 residue 90 GLU Chi-restraints excluded: chain B3 residue 19 VAL Chi-restraints excluded: chain C2 residue 50 VAL Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain A9 residue 339 ILE Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 65 HIS Chi-restraints excluded: chain S2 residue 202 LEU Chi-restraints excluded: chain S2 residue 227 MET Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 173 ILE Chi-restraints excluded: chain V1 residue 174 ARG Chi-restraints excluded: chain V1 residue 285 ASN Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 50 ASP Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 74 THR Chi-restraints excluded: chain AL residue 158 GLN Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 470 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 454 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 483 optimal weight: 7.9990 chunk 518 optimal weight: 3.9990 chunk 375 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 597 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 82 HIS A8 86 GLN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 49 GLN BL 68 GLN ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 228 HIS V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN 6 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.255 68187 Z= 0.550 Angle : 1.566 50.675 92095 Z= 1.011 Chirality : 0.313 6.394 9832 Planarity : 0.003 0.059 11493 Dihedral : 11.143 178.199 10375 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.88 % Allowed : 14.41 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 7942 helix: 1.34 (0.08), residues: 4165 sheet: -0.56 (0.27), residues: 414 loop : -0.33 (0.11), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPS4 152 HIS 0.011 0.001 HISS8 106 PHE 0.027 0.001 PHE 5 307 TYR 0.025 0.001 TYRB2 33 ARG 0.007 0.000 ARGS8 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 936 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S1 70 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (mp) REVERT: S1 409 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: S3 90 ILE cc_start: 0.9073 (pt) cc_final: 0.8760 (pt) REVERT: S3 166 ASN cc_start: 0.8062 (t0) cc_final: 0.7821 (t0) REVERT: S8 213 ASP cc_start: 0.8054 (t70) cc_final: 0.7727 (t70) REVERT: 3 81 MET cc_start: 0.8243 (tmm) cc_final: 0.7917 (ttt) REVERT: 5 102 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6721 (mpp) REVERT: 5 487 LEU cc_start: 0.7730 (tp) cc_final: 0.7509 (mt) REVERT: S5 38 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7907 (m-10) REVERT: B8 143 LEU cc_start: 0.8843 (mm) cc_final: 0.8532 (mm) REVERT: AC 101 ILE cc_start: 0.8895 (mm) cc_final: 0.8644 (mm) REVERT: S4 131 MET cc_start: 0.7780 (ttp) cc_final: 0.7501 (ttp) REVERT: S4 147 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8435 (mtm180) REVERT: A9 332 PHE cc_start: 0.8233 (t80) cc_final: 0.8023 (t80) REVERT: S2 376 MET cc_start: 0.8534 (tmm) cc_final: 0.8253 (ttp) REVERT: S2 392 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: V1 173 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8023 (mm) REVERT: V1 174 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7032 (mtp180) REVERT: 4L 81 MET cc_start: 0.8553 (mtt) cc_final: 0.8232 (mtt) REVERT: A5 94 MET cc_start: 0.7930 (mmp) cc_final: 0.7504 (mmt) REVERT: AL 194 ASP cc_start: 0.8512 (t70) cc_final: 0.7960 (t0) REVERT: AB 116 MET cc_start: 0.8274 (ptp) cc_final: 0.7995 (mtm) REVERT: AB 120 ASP cc_start: 0.5725 (m-30) cc_final: 0.5456 (m-30) outliers start: 131 outliers final: 101 residues processed: 1017 average time/residue: 0.6244 time to fit residues: 1092.0714 Evaluate side-chains 1016 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 908 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 65 ILE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 70 ILE Chi-restraints excluded: chain S1 residue 110 TRP Chi-restraints excluded: chain S1 residue 169 THR Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 211 THR Chi-restraints excluded: chain S1 residue 320 MET Chi-restraints excluded: chain S1 residue 325 ASN Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 217 GLU Chi-restraints excluded: chain V2 residue 190 THR Chi-restraints excluded: chain S8 residue 66 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 223 MET Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 4 residue 437 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 5 residue 106 ILE Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 166 SER Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 226 VAL Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 14 LEU Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 38 PHE Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 9 THR Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B6 residue 80 VAL Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain B9 residue 90 GLU Chi-restraints excluded: chain BM residue 69 VAL Chi-restraints excluded: chain C2 residue 50 VAL Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 65 HIS Chi-restraints excluded: chain S2 residue 202 LEU Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 173 ILE Chi-restraints excluded: chain V1 residue 174 ARG Chi-restraints excluded: chain V1 residue 285 ASN Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 74 THR Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 87 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 691 optimal weight: 0.4980 chunk 728 optimal weight: 2.9990 chunk 664 optimal weight: 0.6980 chunk 708 optimal weight: 6.9990 chunk 426 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 556 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 640 optimal weight: 3.9990 chunk 670 optimal weight: 2.9990 chunk 706 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AN 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 191 ASN 5 304 HIS A8 86 GLN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 49 GLN B4 28 GLN ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 50 ASN ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN AL 274 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 68187 Z= 0.552 Angle : 1.568 50.690 92095 Z= 1.012 Chirality : 0.313 6.401 9832 Planarity : 0.004 0.059 11493 Dihedral : 10.959 178.488 10375 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.93 % Allowed : 14.68 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 7942 helix: 1.37 (0.08), residues: 4166 sheet: -0.54 (0.27), residues: 415 loop : -0.32 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPS4 152 HIS 0.011 0.001 HISS8 106 PHE 0.026 0.001 PHE 5 307 TYR 0.022 0.001 TYRB2 33 ARG 0.008 0.000 ARGS8 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 922 time to evaluate : 5.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S1 70 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7673 (mp) REVERT: S1 282 ASN cc_start: 0.7771 (t0) cc_final: 0.7523 (t0) REVERT: S1 409 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: S1 726 LYS cc_start: 0.7422 (mmmt) cc_final: 0.6917 (mmmt) REVERT: S3 90 ILE cc_start: 0.9072 (pt) cc_final: 0.8725 (pt) REVERT: S3 166 ASN cc_start: 0.8046 (t0) cc_final: 0.7805 (t0) REVERT: V2 238 LEU cc_start: 0.8402 (mm) cc_final: 0.8119 (tp) REVERT: S8 213 ASP cc_start: 0.8039 (t70) cc_final: 0.7710 (t70) REVERT: 3 81 MET cc_start: 0.8237 (tmm) cc_final: 0.7957 (ttt) REVERT: 5 102 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6749 (mpp) REVERT: 5 487 LEU cc_start: 0.7727 (tp) cc_final: 0.7497 (mt) REVERT: B6 117 ASN cc_start: 0.7341 (t0) cc_final: 0.7007 (t0) REVERT: B4 108 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7128 (ttm170) REVERT: B9 50 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7975 (t160) REVERT: B8 130 TYR cc_start: 0.8479 (t80) cc_final: 0.8215 (t80) REVERT: B8 143 LEU cc_start: 0.8849 (mm) cc_final: 0.8547 (mm) REVERT: AC 101 ILE cc_start: 0.8896 (mm) cc_final: 0.8647 (mm) REVERT: S4 131 MET cc_start: 0.7785 (ttp) cc_final: 0.7519 (ttp) REVERT: A9 332 PHE cc_start: 0.8252 (t80) cc_final: 0.8046 (t80) REVERT: S2 376 MET cc_start: 0.8543 (tmm) cc_final: 0.8267 (ttp) REVERT: S2 392 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: V1 173 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7856 (mm) REVERT: V1 174 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6826 (mtp180) REVERT: V1 316 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6938 (mm-30) REVERT: 4L 81 MET cc_start: 0.8548 (mtt) cc_final: 0.8217 (mtt) REVERT: A5 94 MET cc_start: 0.7949 (mmp) cc_final: 0.7526 (mmt) REVERT: AL 194 ASP cc_start: 0.8521 (t70) cc_final: 0.7968 (t0) REVERT: AB 116 MET cc_start: 0.8276 (ptp) cc_final: 0.8012 (mtm) REVERT: AB 120 ASP cc_start: 0.5719 (m-30) cc_final: 0.5454 (m-30) outliers start: 134 outliers final: 108 residues processed: 1003 average time/residue: 0.6254 time to fit residues: 1077.1797 Evaluate side-chains 1024 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 909 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 65 ILE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 70 ILE Chi-restraints excluded: chain S1 residue 110 TRP Chi-restraints excluded: chain S1 residue 169 THR Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 211 THR Chi-restraints excluded: chain S1 residue 320 MET Chi-restraints excluded: chain S1 residue 325 ASN Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 694 ARG Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 217 GLU Chi-restraints excluded: chain V2 residue 190 THR Chi-restraints excluded: chain V2 residue 194 MET Chi-restraints excluded: chain S8 residue 66 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 223 MET Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 4 residue 437 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 58 MET Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 226 VAL Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 14 LEU Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 9 THR Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B6 residue 80 VAL Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 144 GLU Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 50 ASN Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain B9 residue 90 GLU Chi-restraints excluded: chain BM residue 69 VAL Chi-restraints excluded: chain C2 residue 50 VAL Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain S2 residue 99 VAL Chi-restraints excluded: chain S2 residue 202 LEU Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 173 ILE Chi-restraints excluded: chain V1 residue 174 ARG Chi-restraints excluded: chain V1 residue 285 ASN Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 50 ASP Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 74 THR Chi-restraints excluded: chain AL residue 158 GLN Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 81 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 789 random chunks: chunk 465 optimal weight: 1.9990 chunk 749 optimal weight: 2.9990 chunk 457 optimal weight: 0.9980 chunk 355 optimal weight: 3.9990 chunk 520 optimal weight: 0.7980 chunk 786 optimal weight: 7.9990 chunk 723 optimal weight: 0.8980 chunk 625 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 483 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AN 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 274 ASN ** S1 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 304 HIS A8 86 GLN ** A1 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 49 GLN ** B5 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 65 HIS S2 92 GLN V1 193 GLN ** V1 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 68187 Z= 0.559 Angle : 1.573 50.718 92095 Z= 1.014 Chirality : 0.314 6.408 9832 Planarity : 0.004 0.059 11493 Dihedral : 10.896 178.668 10375 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.81 % Allowed : 14.84 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 7942 helix: 1.35 (0.08), residues: 4166 sheet: -0.57 (0.27), residues: 415 loop : -0.31 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRPS4 152 HIS 0.012 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.021 0.001 TYR 5 394 ARG 0.009 0.000 ARGB9 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 927 time to evaluate : 5.780 Fit side-chains revert: symmetry clash REVERT: S1 70 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7715 (mp) REVERT: S1 282 ASN cc_start: 0.7837 (t0) cc_final: 0.7554 (t0) REVERT: S1 409 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: S1 726 LYS cc_start: 0.7529 (mmmt) cc_final: 0.6990 (mmmt) REVERT: S3 90 ILE cc_start: 0.9066 (pt) cc_final: 0.8739 (pt) REVERT: S3 166 ASN cc_start: 0.8082 (t0) cc_final: 0.7815 (t0) REVERT: V2 238 LEU cc_start: 0.8433 (mm) cc_final: 0.8169 (tp) REVERT: S8 213 ASP cc_start: 0.8076 (t70) cc_final: 0.7751 (t70) REVERT: 3 35 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7667 (tttt) REVERT: 3 81 MET cc_start: 0.8236 (tmm) cc_final: 0.7976 (ttt) REVERT: 5 102 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6727 (mpp) REVERT: 5 366 MET cc_start: 0.8242 (tpp) cc_final: 0.7840 (tpt) REVERT: B6 117 ASN cc_start: 0.7401 (t0) cc_final: 0.7094 (t0) REVERT: B4 108 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.7163 (ttm170) REVERT: B8 130 TYR cc_start: 0.8500 (t80) cc_final: 0.8218 (t80) REVERT: B8 143 LEU cc_start: 0.8870 (mm) cc_final: 0.8558 (mm) REVERT: AC 101 ILE cc_start: 0.8895 (mm) cc_final: 0.8663 (mm) REVERT: S4 131 MET cc_start: 0.7798 (ttp) cc_final: 0.7516 (ttp) REVERT: A9 332 PHE cc_start: 0.8260 (t80) cc_final: 0.8059 (t80) REVERT: S2 376 MET cc_start: 0.8569 (tmm) cc_final: 0.8285 (ttp) REVERT: S2 392 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: V1 173 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7976 (mm) REVERT: V1 174 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: 4L 81 MET cc_start: 0.8552 (mtt) cc_final: 0.8227 (mtt) REVERT: A5 94 MET cc_start: 0.7984 (mmp) cc_final: 0.7625 (mmt) REVERT: AL 194 ASP cc_start: 0.8526 (t70) cc_final: 0.7970 (t0) REVERT: AB 116 MET cc_start: 0.8297 (ptp) cc_final: 0.8021 (mtm) REVERT: AB 120 ASP cc_start: 0.5693 (m-30) cc_final: 0.5435 (m-30) outliers start: 126 outliers final: 112 residues processed: 1002 average time/residue: 0.6630 time to fit residues: 1144.7749 Evaluate side-chains 1026 residues out of total 6963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 908 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 28 LEU Chi-restraints excluded: chain AN residue 65 ILE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain S1 residue 68 VAL Chi-restraints excluded: chain S1 residue 70 ILE Chi-restraints excluded: chain S1 residue 110 TRP Chi-restraints excluded: chain S1 residue 169 THR Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 211 THR Chi-restraints excluded: chain S1 residue 274 ASN Chi-restraints excluded: chain S1 residue 320 MET Chi-restraints excluded: chain S1 residue 325 ASN Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 694 ARG Chi-restraints excluded: chain S1 residue 699 THR Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 217 GLU Chi-restraints excluded: chain V2 residue 190 THR Chi-restraints excluded: chain V2 residue 194 MET Chi-restraints excluded: chain S8 residue 66 MET Chi-restraints excluded: chain S8 residue 78 THR Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 ASP Chi-restraints excluded: chain 3 residue 54 SER Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 184 ILE Chi-restraints excluded: chain 1 residue 313 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 223 MET Chi-restraints excluded: chain 4 residue 398 LEU Chi-restraints excluded: chain 4 residue 437 LEU Chi-restraints excluded: chain 5 residue 15 ILE Chi-restraints excluded: chain 5 residue 71 SER Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 5 residue 106 ILE Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 154 LEU Chi-restraints excluded: chain 5 residue 168 ASN Chi-restraints excluded: chain 5 residue 202 PHE Chi-restraints excluded: chain 5 residue 226 VAL Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 256 THR Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 399 VAL Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain AO residue 65 GLU Chi-restraints excluded: chain AO residue 100 GLU Chi-restraints excluded: chain AO residue 112 THR Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 14 LEU Chi-restraints excluded: chain S5 residue 24 TYR Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 43 LEU Chi-restraints excluded: chain B6 residue 9 THR Chi-restraints excluded: chain B6 residue 22 VAL Chi-restraints excluded: chain B6 residue 50 HIS Chi-restraints excluded: chain B6 residue 80 VAL Chi-restraints excluded: chain B4 residue 65 THR Chi-restraints excluded: chain B7 residue 87 THR Chi-restraints excluded: chain B5 residue 44 HIS Chi-restraints excluded: chain B5 residue 47 ILE Chi-restraints excluded: chain B5 residue 144 GLU Chi-restraints excluded: chain B9 residue 9 VAL Chi-restraints excluded: chain B9 residue 28 SER Chi-restraints excluded: chain B9 residue 87 CYS Chi-restraints excluded: chain B9 residue 90 GLU Chi-restraints excluded: chain BM residue 69 VAL Chi-restraints excluded: chain B8 residue 145 LEU Chi-restraints excluded: chain C2 residue 50 VAL Chi-restraints excluded: chain C2 residue 52 SER Chi-restraints excluded: chain C2 residue 108 VAL Chi-restraints excluded: chain C2 residue 113 VAL Chi-restraints excluded: chain S4 residue 79 ILE Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 143 ASP Chi-restraints excluded: chain A9 residue 191 VAL Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain S2 residue 99 VAL Chi-restraints excluded: chain S2 residue 202 LEU Chi-restraints excluded: chain S2 residue 392 GLN Chi-restraints excluded: chain S2 residue 422 SER Chi-restraints excluded: chain V1 residue 58 THR Chi-restraints excluded: chain V1 residue 173 ILE Chi-restraints excluded: chain V1 residue 174 ARG Chi-restraints excluded: chain V1 residue 285 ASN Chi-restraints excluded: chain V1 residue 349 ASP Chi-restraints excluded: chain V1 residue 397 CYS Chi-restraints excluded: chain V1 residue 398 THR Chi-restraints excluded: chain 2 residue 82 ASN Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 141 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 280 MET Chi-restraints excluded: chain 6 residue 100 PHE Chi-restraints excluded: chain 6 residue 107 SER Chi-restraints excluded: chain A5 residue 119 ILE Chi-restraints excluded: chain A3 residue 50 ASP Chi-restraints excluded: chain A3 residue 63 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain A6 residue 17 ILE Chi-restraints excluded: chain AL residue 74 THR Chi-restraints excluded: chain AL residue 158 GLN Chi-restraints excluded: chain AL residue 240 ASP Chi-restraints excluded: chain AL residue 252 ASP Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.9707 > 50: distance: 121 - 125: 21.510 distance: 125 - 126: 12.746 distance: 126 - 127: 8.087 distance: 126 - 129: 26.006 distance: 127 - 128: 43.005 distance: 127 - 134: 33.464 distance: 129 - 130: 5.795 distance: 130 - 131: 18.883 distance: 131 - 132: 12.820 distance: 131 - 133: 10.295 distance: 134 - 135: 28.339 distance: 135 - 136: 31.116 distance: 136 - 137: 37.871 distance: 136 - 138: 10.543 distance: 138 - 139: 4.555 distance: 139 - 142: 12.074 distance: 140 - 141: 8.232 distance: 140 - 147: 24.210 distance: 142 - 143: 3.747 distance: 143 - 144: 17.187 distance: 144 - 145: 9.007 distance: 145 - 146: 13.921 distance: 147 - 148: 28.145 distance: 147 - 153: 15.445 distance: 148 - 149: 31.055 distance: 148 - 151: 21.815 distance: 149 - 150: 27.947 distance: 149 - 154: 25.192 distance: 152 - 153: 33.562 distance: 154 - 155: 22.427 distance: 155 - 156: 9.792 distance: 155 - 158: 17.648 distance: 156 - 157: 9.039 distance: 156 - 165: 5.545 distance: 158 - 159: 14.284 distance: 159 - 160: 10.954 distance: 160 - 161: 11.778 distance: 161 - 162: 5.480 distance: 162 - 163: 9.062 distance: 162 - 164: 15.585 distance: 165 - 166: 19.054 distance: 166 - 167: 12.896 distance: 166 - 169: 16.209 distance: 167 - 173: 10.067 distance: 169 - 170: 4.104 distance: 170 - 171: 9.896 distance: 170 - 172: 35.718 distance: 173 - 174: 19.950 distance: 174 - 175: 24.451 distance: 174 - 177: 14.960 distance: 175 - 176: 14.883 distance: 175 - 182: 9.744 distance: 177 - 178: 18.990 distance: 178 - 179: 30.887 distance: 179 - 180: 14.997 distance: 180 - 181: 5.136 distance: 182 - 183: 18.109 distance: 182 - 188: 17.872 distance: 189 - 190: 31.875 distance: 189 - 195: 3.291 distance: 190 - 191: 8.702 distance: 190 - 193: 26.754 distance: 191 - 196: 25.616 distance: 193 - 194: 41.974 distance: 194 - 195: 37.517 distance: 196 - 197: 25.009 distance: 197 - 198: 9.439 distance: 197 - 200: 20.933 distance: 198 - 199: 19.774 distance: 198 - 207: 7.163 distance: 200 - 201: 7.790 distance: 201 - 202: 11.469 distance: 201 - 203: 38.760 distance: 202 - 204: 16.541 distance: 203 - 205: 4.807 distance: 204 - 206: 24.814 distance: 205 - 206: 15.583