Starting phenix.real_space_refine on Thu Mar 14 18:53:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esz_28582/03_2024/8esz_28582_updated.pdb" } resolution = 3.4 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= 0.089 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 62 5.49 5 S 479 5.16 5 C 44063 2.51 5 N 10976 2.21 5 O 12148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AN TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 ASP 104": "OD1" <-> "OD2" Residue "S6 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 69": "OE1" <-> "OE2" Residue "S1 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 258": "OE1" <-> "OE2" Residue "S1 GLU 283": "OE1" <-> "OE2" Residue "S1 GLU 298": "OE1" <-> "OE2" Residue "S1 GLU 327": "OE1" <-> "OE2" Residue "S1 GLU 334": "OE1" <-> "OE2" Residue "S1 TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 454": "OE1" <-> "OE2" Residue "S1 GLU 506": "OE1" <-> "OE2" Residue "S3 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 ASP 156": "OD1" <-> "OD2" Residue "S3 ASP 236": "OD1" <-> "OD2" Residue "V2 GLU 57": "OE1" <-> "OE2" Residue "V2 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 GLU 50": "OE1" <-> "OE2" Residue "S8 TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 GLU 174": "OE1" <-> "OE2" Residue "S8 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 58": "OD1" <-> "OD2" Residue "1 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 221": "OE1" <-> "OE2" Residue "1 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 366": "OE1" <-> "OE2" Residue "4 GLU 421": "OE1" <-> "OE2" Residue "4 GLU 440": "OE1" <-> "OE2" Residue "5 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 84": "OD1" <-> "OD2" Residue "5 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 GLU 39": "OE1" <-> "OE2" Residue "A8 ASP 119": "OD1" <-> "OD2" Residue "A8 GLU 139": "OE1" <-> "OE2" Residue "A8 GLU 145": "OE1" <-> "OE2" Residue "A8 ASP 151": "OD1" <-> "OD2" Residue "A8 GLU 158": "OE1" <-> "OE2" Residue "A1 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ASP 13": "OD1" <-> "OD2" Residue "AO GLU 97": "OE1" <-> "OE2" Residue "AO GLU 100": "OE1" <-> "OE2" Residue "AO GLU 134": "OE1" <-> "OE2" Residue "S5 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S5 GLU 49": "OE1" <-> "OE2" Residue "AM TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 85": "OD1" <-> "OD2" Residue "AM ASP 152": "OD1" <-> "OD2" Residue "AM GLU 166": "OE1" <-> "OE2" Residue "BL TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 64": "OE1" <-> "OE2" Residue "BL TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 143": "OE1" <-> "OE2" Residue "B4 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 GLU 39": "OE1" <-> "OE2" Residue "B4 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 GLU 91": "OE1" <-> "OE2" Residue "B7 GLU 103": "OE1" <-> "OE2" Residue "B5 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 146": "OE1" <-> "OE2" Residue "B5 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 GLU 175": "OE1" <-> "OE2" Residue "B5 GLU 179": "OE1" <-> "OE2" Residue "B9 GLU 68": "OE1" <-> "OE2" Residue "B9 GLU 92": "OE1" <-> "OE2" Residue "B9 ASP 101": "OD1" <-> "OD2" Residue "B8 TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 GLU 60": "OE1" <-> "OE2" Residue "B8 GLU 61": "OE1" <-> "OE2" Residue "B8 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 GLU 115": "OE1" <-> "OE2" Residue "B8 GLU 174": "OE1" <-> "OE2" Residue "B3 ASP 39": "OD1" <-> "OD2" Residue "AC ASP 87": "OD1" <-> "OD2" Residue "AC GLU 97": "OE1" <-> "OE2" Residue "AC ASP 120": "OD1" <-> "OD2" Residue "AC GLU 121": "OE1" <-> "OE2" Residue "AC PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 77": "OE1" <-> "OE2" Residue "C2 GLU 101": "OE1" <-> "OE2" Residue "C2 GLU 110": "OE1" <-> "OE2" Residue "A9 ASP 98": "OD1" <-> "OD2" Residue "A9 ASP 143": "OD1" <-> "OD2" Residue "A9 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 GLU 348": "OE1" <-> "OE2" Residue "A9 GLU 393": "OE1" <-> "OE2" Residue "B2 GLU 66": "OE1" <-> "OE2" Residue "S2 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ASP 60": "OD1" <-> "OD2" Residue "S2 GLU 105": "OE1" <-> "OE2" Residue "S2 ASP 107": "OD1" <-> "OD2" Residue "S2 GLU 109": "OE1" <-> "OE2" Residue "S2 GLU 161": "OE1" <-> "OE2" Residue "S2 PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ASP 451": "OD1" <-> "OD2" Residue "V1 GLU 136": "OE1" <-> "OE2" Residue "V1 GLU 180": "OE1" <-> "OE2" Residue "V1 TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 GLU 305": "OE1" <-> "OE2" Residue "V1 ASP 373": "OD1" <-> "OD2" Residue "2 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A7 ASP 7": "OD1" <-> "OD2" Residue "A7 GLU 31": "OE1" <-> "OE2" Residue "A3 ASP 22": "OD1" <-> "OD2" Residue "A3 ASP 76": "OD1" <-> "OD2" Residue "4L GLU 56": "OE1" <-> "OE2" Residue "4L ASP 88": "OD1" <-> "OD2" Residue "6 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 40": "OE1" <-> "OE2" Residue "3 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL GLU 80": "OE1" <-> "OE2" Residue "AL ASP 117": "OD1" <-> "OD2" Residue "AL TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL GLU 188": "OE1" <-> "OE2" Residue "AL TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL GLU 217": "OE1" <-> "OE2" Residue "AL TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL GLU 298": "OE1" <-> "OE2" Residue "AL TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67757 Number of models: 1 Model: "" Number of chains: 68 Chain: "AN" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1145 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "S6" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 716 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "S1" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5181 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 1 Chain: "S3" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1699 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} 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: {'PCIS': 1, 'PTRANS': 16, '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: "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: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 305} Chain: "4" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3606 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 434} 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: "5" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4606 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, '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: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1202 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 133} 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: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1281 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 9, 'TRANS': 158} Chain: "BL" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1266 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 884 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "B7" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 972 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} 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: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1148 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 680 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "C2" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 908 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} 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: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1214 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "A9" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3030 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 355} Chain: "B2" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "S2" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3427 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 403} Chain: "V3" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "V1" Number of atoms: 3361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3361 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 413} 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: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 333} Chain: "A7" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 81} Chain breaks: 1 Chain: "A3" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 519 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "4L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "6" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1404 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 170} Chain: "3" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 956 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "A5" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} 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: "A6" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 977 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "AB" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 670 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "AN" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'3PE': 2, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 168 Unusual residues: {'3PE': 1, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 230 Unusual residues: {'3PE': 4, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 82 Chain: "5" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 309 Unusual residues: {'3PE': 7, 'PC1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "AO" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'C14': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 261 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 103 Chain: "B6" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 75 Chain: "B4" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B5" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'C14': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Chain: "AC" 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'3PE': 1, 'C14': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'3PE': 1, 'D12': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A9" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'D12': 2, 'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'3PE': 1, 'CDL': 1, 'WSF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "3" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1604 SG CYSS6 87 64.434 86.667 244.665 1.00 42.18 S ATOM 1780 SG CYSS6 111 66.504 83.868 243.040 1.00 40.81 S ATOM 1802 SG CYSS6 114 67.437 87.428 242.737 1.00 39.61 S ATOM 2694 SG CYSS1 147 60.718 67.763 233.598 1.00 34.64 S ATOM 2633 SG CYSS1 138 59.735 74.381 233.704 1.00 32.53 S ATOM 2654 SG CYSS1 141 65.043 71.350 236.021 1.00 35.31 S ATOM 3056 SG CYSS1 193 61.044 58.879 240.462 1.00 36.25 S ATOM 3032 SG CYSS1 190 62.227 63.691 244.898 1.00 36.63 S ATOM 3080 SG CYSS1 196 66.341 58.659 244.204 1.00 40.00 S ATOM 3409 SG CYSS1 240 65.631 63.120 239.397 1.00 38.29 S ATOM 2133 SG CYSS1 74 55.879 54.554 239.732 1.00 38.93 S ATOM 2218 SG CYSS1 85 54.110 57.353 238.608 1.00 41.07 S ATOM 2243 SG CYSS1 88 50.243 53.268 236.522 1.00 41.16 S ATOM 2344 SG CYSS1 102 52.800 50.947 238.147 1.00 44.47 S ATOM 9563 SG CYSV2 128 44.065 64.966 271.066 1.00 75.30 S ATOM 9597 SG CYSV2 133 41.092 64.532 273.080 1.00 75.25 S ATOM 9878 SG CYSV2 169 43.028 60.268 268.351 1.00 73.37 S ATOM 9901 SG CYSV2 173 39.727 60.118 270.462 1.00 79.98 S ATOM 10870 SG CYSS7 97 64.337 95.493 203.362 1.00 30.12 S ATOM 11371 SG CYSS7 161 65.883 89.773 203.200 1.00 26.05 S ATOM 11602 SG CYSS7 191 63.337 92.255 208.226 1.00 29.30 S ATOM 10864 SG CYSS7 96 60.539 92.669 202.402 1.00 31.21 S ATOM 12882 SG CYSS8 160 61.353 87.924 215.787 1.00 27.90 S ATOM 12856 SG CYSS8 157 66.932 91.175 214.860 1.00 26.56 S ATOM 12903 SG CYSS8 163 64.876 89.001 220.915 1.00 27.11 S ATOM 12628 SG CYSS8 128 66.967 84.878 216.228 1.00 25.34 S ATOM 12577 SG CYSS8 121 65.838 80.922 229.076 1.00 27.13 S ATOM 12932 SG CYSS8 167 64.771 87.043 228.725 1.00 29.40 S ATOM 12558 SG CYSS8 118 71.053 85.196 229.294 1.00 29.39 S ATOM 12600 SG CYSS8 124 67.772 84.128 223.778 1.00 26.09 S ATOM 51975 SG CYSV1 397 48.927 57.387 247.066 1.00 39.86 S ATOM 51995 SG CYSV1 400 47.295 60.566 251.592 1.00 41.43 S ATOM 52317 SG CYSV1 440 46.958 53.928 252.287 1.00 46.83 S ATOM 51956 SG CYSV1 394 52.577 56.640 252.805 1.00 46.13 S Time building chain proxies: 26.08, per 1000 atoms: 0.38 Number of scatterers: 67757 At special positions: 0 Unit cell: (133.76, 190.96, 303.6, 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 479 16.00 P 62 15.00 O 12148 8.00 N 10976 7.00 C 44063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.02 Simple disulfide: pdb=" SG CYSA8 80 " - pdb=" SG CYSA8 113 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 90 " - pdb=" SG CYSA8 103 " distance=2.04 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=2.04 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 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.74 Conformation dependent library (CDL) restraints added in 9.1 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 128 " pdb="FE1 FESV2 301 " - pdb=" SG CYSV2 133 " pdb="FE2 FESV2 301 " - pdb=" SG CYSV2 173 " pdb="FE2 FESV2 301 " - pdb=" SG CYSV2 169 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 134 " 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=" SF4S1 802 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 196 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 193 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 240 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 190 " pdb=" SF4S7 301 " pdb="FE1 SF4S7 301 " - pdb=" SG CYSS7 97 " pdb="FE4 SF4S7 301 " - pdb=" SG CYSS7 96 " pdb="FE2 SF4S7 301 " - pdb=" SG CYSS7 161 " pdb="FE3 SF4S7 301 " - pdb=" SG CYSS7 191 " pdb=" SF4S8 301 " pdb="FE3 SF4S8 301 " - pdb=" SG CYSS8 163 " pdb="FE2 SF4S8 301 " - pdb=" SG CYSS8 157 " pdb="FE2 SF4S8 301 " - pdb=" NE2 HISS8 106 " 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="FE1 SF4S8 302 " - pdb=" SG CYSS8 121 " pdb="FE3 SF4S8 302 " - pdb=" SG CYSS8 118 " pdb="FE2 SF4S8 302 " - pdb=" SG CYSS8 167 " pdb=" SF4V1 502 " pdb="FE2 SF4V1 502 " - pdb=" SG CYSV1 400 " pdb="FE4 SF4V1 502 " - pdb=" SG CYSV1 394 " pdb="FE1 SF4V1 502 " - pdb=" SG CYSV1 397 " pdb="FE3 SF4V1 502 " - pdb=" SG CYSV1 440 " 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 114 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 111 " Number of angles added : 3 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 28 sheets defined 50.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.71 Creating SS restraints... Processing helix chain 'AN' and resid 7 through 20 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: 3.854A 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 46 through 48 No H-bonds generated for 'chain 'S1' and resid 46 through 48' Processing helix chain 'S1' and resid 59 through 66 Processing helix chain 'S1' and resid 117 through 131 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 154 Processing helix chain 'S1' and resid 164 through 166 No H-bonds generated for 'chain 'S1' and resid 164 through 166' Processing helix chain 'S1' and resid 187 through 189 No H-bonds generated for 'chain 'S1' and resid 187 through 189' 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 302 through 305 No H-bonds generated for 'chain 'S1' and resid 302 through 305' 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 396 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 423 through 435 Processing helix chain 'S1' and resid 461 through 468 Processing helix chain 'S1' and resid 472 through 479 Processing helix chain 'S1' and resid 489 through 493 Processing helix chain 'S1' and resid 496 through 510 removed outlier: 3.565A pdb=" N ILES1 500 " --> pdb=" O ASPS1 496 " (cutoff:3.500A) Processing helix chain 'S1' and resid 528 through 534 Processing helix chain 'S1' and resid 540 through 546 removed outlier: 4.150A pdb=" N VALS1 544 " --> pdb=" O ALAS1 540 " (cutoff:3.500A) Processing helix chain 'S1' and resid 625 through 636 Processing helix chain 'S1' and resid 645 through 655 Processing helix chain 'S1' and resid 657 through 659 No H-bonds generated for 'chain 'S1' and resid 657 through 659' 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 726 Processing helix chain 'S3' and resid 54 through 70 Processing helix chain 'S3' and resid 95 through 104 removed outlier: 4.170A pdb=" N LEUS3 99 " --> pdb=" O VALS3 95 " (cutoff:3.500A) Processing helix chain 'S3' and resid 158 through 160 No H-bonds generated for 'chain 'S3' and resid 158 through 160' Processing helix chain 'S3' and resid 164 through 175 removed outlier: 5.349A pdb=" N GLUS3 169 " --> pdb=" O ASNS3 166 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N METS3 175 " --> pdb=" O ILES3 172 " (cutoff:3.500A) Processing helix chain 'V2' and resid 50 through 59 Processing helix chain 'V2' and resid 68 through 80 removed outlier: 3.951A pdb=" N ILEV2 73 " --> pdb=" O GLYV2 70 " (cutoff:3.500A) Proline residue: V2 74 - end of helix 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 201 Processing helix chain 'S7' and resid 46 through 51 Processing helix chain 'S7' and resid 67 through 84 Processing helix chain 'S7' and resid 96 through 105 Processing helix chain 'S7' and resid 111 through 114 Processing helix chain 'S7' and resid 139 through 148 Processing helix chain 'S7' and resid 160 through 164 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 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 82 Processing helix chain 'S8' and resid 123 through 127 Processing helix chain 'S8' and resid 162 through 166 Processing helix chain 'S8' and resid 186 through 188 No H-bonds generated for 'chain 'S8' and resid 186 through 188' Processing helix chain 'S8' and resid 192 through 201 Processing helix chain 'S8' and resid 203 through 211 Processing helix chain '1' and resid 3 through 38 removed outlier: 3.501A pdb=" N ILE 1 7 " --> pdb=" O TYR 1 3 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY 1 36 " --> pdb=" O ARG 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 52 through 62 Proline residue: 1 55 - end of helix removed outlier: 3.689A pdb=" N ILE 1 60 " --> pdb=" O CYS 1 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS 1 61 " --> pdb=" O ASP 1 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 1 62 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 78 No H-bonds generated for 'chain '1' and resid 75 through 78' Processing helix chain '1' and resid 81 through 95 removed outlier: 4.555A pdb=" N TRP 1 93 " --> pdb=" O SER 1 89 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET 1 94 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS 1 95 " --> pdb=" O PHE 1 91 " (cutoff:3.500A) Processing helix chain '1' and resid 108 through 128 removed outlier: 3.770A pdb=" N VAL 1 120 " --> pdb=" O THR 1 116 " (cutoff:3.500A) Processing helix chain '1' and resid 133 through 164 removed outlier: 5.136A pdb=" N VAL 1 151 " --> pdb=" O ILE 1 147 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER 1 152 " --> pdb=" O SER 1 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 1 163 " --> pdb=" O SER 1 159 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 176 removed outlier: 3.719A pdb=" N PHE 1 174 " --> pdb=" O TYR 1 171 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR 1 175 " --> pdb=" O PHE 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 199 Processing helix chain '1' and resid 217 through 219 No H-bonds generated for 'chain '1' and resid 217 through 219' Processing helix chain '1' and resid 226 through 248 Processing helix chain '1' and resid 257 through 274 removed outlier: 3.754A pdb=" N ARG 1 274 " --> pdb=" O PHE 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 288 Processing helix chain '1' and resid 293 through 314 removed outlier: 3.531A pdb=" N LEU 1 314 " --> pdb=" O LEU 1 310 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 14 Proline residue: 4 13 - end of helix Processing helix chain '4' and resid 21 through 37 Processing helix chain '4' and resid 56 through 75 Processing helix chain '4' and resid 78 through 82 removed outlier: 3.516A pdb=" N HIS 4 82 " --> pdb=" O MET 4 78 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 78 through 82' Processing helix chain '4' and resid 86 through 104 Processing helix chain '4' and resid 109 through 129 removed outlier: 3.875A pdb=" N LEU 4 120 " --> pdb=" O PHE 4 116 " (cutoff:3.500A) removed outlier: 4.398A 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: 4.178A pdb=" N LEU 4 137 " --> pdb=" O PRO 4 134 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN 4 138 " --> pdb=" O GLU 4 135 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY 4 140 " --> pdb=" O LEU 4 137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU 4 141 " --> pdb=" O GLN 4 138 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 4 143 " --> pdb=" O GLY 4 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 4 144 " --> pdb=" O LEU 4 141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 4 145 " --> pdb=" O TYR 4 142 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR 4 146 " --> pdb=" O LEU 4 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR 4 147 " --> pdb=" O LEU 4 144 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU 4 149 " --> pdb=" O TYR 4 146 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 4 150 " --> pdb=" O THR 4 147 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU 4 152 " --> pdb=" O LEU 4 149 " (cutoff:3.500A) Proline residue: 4 153 - end of helix removed outlier: 3.520A pdb=" N MET 4 162 " --> pdb=" O PHE 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 194 removed outlier: 4.153A pdb=" N ALA 4 190 " --> pdb=" O CYS 4 186 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE 4 191 " --> pdb=" O LEU 4 187 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 210 Proline residue: 4 205 - end of helix removed outlier: 4.121A pdb=" N VAL 4 209 " --> pdb=" O LYS 4 206 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU 4 210 " --> pdb=" O ALA 4 207 " (cutoff:3.500A) Processing helix chain '4' and resid 213 through 220 removed outlier: 6.488A pdb=" N ILE 4 218 " --> pdb=" O SER 4 214 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU 4 219 " --> pdb=" O GLY 4 215 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 237 removed outlier: 4.134A pdb=" N MET 4 231 " --> pdb=" O GLY 4 227 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER 4 236 " --> pdb=" O LEU 4 232 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE 4 237 " --> pdb=" O ARG 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 239 through 255 removed outlier: 5.735A pdb=" N PHE 4 247 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL 4 248 " --> pdb=" O LYS 4 244 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP 4 249 " --> pdb=" O TYR 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 259 through 266 removed outlier: 3.736A pdb=" N LEU 4 265 " --> pdb=" O SER 4 261 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG 4 266 " --> pdb=" O LEU 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 290 removed outlier: 3.587A pdb=" N ILE 4 274 " --> pdb=" O LEU 4 270 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL 4 279 " --> pdb=" O ALA 4 275 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 4 281 " --> pdb=" O SER 4 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET 4 282 " --> pdb=" O SER 4 278 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 4 290 " --> pdb=" O LEU 4 286 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 325 removed outlier: 3.816A pdb=" N ASN 4 319 " --> pdb=" O PHE 4 315 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 4 320 " --> pdb=" O CYS 4 316 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER 4 321 " --> pdb=" O LEU 4 317 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR 4 322 " --> pdb=" O ALA 4 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG 4 324 " --> pdb=" O VAL 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 341 through 354 removed outlier: 4.082A pdb=" N LEU 4 345 " --> pdb=" O PRO 4 341 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP 4 346 " --> pdb=" O SER 4 342 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA 4 353 " --> pdb=" O LEU 4 349 " (cutoff:3.500A) Processing helix chain '4' and resid 361 through 376 removed outlier: 3.655A pdb=" N SER 4 368 " --> pdb=" O LEU 4 364 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN 4 371 " --> pdb=" O ILE 4 367 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 4 373 " --> pdb=" O LEU 4 369 " (cutoff:3.500A) Processing helix chain '4' and resid 379 through 402 removed outlier: 3.576A pdb=" N ILE 4 382 " --> pdb=" O ILE 4 379 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU 4 383 " --> pdb=" O SER 4 380 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 4 385 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE 4 386 " --> pdb=" O LEU 4 383 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER 4 388 " --> pdb=" O SER 4 385 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE 4 389 " --> pdb=" O PHE 4 386 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE 4 390 " --> pdb=" O LEU 4 387 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA 4 392 " --> pdb=" O PHE 4 389 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR 4 395 " --> pdb=" O ALA 4 392 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU 4 396 " --> pdb=" O ALA 4 393 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU 4 398 " --> pdb=" O THR 4 395 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR 4 399 " --> pdb=" O LEU 4 396 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE 4 401 " --> pdb=" O LEU 4 398 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 4 402 " --> pdb=" O TYR 4 399 " (cutoff:3.500A) Processing helix chain '4' and resid 419 through 434 removed outlier: 3.725A pdb=" N HIS 4 428 " --> pdb=" O LEU 4 424 " (cutoff:3.500A) Proline residue: 4 431 - end of helix Processing helix chain '4' and resid 439 through 443 removed outlier: 3.603A pdb=" N MET 4 443 " --> pdb=" O GLU 4 440 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 31 removed outlier: 3.557A pdb=" N TYR 5 27 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 5 29 " --> pdb=" O SER 5 25 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU 5 30 " --> pdb=" O LEU 5 26 " (cutoff:3.500A) Processing helix chain '5' and resid 57 through 81 removed outlier: 4.531A pdb=" N GLU 5 79 " --> pdb=" O PHE 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 105 Processing helix chain '5' and resid 110 through 128 removed outlier: 3.669A pdb=" N GLY 5 119 " --> pdb=" O LEU 5 115 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 163 removed outlier: 4.158A pdb=" N GLY 5 150 " --> pdb=" O SER 5 146 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 5 162 " --> pdb=" O ILE 5 158 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN 5 163 " --> pdb=" O ALA 5 159 " (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 197 Processing helix chain '5' and resid 205 through 211 removed outlier: 4.461A pdb=" N ALA 5 211 " --> pdb=" O PRO 5 207 " (cutoff:3.500A) Processing helix chain '5' and resid 214 through 222 Processing helix chain '5' and resid 225 through 235 removed outlier: 4.078A pdb=" N GLY 5 229 " --> pdb=" O LEU 5 225 " (cutoff:3.500A) removed outlier: 4.350A 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 removed outlier: 3.672A pdb=" N GLY 5 254 " --> pdb=" O LEU 5 250 " (cutoff:3.500A) Processing helix chain '5' and resid 270 through 290 Processing helix chain '5' and resid 294 through 321 removed outlier: 3.748A pdb=" N THR 5 303 " --> pdb=" O PHE 5 299 " (cutoff:3.500A) 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 341 through 353 Processing helix chain '5' and resid 359 through 373 removed outlier: 3.904A pdb=" N SER 5 363 " --> pdb=" O ALA 5 359 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET 5 366 " --> pdb=" O TYR 5 362 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER 5 372 " --> pdb=" O LEU 5 368 " (cutoff:3.500A) Processing helix chain '5' and resid 378 through 402 removed outlier: 3.747A pdb=" N TYR 5 385 " --> pdb=" O PHE 5 381 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 440 removed outlier: 4.013A pdb=" N GLY 5 425 " --> pdb=" O ILE 5 421 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY 5 437 " --> pdb=" O SER 5 433 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N SER 5 438 " --> pdb=" O ILE 5 434 " (cutoff:3.500A) 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 Processing helix chain '5' and resid 485 through 488 No H-bonds generated for 'chain '5' and resid 485 through 488' Processing helix chain '5' and resid 490 through 496 removed outlier: 4.175A pdb=" N PHE 5 495 " --> pdb=" O ASN 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 498 through 507 removed outlier: 3.581A pdb=" N MET 5 502 " --> pdb=" O MET 5 499 " (cutoff:3.500A) Proline residue: 5 503 - end of helix removed outlier: 4.199A pdb=" N SER 5 506 " --> pdb=" O PRO 5 503 " (cutoff:3.500A) Processing helix chain '5' and resid 511 through 524 removed outlier: 3.542A pdb=" N TYR 5 517 " --> pdb=" O TYR 5 513 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN 5 519 " --> pdb=" O LEU 5 515 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL 5 522 " --> pdb=" O GLY 5 518 " (cutoff:3.500A) Processing helix chain '5' and resid 529 through 532 No H-bonds generated for 'chain '5' and resid 529 through 532' Processing helix chain '5' and resid 535 through 553 removed outlier: 3.680A pdb=" N HIS 5 553 " --> pdb=" O LEU 5 549 " (cutoff:3.500A) Processing helix chain '5' and resid 557 through 576 removed outlier: 3.575A pdb=" N LEU 5 575 " --> pdb=" O LEU 5 571 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE 5 576 " --> pdb=" O LEU 5 572 " (cutoff:3.500A) Processing helix chain 'A8' and resid 24 through 28 Processing helix chain 'A8' and resid 31 through 37 removed outlier: 3.595A pdb=" N GLYA8 35 " --> pdb=" O ALAA8 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYSA8 36 " --> pdb=" O PHEA8 32 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLNA8 37 " --> pdb=" O HISA8 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A8' and resid 31 through 37' Processing helix chain 'A8' and resid 39 through 52 Processing helix chain 'A8' and resid 59 through 78 Processing helix chain 'A8' and resid 81 through 93 Processing helix chain 'A8' and resid 105 through 117 Processing helix chain 'A1' and resid 2 through 5 removed outlier: 3.507A pdb=" N ILEA1 5 " --> pdb=" O TRPA1 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A1' and resid 2 through 5' Processing helix chain 'A1' and resid 10 through 15 Processing helix chain 'A1' and resid 18 through 30 removed outlier: 4.342A pdb=" N META1 23 " --> pdb=" O PROA1 19 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYSA1 28 " --> pdb=" O TYRA1 24 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N META1 30 " --> pdb=" O LEUA1 26 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 54 Processing helix chain 'AO' and resid 36 through 103 Proline residue: AO 77 - end of helix removed outlier: 3.937A pdb=" N LYSAO 103 " --> pdb=" O ALAAO 99 " (cutoff:3.500A) 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 147 Processing helix chain 'AO' and resid 150 through 153 No H-bonds generated for 'chain 'AO' and resid 150 through 153' Processing helix chain 'S5' and resid 10 through 17 removed outlier: 4.137A pdb=" N LEUS5 14 " --> pdb=" O LEUS5 11 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLYS5 16 " --> pdb=" O ASPS5 13 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYSS5 17 " --> pdb=" O LEUS5 14 " (cutoff:3.500A) Processing helix chain 'S5' and resid 28 through 40 Processing helix chain 'S5' and resid 46 through 49 No H-bonds generated for 'chain 'S5' and resid 46 through 49' Processing helix chain 'S5' and resid 51 through 61 Processing helix chain 'S5' and resid 64 through 83 removed outlier: 3.661A pdb=" N ARGS5 77 " --> pdb=" O METS5 73 " (cutoff:3.500A) Processing helix chain 'AM' and resid 18 through 40 Processing helix chain 'AM' and resid 49 through 80 removed outlier: 3.621A pdb=" N LEUAM 53 " --> pdb=" O TYRAM 49 " (cutoff:3.500A) Proline residue: AM 62 - end of helix Processing helix chain 'AM' and resid 87 through 104 Processing helix chain 'AM' and resid 107 through 130 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: 3.861A pdb=" N GLUBL 64 " --> pdb=" O VALBL 60 " (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 120 Processing helix chain 'BL' and resid 129 through 145 Processing helix chain 'B6' and resid 19 through 22 removed outlier: 4.173A 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 25 through 28 No H-bonds generated for 'chain 'B6' and resid 25 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 removed outlier: 3.568A pdb=" N VALB6 77 " --> pdb=" O PROB6 73 " (cutoff:3.500A) Processing helix chain 'B6' and resid 82 through 85 No H-bonds generated for 'chain 'B6' and resid 82 through 85' Processing helix chain 'B6' and resid 87 through 116 removed outlier: 3.818A pdb=" N THRB6 92 " --> pdb=" O GLNB6 88 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VALB6 93 " --> pdb=" O ARGB6 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLYB6 98 " --> pdb=" O ARGB6 94 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALAB6 100 " --> pdb=" O TRPB6 96 " (cutoff:3.500A) Processing helix chain 'B6' and resid 152 through 154 No H-bonds generated for 'chain 'B6' and resid 152 through 154' Processing helix chain 'B4' and resid 8 through 28 Processing helix chain 'B4' and resid 32 through 35 No H-bonds generated for 'chain 'B4' and resid 32 through 35' Processing helix chain 'B4' and resid 46 through 56 Processing helix chain 'B4' and resid 59 through 61 No H-bonds generated for 'chain 'B4' and resid 59 through 61' Processing helix chain 'B4' and resid 66 through 75 Processing helix chain 'B4' and resid 77 through 100 Processing helix chain 'B7' and resid 3 through 9 Processing helix chain 'B7' and resid 41 through 46 Processing helix chain 'B7' and resid 59 through 70 Processing helix chain 'B7' and resid 79 through 114 Processing helix chain 'B5' and resid 53 through 82 Proline residue: B5 72 - end of helix Processing helix chain 'B5' and resid 107 through 115 Processing helix chain 'B5' and resid 120 through 154 removed outlier: 3.568A pdb=" N ARGB5 154 " --> pdb=" O LYSB5 150 " (cutoff:3.500A) Processing helix chain 'B5' and resid 168 through 182 removed outlier: 3.996A pdb=" N ALAB5 182 " --> pdb=" O ASPB5 178 " (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: 4.130A pdb=" N GLNB9 110 " --> pdb=" O LEUB9 106 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYRB9 111 " --> pdb=" O GLUB9 107 " (cutoff:3.500A) Proline residue: B9 112 - end of helix Processing helix chain 'BM' and resid 47 through 51 Processing helix chain 'BM' and resid 68 through 82 removed outlier: 4.435A pdb=" N LYSBM 76 " --> pdb=" O ARGBM 72 " (cutoff:3.500A) Processing helix chain 'BM' and resid 89 through 95 Processing helix chain 'BM' and resid 104 through 119 removed outlier: 3.608A 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 128 through 148 removed outlier: 3.982A pdb=" N PHEB8 132 " --> pdb=" O ASNB8 128 " (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 Processing helix chain 'B3' and resid 40 through 43 removed outlier: 4.361A pdb=" N ARGB3 43 " --> pdb=" O PROB3 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 40 through 43' Processing helix chain 'B3' and resid 57 through 65 Processing helix chain 'B3' and resid 69 through 86 removed outlier: 4.099A pdb=" N ALAB3 85 " --> pdb=" O ALAB3 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUB3 86 " --> pdb=" O VALB3 82 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 85 Processing helix chain 'AC' and resid 108 through 122 removed outlier: 4.042A pdb=" N VALAC 112 " --> pdb=" O SERAC 108 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUAC 113 " --> pdb=" O LEUAC 109 " (cutoff:3.500A) Processing helix chain 'AC' and resid 128 through 133 Processing helix chain 'AC' and resid 137 through 148 removed outlier: 3.533A pdb=" N LYSAC 147 " --> pdb=" O TYRAC 143 " (cutoff:3.500A) Processing helix 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 'C2' and resid 105 through 107 No H-bonds generated for 'chain 'C2' and resid 105 through 107' Processing helix chain 'B1' and resid 7 through 32 removed outlier: 3.825A pdb=" N LEUB1 10 " --> pdb=" O LYSB1 7 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALAB1 13 " --> pdb=" O LEUB1 10 " (cutoff:3.500A) Proline residue: B1 15 - end of helix Processing helix chain 'S4' and resid 40 through 43 No H-bonds generated for 'chain 'S4' and resid 40 through 43' Processing helix chain 'S4' and resid 47 through 56 Processing helix chain 'S4' and resid 69 through 72 No H-bonds generated for 'chain 'S4' and resid 69 through 72' Processing helix chain 'S4' and resid 76 through 81 Processing helix chain 'S4' and resid 138 through 148 Processing helix chain 'A9' and resid 74 through 85 removed outlier: 4.307A pdb=" N TYRA9 78 " --> pdb=" O PHEA9 74 " (cutoff:3.500A) Processing helix chain 'A9' and resid 98 through 105 removed outlier: 4.822A pdb=" N ARGA9 103 " --> pdb=" O SERA9 99 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEUA9 104 " --> pdb=" O ASPA9 100 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYSA9 105 " --> pdb=" O VALA9 101 " (cutoff:3.500A) Processing helix chain 'A9' and resid 123 through 129 Processing helix chain 'A9' and resid 151 through 155 Processing helix chain 'A9' and resid 157 through 168 Processing helix chain 'A9' and resid 196 through 211 Processing helix chain 'A9' and resid 230 through 234 removed outlier: 3.527A pdb=" N TYRA9 234 " --> pdb=" O PHEA9 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A9' and resid 230 through 234' Processing helix chain 'A9' and resid 248 through 251 Processing helix chain 'A9' and resid 261 through 273 Processing helix chain 'A9' and resid 275 through 277 No H-bonds generated for 'chain 'A9' and resid 275 through 277' Processing helix chain 'A9' and resid 292 through 302 Processing helix chain 'A9' and resid 321 through 333 removed outlier: 3.753A pdb=" N LEUA9 325 " --> pdb=" O PROA9 321 " (cutoff:3.500A) 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 373 through 380 Proline residue: A9 378 - end of helix Processing helix chain 'A9' and resid 408 through 415 Processing helix chain 'B2' and resid 42 through 65 Processing helix chain 'B2' and resid 68 through 71 No H-bonds generated for 'chain 'B2' and resid 68 through 71' Processing helix chain 'B2' and resid 84 through 87 No H-bonds generated for 'chain 'B2' and resid 84 through 87' Processing helix chain 'S2' and resid 46 through 49 No H-bonds generated for 'chain 'S2' and resid 46 through 49' 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 94 through 96 No H-bonds generated for 'chain 'S2' and resid 94 through 96' Processing helix chain 'S2' and resid 125 through 131 removed outlier: 3.653A pdb=" N TYRS2 131 " --> pdb=" O LYSS2 127 " (cutoff:3.500A) Processing helix chain 'S2' and resid 134 through 144 Proline residue: S2 139 - end of helix removed outlier: 4.113A pdb=" N ASPS2 142 " --> pdb=" O LEUS2 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARGS2 143 " --> pdb=" O PROS2 139 " (cutoff:3.500A) Processing helix chain 'S2' and resid 150 through 164 Processing helix chain 'S2' and resid 170 through 199 Processing helix chain 'S2' and resid 203 through 223 removed outlier: 4.595A pdb=" N GLUS2 211 " --> pdb=" O TRPS2 207 " (cutoff:3.500A) Processing helix chain 'S2' and resid 245 through 267 removed outlier: 4.308A pdb=" N ALAS2 257 " --> pdb=" O ALAS2 253 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLUS2 258 " --> pdb=" O SERS2 254 " (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 301 removed outlier: 4.303A pdb=" N GLYS2 300 " --> pdb=" O METS2 297 " (cutoff:3.500A) Processing helix chain 'S2' and resid 331 through 354 Processing helix chain 'S2' and resid 373 through 378 Processing helix chain 'S2' and resid 381 through 391 Processing helix chain 'S2' and resid 432 through 443 removed outlier: 4.224A pdb=" N HISS2 436 " --> pdb=" O PROS2 432 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLUS2 441 " --> pdb=" O LEUS2 437 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYSS2 442 " --> pdb=" O ALAS2 438 " (cutoff:3.500A) Processing helix chain 'S2' and resid 449 through 458 Processing helix chain 'S2' and resid 463 through 467 Processing helix chain 'V3' and resid 91 through 97 Processing helix chain 'V1' and resid 68 through 74 removed outlier: 3.580A pdb=" N LYSV1 73 " --> pdb=" O LYSV1 69 " (cutoff:3.500A) 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 115 Processing helix chain 'V1' and resid 141 through 148 Processing helix chain 'V1' and resid 150 through 164 Processing helix chain 'V1' and resid 179 through 194 Processing helix chain 'V1' and resid 220 through 222 No H-bonds generated for 'chain 'V1' and resid 220 through 222' 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 274 through 277 No H-bonds generated for 'chain 'V1' and resid 274 through 277' Processing helix chain 'V1' and resid 311 through 318 removed outlier: 3.601A pdb=" N HISV1 318 " --> pdb=" O LEUV1 314 " (cutoff:3.500A) Processing helix chain 'V1' and resid 344 through 349 removed outlier: 4.475A 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 392 Processing helix chain 'V1' and resid 398 through 416 removed outlier: 4.147A pdb=" N ILEV1 404 " --> pdb=" O CYSV1 400 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLYV1 405 " --> pdb=" O ARGV1 401 " (cutoff:3.500A) Processing helix chain 'V1' and resid 421 through 433 removed outlier: 4.436A pdb=" N ASPV1 425 " --> pdb=" O ALAV1 422 " (cutoff:3.500A) Processing helix chain 'V1' and resid 442 through 472 Proline residue: V1 449 - end of helix Proline residue: V1 459 - end of helix Processing helix chain '2' and resid 5 through 22 Processing helix chain '2' and resid 27 through 43 Proline residue: 2 43 - end of helix Processing helix chain '2' and resid 51 through 81 removed outlier: 4.164A pdb=" N GLU 2 55 " --> pdb=" O LEU 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 105 removed outlier: 3.517A pdb=" N LYS 2 104 " --> pdb=" O ALA 2 100 " (cutoff:3.500A) Processing helix chain '2' and resid 112 through 120 removed outlier: 4.052A pdb=" N ASN 2 116 " --> pdb=" O PHE 2 112 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU 2 119 " --> pdb=" O PRO 2 115 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY 2 120 " --> pdb=" O ASN 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 130 Processing helix chain '2' and resid 132 through 143 removed outlier: 4.473A pdb=" N ALA 2 136 " --> pdb=" O GLN 2 133 " (cutoff:3.500A) Proline residue: 2 137 - end of helix removed outlier: 3.583A pdb=" N SER 2 142 " --> pdb=" O MET 2 139 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR 2 143 " --> pdb=" O LEU 2 140 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 166 removed outlier: 3.703A pdb=" N ALA 2 162 " --> pdb=" O VAL 2 158 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY 2 165 " --> pdb=" O GLY 2 161 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU 2 166 " --> pdb=" O ALA 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 189 removed outlier: 3.685A pdb=" N TRP 2 185 " --> pdb=" O ASN 2 181 " (cutoff:3.500A) Processing helix chain '2' and resid 194 through 218 removed outlier: 3.989A pdb=" N PHE 2 213 " --> pdb=" O PHE 2 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET 2 214 " --> pdb=" O VAL 2 210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 2 215 " --> pdb=" O LEU 2 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE 2 218 " --> pdb=" O MET 2 214 " (cutoff:3.500A) Processing helix chain '2' and resid 223 through 227 removed outlier: 3.716A 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: 3.935A pdb=" N MET 2 242 " --> pdb=" O PHE 2 238 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN 2 243 " --> pdb=" O THR 2 239 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE 2 244 " --> pdb=" O LEU 2 240 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU 2 245 " --> pdb=" O PHE 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 254 through 268 Proline residue: 2 258 - end of helix removed outlier: 3.530A pdb=" N GLN 2 264 " --> pdb=" O LEU 2 261 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU 2 268 " --> pdb=" O GLN 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 297 removed outlier: 3.569A pdb=" N LEU 2 283 " --> pdb=" O MET 2 279 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE 2 284 " --> pdb=" O MET 2 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG 2 291 " --> pdb=" O PHE 2 287 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE 2 292 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER 2 295 " --> pdb=" O ARG 2 291 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA 2 296 " --> pdb=" O ILE 2 292 " (cutoff:3.500A) Processing helix chain '2' and resid 315 through 326 removed outlier: 3.685A pdb=" N ILE 2 322 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET 2 323 " --> pdb=" O MET 2 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE 2 325 " --> pdb=" O MET 2 321 " (cutoff:3.500A) Processing helix chain '2' and resid 330 through 333 Processing helix chain 'A7' and resid 10 through 20 Processing helix chain 'A7' and resid 72 through 79 Processing helix chain 'A3' and resid 12 through 19 Processing helix chain 'A3' and resid 21 through 46 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 21 Processing helix chain '4L' and resid 28 through 52 Processing helix chain '4L' and resid 57 through 84 removed outlier: 3.559A pdb=" N MET4L 61 " --> pdb=" O TYR4L 58 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE4L 63 " --> pdb=" O SER4L 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE4L 66 " --> pdb=" O PHE4L 63 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET4L 81 " --> pdb=" O LEU4L 78 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 19 Processing helix chain '6' and resid 23 through 44 removed outlier: 3.757A pdb=" N MET 6 44 " --> pdb=" O LEU 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 49 through 71 removed outlier: 4.063A pdb=" N MET 6 62 " --> pdb=" O PHE 6 58 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 6 63 " --> pdb=" O LEU 6 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL 6 64 " --> pdb=" O GLY 6 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 82 through 100 Processing helix chain '6' and resid 134 through 136 No H-bonds generated for 'chain '6' and resid 134 through 136' Processing helix chain '6' and resid 142 through 162 Processing helix chain '6' and resid 165 through 167 No H-bonds generated for 'chain '6' and resid 165 through 167' Processing helix chain '3' and resid 2 through 24 Processing helix chain '3' and resid 40 through 42 No H-bonds generated for 'chain '3' and resid 40 through 42' Processing helix chain '3' and resid 58 through 73 removed outlier: 3.623A pdb=" N LEU 3 73 " --> pdb=" O VAL 3 69 " (cutoff:3.500A) Processing helix chain '3' and resid 75 through 83 removed outlier: 4.164A pdb=" N ILE 3 78 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 3 80 " --> pdb=" O MET 3 77 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET 3 81 " --> pdb=" O ILE 3 78 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS 3 82 " --> pdb=" O ILE 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 110 Processing helix chain 'A5' and resid 20 through 35 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: 4.065A pdb=" N LEUA5 95 " --> pdb=" O ALAA5 91 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLYA5 96 " --> pdb=" O ARGA5 92 " (cutoff:3.500A) Processing helix chain 'AL' and resid 74 through 76 No H-bonds generated for 'chain 'AL' and resid 74 through 76' Processing helix chain 'AL' and resid 95 through 105 Processing helix chain 'AL' and resid 128 through 130 No H-bonds generated for 'chain 'AL' and resid 128 through 130' Processing helix chain 'AL' and resid 144 through 149 Processing helix chain 'AL' and resid 155 through 181 removed outlier: 4.357A pdb=" N ASPAL 173 " --> pdb=" O SERAL 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HISAL 177 " --> pdb=" O ASPAL 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUAL 179 " --> pdb=" O LEUAL 175 " (cutoff:3.500A) Processing helix chain 'AL' and resid 191 through 204 removed outlier: 3.673A pdb=" N ASPAL 194 " --> pdb=" O PROAL 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHEAL 195 " --> pdb=" O TYRAL 192 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VALAL 196 " --> pdb=" O SERAL 193 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARGAL 203 " --> pdb=" O ALAAL 200 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLNAL 204 " --> pdb=" O METAL 201 " (cutoff:3.500A) Processing helix chain 'AL' and resid 209 through 225 removed outlier: 4.922A pdb=" N GLYAL 224 " --> pdb=" O GLNAL 220 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLUAL 225 " --> pdb=" O ASNAL 221 " (cutoff:3.500A) Processing helix chain 'AL' and resid 239 through 247 removed outlier: 3.891A pdb=" N LYSAL 243 " --> pdb=" O VALAL 239 " (cutoff:3.500A) Processing helix chain 'AL' and resid 252 through 255 No H-bonds generated for 'chain 'AL' and resid 252 through 255' Processing helix chain 'AL' and resid 262 through 280 removed outlier: 5.707A pdb=" N LEUAL 277 " --> pdb=" O LYSAL 273 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYSAL 278 " --> pdb=" O GLNAL 274 " (cutoff:3.500A) Processing helix chain 'AL' and resid 297 through 302 Processing helix chain 'AL' and resid 329 through 340 Processing helix chain 'AL' and resid 343 through 350 removed outlier: 4.322A 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 'A6' and resid 22 through 47 Proline residue: A6 41 - end of helix removed outlier: 3.673A pdb=" N ASPA6 46 " --> pdb=" O TYRA6 42 " (cutoff:3.500A) Processing helix chain 'A6' and resid 53 through 65 Processing helix chain 'A6' and resid 73 through 91 Processing helix chain 'A6' and resid 97 through 103 removed outlier: 3.527A pdb=" N META6 101 " --> pdb=" O LYSA6 97 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARGA6 102 " --> pdb=" O GLYA6 98 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYRA6 103 " --> pdb=" O HISA6 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A6' and resid 97 through 103' Processing helix chain 'A6' and resid 115 through 121 Processing helix chain 'AB' and resid 72 through 84 Processing helix chain 'AB' and resid 108 through 122 removed outlier: 3.942A pdb=" N VALAB 112 " --> pdb=" O SERAB 108 " (cutoff:3.500A) Processing helix chain 'AB' and resid 128 through 133 Processing helix chain 'AB' and resid 137 through 147 Processing sheet with id= A, first strand: chain 'AN' and resid 63 through 66 removed outlier: 6.446A pdb=" N GLUAN 53 " --> pdb=" O LEUAN 41 " (cutoff:3.500A) removed outlier: 5.599A 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 41 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: 3.908A pdb=" N ARGS1 286 " --> pdb=" O SERS1 278 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S1' and resid 319 through 323 removed outlier: 3.810A pdb=" N GLUS1 327 " --> pdb=" O METS1 323 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S1' and resid 351 through 355 removed outlier: 6.291A pdb=" N VALS1 550 " --> pdb=" O ALAS1 352 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILES1 354 " --> pdb=" O VALS1 550 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHES1 552 " --> pdb=" O ILES1 354 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S1' and resid 519 through 522 removed outlier: 7.909A pdb=" N ASNS1 520 " --> pdb=" O PROS1 483 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILES1 485 " --> pdb=" O ASNS1 520 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEUS1 522 " --> pdb=" O ILES1 485 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILES1 487 " --> pdb=" O LEUS1 522 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALAS1 410 " --> pdb=" O ALAS1 484 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILES1 486 " --> pdb=" O ALAS1 410 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEUS1 412 " --> pdb=" O ILES1 486 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLYS1 488 " --> pdb=" O LEUS1 412 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VALS1 414 " --> pdb=" O GLYS1 488 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLNS1 439 " --> pdb=" O VALS1 411 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEUS1 413 " --> pdb=" O GLNS1 439 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALAS1 441 " --> pdb=" O LEUS1 413 " (cutoff:3.500A) removed outlier: 6.695A 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 601 through 603 Processing sheet with id= K, first strand: chain 'S3' and resid 112 through 120 removed outlier: 7.255A pdb=" N ASNS3 133 " --> pdb=" O VALS3 114 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILES3 116 " --> pdb=" O VALS3 131 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VALS3 131 " --> pdb=" O ILES3 116 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLYS3 118 " --> pdb=" O GLUS3 129 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLUS3 129 " --> pdb=" O GLYS3 118 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEUS3 86 " --> pdb=" O ARGS3 144 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LYSS3 146 " --> pdb=" O LEUS3 86 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VALS3 88 " --> pdb=" O LYSS3 146 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TYRS3 148 " --> pdb=" O VALS3 88 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ILES3 90 " --> pdb=" O TYRS3 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLUS3 85 " --> pdb=" O THRS3 81 " (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 123 through 125 Processing sheet with id= N, first strand: chain 'V2' and resid 178 through 181 Processing sheet with id= O, first strand: chain 'S7' and resid 127 through 131 removed outlier: 7.014A pdb=" N TRPS7 154 " --> pdb=" O ILES7 128 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VALS7 130 " --> pdb=" O TRPS7 154 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILES7 156 " --> pdb=" O VALS7 130 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILES7 186 " --> pdb=" O SERS7 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'S8' and resid 106 through 108 Processing sheet with id= Q, first strand: chain 'S8' and resid 133 through 139 removed outlier: 5.910A pdb=" N GLUS8 138 " --> pdb=" O THRS8 147 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THRS8 147 " --> pdb=" O GLUS8 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '5' and resid 35 through 44 removed outlier: 6.691A pdb=" N ILE 5 49 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER 5 43 " --> pdb=" O MET 5 47 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S4' and resid 151 through 154 Processing sheet with id= T, first strand: chain 'S4' and resid 113 through 115 Processing sheet with id= U, first strand: chain 'A9' and resid 135 through 138 removed outlier: 6.387A pdb=" N GLNA9 89 " --> pdb=" O ALAA9 66 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VALA9 68 " --> pdb=" O GLNA9 89 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILEA9 91 " --> pdb=" O VALA9 68 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A9' and resid 177 through 179 removed outlier: 7.027A pdb=" N ILEA9 218 " --> pdb=" O SERA9 178 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A9' and resid 244 through 247 removed outlier: 6.551A pdb=" N META9 313 " --> pdb=" O META9 245 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEUA9 247 " --> pdb=" O META9 313 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYRA9 315 " --> pdb=" O LEUA9 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'S2' and resid 85 through 89 removed outlier: 3.634A pdb=" N ASPS2 115 " --> pdb=" O VALS2 103 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASPS2 107 " --> pdb=" O VALS2 111 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VALS2 111 " --> pdb=" O ASPS2 107 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S2' and resid 399 through 406 removed outlier: 3.695A pdb=" N GLYS2 413 " --> pdb=" O LYSS2 430 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'V1' and resid 254 through 259 removed outlier: 6.205A pdb=" N ALAV1 168 " --> pdb=" O LEUV1 128 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VALV1 130 " --> pdb=" O ALAV1 168 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYRV1 170 " --> pdb=" O VALV1 130 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASPV1 209 " --> pdb=" O ALAV1 169 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILEV1 171 " --> pdb=" O ASPV1 209 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHEV1 211 " --> pdb=" O ILEV1 171 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILEV1 173 " --> pdb=" O PHEV1 211 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HISV1 213 " --> pdb=" O ILEV1 173 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'V1' and resid 301 through 306 Processing sheet with id= AB, first strand: chain 'AL' and resid 285 through 290 removed outlier: 6.155A pdb=" N VALAL 185 " --> pdb=" O ILEAL 85 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VALAL 87 " --> pdb=" O VALAL 185 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEUAL 187 " --> pdb=" O VALAL 87 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLUAL 109 " --> pdb=" O VALAL 186 " (cutoff:3.500A) 2669 hydrogen bonds defined for protein. 7563 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: 21.21 Time building geometry restraints manager: 21.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.43: 28715 1.43 - 1.69: 39823 1.69 - 1.95: 763 1.95 - 2.20: 8 2.20 - 2.46: 75 Bond restraints: 69384 Sorted by residual: bond pdb=" C12 WSF 6 201 " pdb=" C13 WSF 6 201 " ideal model delta sigma weight residual 1.527 2.461 -0.934 2.00e-02 2.50e+03 2.18e+03 bond pdb=" C13 WSF 6 201 " pdb=" C14 WSF 6 201 " ideal model delta sigma weight residual 1.527 2.433 -0.906 2.00e-02 2.50e+03 2.05e+03 bond pdb=" C13 WSF 6 201 " pdb=" C15 WSF 6 201 " ideal model delta sigma weight residual 1.527 2.431 -0.904 2.00e-02 2.50e+03 2.04e+03 bond pdb=" C2' DGTAL 501 " pdb=" C3' DGTAL 501 " ideal model delta sigma weight residual 1.284 1.523 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C3 U10 1 402 " pdb=" O3 U10 1 402 " ideal model delta sigma weight residual 1.230 1.405 -0.175 2.00e-02 2.50e+03 7.66e+01 ... (remaining 69379 not shown) Histogram of bond angle deviations from ideal: 60.13 - 78.12: 79 78.12 - 96.10: 11 96.10 - 114.09: 40701 114.09 - 132.07: 52565 132.07 - 150.06: 209 Bond angle restraints: 93565 Sorted by residual: angle pdb=" C14 WSF 6 201 " pdb=" C13 WSF 6 201 " pdb=" C15 WSF 6 201 " ideal model delta sigma weight residual 109.47 60.13 49.34 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C12 WSF 6 201 " pdb=" C13 WSF 6 201 " pdb=" C15 WSF 6 201 " ideal model delta sigma weight residual 109.47 60.69 48.78 3.00e+00 1.11e-01 2.64e+02 angle pdb=" C12 WSF 6 201 " pdb=" C13 WSF 6 201 " pdb=" C14 WSF 6 201 " ideal model delta sigma weight residual 109.47 60.95 48.52 3.00e+00 1.11e-01 2.62e+02 angle pdb=" C11 WSF 6 201 " pdb=" C12 WSF 6 201 " pdb=" C13 WSF 6 201 " ideal model delta sigma weight residual 109.47 150.06 -40.59 3.00e+00 1.11e-01 1.83e+02 angle pdb=" PA NDPA9 502 " pdb=" O3 NDPA9 502 " pdb=" PN NDPA9 502 " ideal model delta sigma weight residual 107.74 130.30 -22.56 1.95e+00 2.62e-01 1.33e+02 ... (remaining 93560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 40634 35.64 - 71.28: 1218 71.28 - 106.92: 106 106.92 - 142.56: 7 142.56 - 178.20: 6 Dihedral angle restraints: 41971 sinusoidal: 18285 harmonic: 23686 Sorted by residual: dihedral pdb=" CB CYSA8 48 " pdb=" SG CYSA8 48 " pdb=" SG CYSA8 58 " pdb=" CB CYSA8 58 " ideal model delta sinusoidal sigma weight residual 93.00 175.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYSBL 54 " pdb=" SG CYSBL 54 " pdb=" SG CYSBL 61 " pdb=" CB CYSBL 61 " ideal model delta sinusoidal sigma weight residual 93.00 171.56 -78.56 1 1.00e+01 1.00e-02 7.70e+01 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 -163.69 77.69 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 41968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 9908 4.246 - 8.491: 0 8.491 - 12.737: 0 12.737 - 16.982: 0 16.982 - 21.228: 24 Chirality restraints: 9932 Sorted by residual: 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 -10.67 21.23 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 10.63 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S3 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False -10.55 10.62 -21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9929 not shown) Planarity restraints: 11642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.205 2.00e-02 2.50e+03 6.90e-02 2.26e+02 pdb=" C10 FMNV1 501 " 0.003 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.035 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.013 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.026 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.018 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.003 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.129 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.042 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.124 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.039 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.010 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.017 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.034 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.025 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.032 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.051 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 5 2 " 0.027 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C LYS 5 2 " -0.097 2.00e-02 2.50e+03 pdb=" O LYS 5 2 " 0.037 2.00e-02 2.50e+03 pdb=" N TYR 5 3 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERBM 54 " -0.085 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PROBM 55 " 0.219 5.00e-02 4.00e+02 pdb=" CA PROBM 55 " -0.068 5.00e-02 4.00e+02 pdb=" CD PROBM 55 " -0.067 5.00e-02 4.00e+02 ... (remaining 11639 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 2 1.96 - 2.69: 1418 2.69 - 3.43: 92960 3.43 - 4.16: 167711 4.16 - 4.90: 307865 Nonbonded interactions: 569956 Sorted by model distance: nonbonded pdb=" OG SERAC 108 " pdb=" O7 ZMPAC 201 " model vdw 1.219 2.440 nonbonded pdb=" OG SERAC 108 " pdb=" P1 ZMPAC 201 " model vdw 1.505 3.400 nonbonded pdb=" OG SERAC 108 " pdb=" O6 ZMPAC 201 " model vdw 2.038 2.440 nonbonded pdb=" O PHE 4 198 " pdb=" ND1 HIS 4 201 " model vdw 2.198 2.520 nonbonded pdb=" OD2 ASPS2 145 " pdb=" OG SERS2 148 " model vdw 2.223 2.440 ... (remaining 569951 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' selection = (chain 'AC' and (resid 68 through 151 or (resid 201 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 o \ r name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or n \ ame P1 or name S1 )))) } 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 27.980 Check model and map are aligned: 0.790 Set scattering table: 0.610 Process input model: 155.450 Find NCS groups from input model: 2.290 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.009 0.934 69384 Z= 0.527 Angle : 1.074 49.339 93565 Z= 0.559 Chirality : 1.040 21.228 9932 Planarity : 0.008 0.145 11642 Dihedral : 16.722 178.200 26732 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 0.80 % Allowed : 0.85 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.08), residues: 8026 helix: -1.48 (0.07), residues: 4180 sheet: -0.57 (0.26), residues: 412 loop : -1.26 (0.09), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRPS3 167 HIS 0.019 0.001 HIS 2 111 PHE 0.044 0.002 PHE 2 288 TYR 0.050 0.002 TYRS7 167 ARG 0.022 0.001 ARGS2 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1158 time to evaluate : 6.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8296 (t80) cc_final: 0.8070 (t80) REVERT: S1 698 MET cc_start: 0.7662 (mmt) cc_final: 0.7434 (mmt) REVERT: S3 140 ASN cc_start: 0.8668 (t0) cc_final: 0.8447 (t0) REVERT: V2 32 PHE cc_start: 0.8771 (m-80) cc_final: 0.8566 (m-10) REVERT: S7 138 MET cc_start: 0.8325 (tpt) cc_final: 0.7928 (tpt) REVERT: 4 210 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7156 (mm-30) REVERT: 4 354 ASN cc_start: 0.8528 (t0) cc_final: 0.8299 (t0) REVERT: 4 403 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7645 (mm-40) REVERT: 5 108 PRO cc_start: 0.8651 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: 5 322 MET cc_start: 0.7396 (ttp) cc_final: 0.7163 (ttm) REVERT: 5 431 ILE cc_start: 0.8264 (mm) cc_final: 0.8048 (mm) REVERT: A8 142 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6822 (pptt) REVERT: A1 47 MET cc_start: 0.7340 (mmm) cc_final: 0.7111 (mmm) REVERT: AO 13 ASP cc_start: 0.8290 (t70) cc_final: 0.7838 (t0) REVERT: AM 64 MET cc_start: 0.8437 (mmm) cc_final: 0.8196 (mtt) REVERT: BL 78 GLU cc_start: 0.6141 (mp0) cc_final: 0.5919 (mp0) REVERT: B6 41 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7729 (tp-100) REVERT: B4 30 SER cc_start: 0.8831 (t) cc_final: 0.8598 (t) REVERT: B4 108 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: B7 68 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7182 (ttm-80) REVERT: B3 50 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7178 (tm-30) REVERT: AC 109 LEU cc_start: 0.8204 (mt) cc_final: 0.7998 (mt) REVERT: S4 102 ASN cc_start: 0.8103 (t0) cc_final: 0.7742 (p0) REVERT: A9 245 MET cc_start: 0.8939 (tpt) cc_final: 0.8342 (tpt) REVERT: S2 451 ASP cc_start: 0.7867 (m-30) cc_final: 0.7664 (m-30) REVERT: 2 124 MET cc_start: 0.8606 (tpp) cc_final: 0.8243 (mmp) REVERT: 3 40 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7199 (mm-30) REVERT: 3 60 ILE cc_start: 0.8572 (mp) cc_final: 0.8295 (mt) REVERT: 3 77 MET cc_start: 0.7589 (ptt) cc_final: 0.7324 (ptt) REVERT: AL 372 ASP cc_start: 0.7006 (m-30) cc_final: 0.6754 (m-30) REVERT: AB 101 ILE cc_start: 0.6904 (mm) cc_final: 0.6604 (mm) REVERT: AB 116 MET cc_start: 0.7965 (ptt) cc_final: 0.7710 (ptm) outliers start: 56 outliers final: 19 residues processed: 1193 average time/residue: 0.6876 time to fit residues: 1417.9227 Evaluate side-chains 993 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 973 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S1 residue 229 LEU Chi-restraints excluded: chain S7 residue 96 CYS Chi-restraints excluded: chain S7 residue 99 VAL Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 5 residue 8 SER Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 111 ILE Chi-restraints excluded: chain 5 residue 225 LEU Chi-restraints excluded: chain 5 residue 286 MET Chi-restraints excluded: chain 5 residue 288 ILE Chi-restraints excluded: chain 5 residue 387 SER Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain B8 residue 58 LEU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 458 THR Chi-restraints excluded: chain S2 residue 459 LEU Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 46 SER Chi-restraints excluded: chain 6 residue 21 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 670 optimal weight: 0.6980 chunk 601 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 405 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 622 optimal weight: 0.0370 chunk 240 optimal weight: 0.8980 chunk 378 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 721 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S1 84 ASN S1 471 HIS V2 195 GLN 1 131 ASN 4 133 GLN 4 163 ASN 4 362 ASN 4 428 HIS 5 31 ASN ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 321 ASN 5 324 ASN A8 21 ASN A8 50 GLN A1 49 GLN S5 20 ASN S5 58 GLN B6 118 GLN B4 109 GLN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 82 ASN BM 59 GLN S4 132 ASN S4 175 ASN ** S2 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 408 ASN V1 433 GLN 2 85 ASN ** 2 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 19 ASN AL 81 ASN AL 160 GLN A6 96 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.277 69384 Z= 0.508 Angle : 1.554 51.298 93565 Z= 1.009 Chirality : 0.313 6.440 9932 Planarity : 0.005 0.076 11642 Dihedral : 13.390 162.105 10961 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.12 % Allowed : 7.59 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -0.73 (0.09), residues: 8026 helix: -0.10 (0.08), residues: 4225 sheet: -0.41 (0.26), residues: 412 loop : -0.84 (0.10), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPS3 167 HIS 0.009 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.025 0.001 TYR 1 282 ARG 0.006 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1060 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8401 (t80) cc_final: 0.8134 (t80) REVERT: S1 229 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8064 (mt) REVERT: S1 698 MET cc_start: 0.7755 (mmt) cc_final: 0.7545 (mmt) REVERT: V2 185 TYR cc_start: 0.8580 (m-10) cc_final: 0.8080 (m-80) REVERT: S8 151 ASP cc_start: 0.7835 (m-30) cc_final: 0.7528 (m-30) REVERT: 1 1 MET cc_start: 0.7162 (ttt) cc_final: 0.6794 (ttt) REVERT: 1 4 MET cc_start: 0.8342 (tpt) cc_final: 0.8140 (tpp) REVERT: 1 162 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8990 (m-80) REVERT: 4 398 LEU cc_start: 0.8521 (tt) cc_final: 0.8314 (tp) REVERT: 4 403 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7630 (mm110) REVERT: 5 32 ASP cc_start: 0.7957 (t0) cc_final: 0.7601 (t0) REVERT: 5 63 MET cc_start: 0.8126 (ttp) cc_final: 0.7837 (ttp) REVERT: 5 527 GLN cc_start: 0.8820 (pt0) cc_final: 0.8572 (pt0) REVERT: A8 142 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6914 (pptt) REVERT: A1 47 MET cc_start: 0.7554 (mmm) cc_final: 0.7015 (mmm) REVERT: AO 97 GLU cc_start: 0.8623 (tp30) cc_final: 0.8207 (tp30) REVERT: AO 100 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7651 (tm-30) REVERT: AM 27 TYR cc_start: 0.7105 (m-80) cc_final: 0.6850 (m-80) REVERT: BL 103 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6788 (mmm160) REVERT: BL 122 ASP cc_start: 0.8291 (m-30) cc_final: 0.8053 (m-30) REVERT: B6 41 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7817 (tp-100) REVERT: B4 30 SER cc_start: 0.8909 (t) cc_final: 0.8682 (t) REVERT: B4 108 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7746 (ttm-80) REVERT: B7 41 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8040 (tm-30) REVERT: S4 102 ASN cc_start: 0.8155 (t0) cc_final: 0.7860 (p0) REVERT: S2 441 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6081 (mt-10) REVERT: 2 151 LEU cc_start: 0.8593 (tp) cc_final: 0.8374 (tt) REVERT: 4L 4 ILE cc_start: 0.8962 (mm) cc_final: 0.8616 (mp) REVERT: 6 149 MET cc_start: 0.6857 (mtt) cc_final: 0.6619 (mtt) REVERT: AL 372 ASP cc_start: 0.7147 (m-30) cc_final: 0.6862 (m-30) REVERT: A6 85 MET cc_start: 0.8065 (mtt) cc_final: 0.7820 (mtp) REVERT: AB 101 ILE cc_start: 0.6862 (mm) cc_final: 0.6532 (mm) REVERT: AB 116 MET cc_start: 0.8242 (ptt) cc_final: 0.7983 (ptm) outliers start: 79 outliers final: 50 residues processed: 1106 average time/residue: 0.6346 time to fit residues: 1206.1387 Evaluate side-chains 1042 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 988 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain S6 residue 84 VAL Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 229 LEU Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain V2 residue 61 SER Chi-restraints excluded: chain S7 residue 42 THR Chi-restraints excluded: chain S7 residue 151 GLU Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 129 SER Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 154 MET Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 8 SER Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 286 MET Chi-restraints excluded: chain 5 residue 291 MET Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 467 VAL Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain AM residue 21 ILE Chi-restraints excluded: chain B7 residue 12 ASP Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain B8 residue 58 LEU Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 441 GLU Chi-restraints excluded: chain S2 residue 456 ILE Chi-restraints excluded: chain S2 residue 458 THR Chi-restraints excluded: chain S2 residue 459 LEU Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 255 THR Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 46 SER Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain A6 residue 68 ARG Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 400 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 600 optimal weight: 9.9990 chunk 490 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 722 optimal weight: 4.9990 chunk 780 optimal weight: 0.8980 chunk 643 optimal weight: 1.9990 chunk 716 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 579 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V2 195 GLN 1 299 ASN 4 133 GLN ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 324 ASN A8 21 ASN S5 20 ASN AM 88 ASN BL 43 GLN B6 117 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 76 GLN B9 82 ASN BM 57 ASN S4 87 HIS S4 132 ASN S2 136 GLN ** S2 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** 2 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.269 69384 Z= 0.523 Angle : 1.560 50.937 93565 Z= 1.012 Chirality : 0.313 6.406 9932 Planarity : 0.004 0.068 11642 Dihedral : 12.747 162.924 10950 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 11.23 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: -0.08 (0.09), residues: 8026 helix: 0.50 (0.08), residues: 4226 sheet: -0.34 (0.27), residues: 381 loop : -0.62 (0.10), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPS3 167 HIS 0.016 0.001 HISS8 106 PHE 0.029 0.001 PHE 2 288 TYR 0.028 0.001 TYR 5 394 ARG 0.009 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1038 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8431 (t80) cc_final: 0.8182 (t80) REVERT: AN 74 ASP cc_start: 0.7294 (t0) cc_final: 0.6781 (t0) REVERT: S1 113 LYS cc_start: 0.8382 (mttm) cc_final: 0.8163 (mtpt) REVERT: V2 185 TYR cc_start: 0.8651 (m-10) cc_final: 0.8088 (m-80) REVERT: V2 188 ASP cc_start: 0.7519 (m-30) cc_final: 0.7272 (m-30) REVERT: V2 195 GLN cc_start: 0.7974 (mt0) cc_final: 0.7618 (mt0) REVERT: S8 53 MET cc_start: 0.8654 (mmp) cc_final: 0.8205 (mmt) REVERT: S8 151 ASP cc_start: 0.7888 (m-30) cc_final: 0.7644 (m-30) REVERT: 1 162 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: 4 154 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: 4 287 SER cc_start: 0.8934 (p) cc_final: 0.8723 (p) REVERT: 4 403 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7714 (mm110) REVERT: 5 3 TYR cc_start: 0.8201 (m-80) cc_final: 0.7997 (m-80) REVERT: 5 32 ASP cc_start: 0.7994 (t0) cc_final: 0.7624 (t0) REVERT: 5 115 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8215 (tp) REVERT: 5 527 GLN cc_start: 0.8866 (pt0) cc_final: 0.8592 (pt0) REVERT: A8 142 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7206 (pptt) REVERT: AO 100 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7718 (tm-30) REVERT: AM 167 LYS cc_start: 0.8142 (mttp) cc_final: 0.7767 (mppt) REVERT: BL 99 MET cc_start: 0.8335 (mmm) cc_final: 0.8047 (mmm) REVERT: BL 103 ARG cc_start: 0.7485 (mmm160) cc_final: 0.6955 (mmm160) REVERT: BL 120 TYR cc_start: 0.8889 (m-80) cc_final: 0.8539 (m-80) REVERT: BL 122 ASP cc_start: 0.8441 (m-30) cc_final: 0.8165 (m-30) REVERT: B6 41 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7922 (tp-100) REVERT: B4 92 ASP cc_start: 0.7753 (m-30) cc_final: 0.7307 (m-30) REVERT: B8 118 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.8091 (t60) REVERT: B8 139 MET cc_start: 0.8636 (mmp) cc_final: 0.8357 (mmm) REVERT: S4 71 ILE cc_start: 0.7991 (mm) cc_final: 0.7790 (mt) REVERT: S4 102 ASN cc_start: 0.8086 (t0) cc_final: 0.7813 (p0) REVERT: S4 170 ILE cc_start: 0.9155 (mm) cc_final: 0.8842 (mt) REVERT: B2 64 TRP cc_start: 0.8515 (t60) cc_final: 0.7980 (t60) REVERT: B2 81 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8026 (pttp) REVERT: S2 247 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5630 (t0) REVERT: S2 286 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: 2 151 LEU cc_start: 0.8570 (tp) cc_final: 0.8362 (tt) REVERT: 2 271 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: 4L 4 ILE cc_start: 0.9205 (mm) cc_final: 0.8919 (mp) REVERT: 6 149 MET cc_start: 0.6958 (mtt) cc_final: 0.6749 (mtt) REVERT: A5 38 MET cc_start: 0.8681 (mmm) cc_final: 0.8007 (mmm) REVERT: AL 194 ASP cc_start: 0.8303 (t0) cc_final: 0.7964 (t0) REVERT: AL 372 ASP cc_start: 0.7231 (m-30) cc_final: 0.6963 (m-30) outliers start: 121 outliers final: 80 residues processed: 1101 average time/residue: 0.6476 time to fit residues: 1227.9956 Evaluate side-chains 1057 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 969 time to evaluate : 7.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain S6 residue 84 VAL Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 229 LEU Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 223 CYS Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S7 residue 42 THR Chi-restraints excluded: chain S7 residue 149 MET Chi-restraints excluded: chain S7 residue 151 GLU Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 129 SER Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 154 MET Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 102 MET Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 286 MET Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 5 residue 494 THR Chi-restraints excluded: chain A8 residue 2 VAL Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 12 ASP Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 84 VAL Chi-restraints excluded: chain B9 residue 76 GLN Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 58 LEU Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 194 THR Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 458 THR Chi-restraints excluded: chain S2 residue 459 LEU Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 255 THR Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 4L residue 5 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain A5 residue 118 GLN Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 104 LEU Chi-restraints excluded: chain AB residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 713 optimal weight: 5.9990 chunk 543 optimal weight: 6.9990 chunk 374 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 485 optimal weight: 6.9990 chunk 724 optimal weight: 0.9980 chunk 767 optimal weight: 0.9990 chunk 378 optimal weight: 2.9990 chunk 687 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S1 515 ASN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 267 GLN ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S5 20 ASN AM 151 ASN BL 43 GLN ** B6 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 74 HIS B9 76 GLN S4 132 ASN ** S2 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN S2 446 GLN ** 2 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 24 HIS A3 63 HIS ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 138 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 69384 Z= 0.495 Angle : 1.542 50.695 93565 Z= 1.004 Chirality : 0.312 6.501 9932 Planarity : 0.004 0.059 11642 Dihedral : 12.414 162.741 10948 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.77 % Allowed : 12.83 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.28 (0.09), residues: 8026 helix: 0.84 (0.08), residues: 4242 sheet: -0.26 (0.26), residues: 411 loop : -0.50 (0.10), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPB6 42 HIS 0.013 0.001 HISS8 106 PHE 0.026 0.001 PHE 5 307 TYR 0.022 0.001 TYR 5 394 ARG 0.009 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1003 time to evaluate : 6.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8451 (t80) cc_final: 0.8163 (t80) REVERT: AN 74 ASP cc_start: 0.7271 (t0) cc_final: 0.6805 (t0) REVERT: AN 90 TYR cc_start: 0.9110 (m-80) cc_final: 0.8723 (m-80) REVERT: S1 113 LYS cc_start: 0.8362 (mttm) cc_final: 0.8151 (mtpt) REVERT: V2 185 TYR cc_start: 0.8621 (m-10) cc_final: 0.8091 (m-80) REVERT: V2 188 ASP cc_start: 0.7674 (m-30) cc_final: 0.7309 (m-30) REVERT: S8 53 MET cc_start: 0.8695 (mmp) cc_final: 0.8280 (mmt) REVERT: S8 151 ASP cc_start: 0.7920 (m-30) cc_final: 0.7585 (m-30) REVERT: 1 162 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: 1 183 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7385 (mt) REVERT: 1 286 MET cc_start: 0.8391 (ttm) cc_final: 0.8057 (mtt) REVERT: 4 403 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7720 (mm110) REVERT: 4 406 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8049 (mtpp) REVERT: 5 32 ASP cc_start: 0.7898 (t0) cc_final: 0.7530 (t0) REVERT: 5 115 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8217 (tp) REVERT: 5 527 GLN cc_start: 0.8867 (pt0) cc_final: 0.8630 (pt0) REVERT: A8 142 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7155 (pptt) REVERT: A8 153 THR cc_start: 0.8908 (m) cc_final: 0.8650 (m) REVERT: BL 99 MET cc_start: 0.8288 (mmm) cc_final: 0.8084 (mmm) REVERT: BL 120 TYR cc_start: 0.8906 (m-80) cc_final: 0.8548 (m-80) REVERT: BL 122 ASP cc_start: 0.8422 (m-30) cc_final: 0.8190 (m-30) REVERT: B6 41 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7926 (tp-100) REVERT: B4 92 ASP cc_start: 0.7750 (m-30) cc_final: 0.7286 (m-30) REVERT: B8 118 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.8219 (t60) REVERT: B8 139 MET cc_start: 0.8677 (mmp) cc_final: 0.8368 (mmm) REVERT: B1 7 LYS cc_start: 0.7759 (mttp) cc_final: 0.7500 (pptt) REVERT: S4 71 ILE cc_start: 0.7971 (mm) cc_final: 0.7761 (mt) REVERT: S4 102 ASN cc_start: 0.8072 (t0) cc_final: 0.7776 (p0) REVERT: S4 170 ILE cc_start: 0.9205 (mm) cc_final: 0.8908 (mt) REVERT: B2 64 TRP cc_start: 0.8558 (t60) cc_final: 0.8008 (t60) REVERT: B2 81 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8042 (pttp) REVERT: S2 247 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5543 (t0) REVERT: 2 271 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: 4L 4 ILE cc_start: 0.9208 (mm) cc_final: 0.8936 (mp) REVERT: AL 194 ASP cc_start: 0.8273 (t0) cc_final: 0.7971 (t0) REVERT: AL 372 ASP cc_start: 0.7180 (m-30) cc_final: 0.6880 (m-30) REVERT: AL 373 VAL cc_start: 0.8969 (t) cc_final: 0.8719 (t) REVERT: AL 380 MET cc_start: 0.8018 (mtp) cc_final: 0.7633 (ttp) REVERT: AB 110 ASP cc_start: 0.8829 (m-30) cc_final: 0.8543 (m-30) REVERT: AB 116 MET cc_start: 0.7850 (ptp) cc_final: 0.7633 (ptm) outliers start: 124 outliers final: 80 residues processed: 1085 average time/residue: 0.6560 time to fit residues: 1209.0696 Evaluate side-chains 1044 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 957 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 223 CYS Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain V2 residue 213 ASN Chi-restraints excluded: chain S7 residue 149 MET Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 144 SER Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 86 HIS Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 102 LEU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 58 LEU Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain AC residue 107 ASP Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 458 THR Chi-restraints excluded: chain S2 residue 459 LEU Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 255 THR Chi-restraints excluded: chain 2 residue 45 LEU Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain A6 residue 45 MET Chi-restraints excluded: chain A6 residue 71 THR Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 639 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 571 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 654 optimal weight: 0.8980 chunk 530 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 391 optimal weight: 0.5980 chunk 688 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 GLN ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 300 HIS 5 304 HIS S5 20 ASN BL 43 GLN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 57 ASN B8 98 HIS S4 132 ASN ** S2 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN 2 133 GLN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN 6 3 GLN ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 160 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 69384 Z= 0.487 Angle : 1.537 50.683 93565 Z= 1.002 Chirality : 0.312 6.377 9932 Planarity : 0.004 0.061 11642 Dihedral : 12.091 162.397 10943 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.11 % Allowed : 13.60 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.51 (0.09), residues: 8026 helix: 1.06 (0.08), residues: 4241 sheet: -0.28 (0.26), residues: 417 loop : -0.42 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPB6 42 HIS 0.014 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.023 0.001 TYR 5 394 ARG 0.010 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 982 time to evaluate : 6.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8474 (t80) cc_final: 0.8191 (t80) REVERT: AN 74 ASP cc_start: 0.7257 (t0) cc_final: 0.6814 (t0) REVERT: AN 90 TYR cc_start: 0.9099 (m-80) cc_final: 0.8716 (m-80) REVERT: S1 48 ASP cc_start: 0.6760 (t0) cc_final: 0.6544 (t0) REVERT: S1 148 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8054 (t0) REVERT: S3 60 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7990 (mm) REVERT: V2 185 TYR cc_start: 0.8601 (m-10) cc_final: 0.8025 (m-80) REVERT: V2 188 ASP cc_start: 0.7658 (m-30) cc_final: 0.7306 (m-30) REVERT: S8 53 MET cc_start: 0.8684 (mmp) cc_final: 0.8269 (mmt) REVERT: S8 151 ASP cc_start: 0.7897 (m-30) cc_final: 0.7543 (m-30) REVERT: S8 159 TYR cc_start: 0.8615 (m-80) cc_final: 0.8385 (m-80) REVERT: 1 50 MET cc_start: 0.8065 (tpt) cc_final: 0.7856 (tpt) REVERT: 1 162 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: 1 183 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7339 (mt) REVERT: 1 286 MET cc_start: 0.8336 (ttm) cc_final: 0.8046 (mtt) REVERT: 4 154 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8410 (ttp) REVERT: 4 403 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7764 (mm110) REVERT: 4 406 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8059 (mtpp) REVERT: 5 32 ASP cc_start: 0.7884 (t0) cc_final: 0.7522 (t0) REVERT: 5 115 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8199 (tp) REVERT: 5 390 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8058 (mp) REVERT: 5 431 ILE cc_start: 0.7998 (mm) cc_final: 0.7745 (mt) REVERT: A8 142 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7213 (pptt) REVERT: A8 153 THR cc_start: 0.8921 (m) cc_final: 0.8650 (m) REVERT: BL 120 TYR cc_start: 0.8955 (m-80) cc_final: 0.8554 (m-80) REVERT: B6 41 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7934 (tp-100) REVERT: B4 108 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7585 (ttm-80) REVERT: BM 57 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7570 (t0) REVERT: B8 118 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.8214 (t60) REVERT: B8 139 MET cc_start: 0.8689 (mmp) cc_final: 0.8385 (mmm) REVERT: B1 7 LYS cc_start: 0.7719 (mttp) cc_final: 0.7488 (pptt) REVERT: S4 102 ASN cc_start: 0.8028 (t0) cc_final: 0.7746 (p0) REVERT: S4 170 ILE cc_start: 0.9220 (mm) cc_final: 0.8935 (mt) REVERT: B2 64 TRP cc_start: 0.8590 (t60) cc_final: 0.8041 (t60) REVERT: B2 81 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8032 (pttp) REVERT: S2 286 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: V1 212 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7766 (ttt) REVERT: 2 213 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8557 (m-10) REVERT: 2 271 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: 4L 4 ILE cc_start: 0.9183 (mm) cc_final: 0.8938 (mp) REVERT: A5 50 GLN cc_start: 0.8483 (tt0) cc_final: 0.8239 (tt0) REVERT: AL 194 ASP cc_start: 0.8314 (t0) cc_final: 0.8085 (t0) REVERT: AL 201 MET cc_start: 0.7649 (mtt) cc_final: 0.7301 (mtt) REVERT: AL 372 ASP cc_start: 0.7178 (m-30) cc_final: 0.6906 (m-30) REVERT: AL 373 VAL cc_start: 0.8956 (t) cc_final: 0.8708 (t) REVERT: AL 380 MET cc_start: 0.7983 (mtp) cc_final: 0.7711 (ttm) REVERT: AB 110 ASP cc_start: 0.8809 (m-30) cc_final: 0.8491 (m-30) outliers start: 148 outliers final: 95 residues processed: 1074 average time/residue: 0.6432 time to fit residues: 1188.3271 Evaluate side-chains 1055 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 946 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain S6 residue 65 GLU Chi-restraints excluded: chain S6 residue 84 VAL Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 148 ASP Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 144 SER Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 154 MET Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 86 HIS Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 390 LEU Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 57 ASN Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 255 THR Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain 3 residue 70 GLU Chi-restraints excluded: chain A5 residue 118 GLN Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain A6 residue 40 ILE Chi-restraints excluded: chain AB residue 82 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 258 optimal weight: 0.9980 chunk 691 optimal weight: 0.4980 chunk 151 optimal weight: 0.4980 chunk 450 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 768 optimal weight: 2.9990 chunk 637 optimal weight: 8.9990 chunk 355 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 403 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 527 GLN AO 138 HIS S5 20 ASN BL 43 GLN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 152 ASN ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 51 ASN ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.261 69384 Z= 0.497 Angle : 1.542 50.694 93565 Z= 1.004 Chirality : 0.312 6.416 9932 Planarity : 0.004 0.060 11642 Dihedral : 11.885 159.868 10936 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 14.17 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.61 (0.09), residues: 8026 helix: 1.16 (0.08), residues: 4233 sheet: -0.22 (0.26), residues: 415 loop : -0.39 (0.11), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPB6 42 HIS 0.012 0.001 HISS8 106 PHE 0.027 0.001 PHE 4 442 TYR 0.022 0.001 TYR 5 394 ARG 0.010 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 976 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8503 (t80) cc_final: 0.8208 (t80) REVERT: AN 74 ASP cc_start: 0.7289 (t0) cc_final: 0.6858 (t0) REVERT: AN 90 TYR cc_start: 0.9084 (m-80) cc_final: 0.8693 (m-80) REVERT: S1 85 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (p) REVERT: S1 148 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: S3 60 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7980 (mm) REVERT: V2 185 TYR cc_start: 0.8644 (m-10) cc_final: 0.8061 (m-80) REVERT: V2 188 ASP cc_start: 0.7741 (m-30) cc_final: 0.7350 (m-30) REVERT: S8 53 MET cc_start: 0.8725 (mmp) cc_final: 0.8309 (mmt) REVERT: S8 151 ASP cc_start: 0.7904 (m-30) cc_final: 0.7504 (m-30) REVERT: S8 159 TYR cc_start: 0.8693 (m-80) cc_final: 0.8411 (m-80) REVERT: S8 213 ASP cc_start: 0.8004 (t70) cc_final: 0.7790 (t70) REVERT: 1 50 MET cc_start: 0.8070 (tpt) cc_final: 0.7852 (tpt) REVERT: 1 162 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: 1 183 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7339 (mt) REVERT: 1 286 MET cc_start: 0.8341 (ttm) cc_final: 0.8050 (mtt) REVERT: 4 133 GLN cc_start: 0.8131 (mt0) cc_final: 0.7876 (mt0) REVERT: 4 154 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8497 (ttp) REVERT: 4 403 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7866 (mm110) REVERT: 4 406 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8082 (mtpp) REVERT: 5 32 ASP cc_start: 0.7909 (t0) cc_final: 0.7509 (t0) REVERT: 5 115 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (tp) REVERT: 5 390 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8089 (mp) REVERT: 5 431 ILE cc_start: 0.8009 (mm) cc_final: 0.7737 (mt) REVERT: A8 142 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7354 (pptt) REVERT: A8 153 THR cc_start: 0.8955 (m) cc_final: 0.8712 (m) REVERT: BL 99 MET cc_start: 0.8337 (mmm) cc_final: 0.8112 (mmm) REVERT: BL 120 TYR cc_start: 0.8934 (m-80) cc_final: 0.8480 (m-80) REVERT: B6 41 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7977 (tp-100) REVERT: B4 108 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7628 (ttm-80) REVERT: B7 9 MET cc_start: 0.7724 (mmt) cc_final: 0.7522 (mmm) REVERT: B8 118 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8239 (t60) REVERT: B8 139 MET cc_start: 0.8690 (mmp) cc_final: 0.8396 (mmm) REVERT: B1 7 LYS cc_start: 0.7709 (mttp) cc_final: 0.7485 (pptt) REVERT: S4 102 ASN cc_start: 0.8029 (t0) cc_final: 0.7740 (p0) REVERT: S4 170 ILE cc_start: 0.9238 (mm) cc_final: 0.8953 (mt) REVERT: B2 64 TRP cc_start: 0.8624 (t60) cc_final: 0.8047 (t60) REVERT: S2 247 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5601 (t0) REVERT: S2 286 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: V1 212 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7715 (ttt) REVERT: 2 202 PHE cc_start: 0.8018 (t80) cc_final: 0.7666 (t80) REVERT: 2 213 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: 2 271 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: 4L 4 ILE cc_start: 0.9206 (mm) cc_final: 0.8964 (mp) REVERT: A5 50 GLN cc_start: 0.8441 (tt0) cc_final: 0.8225 (tt0) REVERT: AL 194 ASP cc_start: 0.8395 (t0) cc_final: 0.8142 (t0) REVERT: AL 201 MET cc_start: 0.7664 (mtt) cc_final: 0.7384 (mtt) REVERT: AL 339 TYR cc_start: 0.8673 (m-80) cc_final: 0.8115 (m-80) REVERT: AL 372 ASP cc_start: 0.7222 (m-30) cc_final: 0.6963 (m-30) REVERT: AL 373 VAL cc_start: 0.8951 (t) cc_final: 0.8690 (t) REVERT: AB 110 ASP cc_start: 0.8766 (m-30) cc_final: 0.8451 (m-30) outliers start: 159 outliers final: 114 residues processed: 1090 average time/residue: 0.6413 time to fit residues: 1198.6007 Evaluate side-chains 1066 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 937 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 58 PHE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain AN residue 127 THR Chi-restraints excluded: chain S6 residue 65 GLU Chi-restraints excluded: chain S6 residue 84 VAL Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 85 CYS Chi-restraints excluded: chain S1 residue 148 ASP Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain V2 residue 213 ASN Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 144 SER Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 154 MET Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 257 MET Chi-restraints excluded: chain 5 residue 312 PHE Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 390 LEU Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 5 residue 522 VAL Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain S5 residue 82 LEU Chi-restraints excluded: chain BL residue 50 THR Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 102 LEU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 46 SER Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 107 ASP Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain B1 residue 42 LEU Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 149 MET Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 417 ILE Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 255 THR Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain A6 residue 40 ILE Chi-restraints excluded: chain A6 residue 51 MET Chi-restraints excluded: chain A6 residue 71 THR Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 740 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 437 optimal weight: 0.6980 chunk 561 optimal weight: 1.9990 chunk 434 optimal weight: 1.9990 chunk 646 optimal weight: 0.7980 chunk 428 optimal weight: 2.9990 chunk 765 optimal weight: 1.9990 chunk 478 optimal weight: 0.0770 chunk 466 optimal weight: 3.9990 chunk 353 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S8 211 GLN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 265 ASN 5 527 GLN A1 49 GLN S5 20 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 57 ASN B2 69 HIS ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 69384 Z= 0.497 Angle : 1.542 50.718 93565 Z= 1.004 Chirality : 0.312 6.398 9932 Planarity : 0.004 0.062 11642 Dihedral : 11.706 160.034 10934 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.46 % Allowed : 14.64 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.70 (0.09), residues: 8026 helix: 1.23 (0.08), residues: 4229 sheet: -0.24 (0.26), residues: 415 loop : -0.35 (0.11), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPB2 82 HIS 0.016 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.028 0.001 TYRS7 167 ARG 0.012 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 970 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8531 (t80) cc_final: 0.8175 (t80) REVERT: AN 74 ASP cc_start: 0.7366 (t0) cc_final: 0.6921 (t0) REVERT: AN 90 TYR cc_start: 0.9074 (m-80) cc_final: 0.8656 (m-80) REVERT: S1 85 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (p) REVERT: S3 60 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7984 (mm) REVERT: V2 185 TYR cc_start: 0.8647 (m-10) cc_final: 0.8071 (m-80) REVERT: V2 188 ASP cc_start: 0.7747 (m-30) cc_final: 0.7384 (m-30) REVERT: S8 53 MET cc_start: 0.8755 (mmp) cc_final: 0.8345 (mmt) REVERT: S8 151 ASP cc_start: 0.7881 (m-30) cc_final: 0.7517 (m-30) REVERT: S8 159 TYR cc_start: 0.8671 (m-80) cc_final: 0.8402 (m-80) REVERT: 1 50 MET cc_start: 0.8023 (tpt) cc_final: 0.7822 (tpt) REVERT: 1 162 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: 1 183 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7364 (mt) REVERT: 1 286 MET cc_start: 0.8313 (ttm) cc_final: 0.8047 (mtt) REVERT: 4 154 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8538 (ttp) REVERT: 4 403 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7791 (mm-40) REVERT: 4 406 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8072 (mtpp) REVERT: 5 32 ASP cc_start: 0.7901 (t0) cc_final: 0.7521 (t0) REVERT: 5 115 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (tp) REVERT: 5 390 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8095 (mp) REVERT: 5 431 ILE cc_start: 0.8037 (mm) cc_final: 0.7781 (mt) REVERT: A8 142 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7338 (pptt) REVERT: AO 100 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7746 (tm-30) REVERT: BL 120 TYR cc_start: 0.8943 (m-80) cc_final: 0.8404 (m-80) REVERT: B6 41 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7970 (tp-100) REVERT: B7 9 MET cc_start: 0.7754 (mmt) cc_final: 0.7541 (mmm) REVERT: B8 118 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.8191 (t60) REVERT: B8 139 MET cc_start: 0.8677 (mmp) cc_final: 0.8400 (mmm) REVERT: B1 7 LYS cc_start: 0.7720 (mttp) cc_final: 0.7463 (pptt) REVERT: S4 102 ASN cc_start: 0.8015 (t0) cc_final: 0.7746 (p0) REVERT: S4 170 ILE cc_start: 0.9233 (mm) cc_final: 0.8963 (mt) REVERT: A9 412 LEU cc_start: 0.8436 (mm) cc_final: 0.7886 (pp) REVERT: B2 64 TRP cc_start: 0.8617 (t60) cc_final: 0.8066 (t60) REVERT: B2 82 TRP cc_start: 0.7470 (m-10) cc_final: 0.7182 (m-10) REVERT: S2 247 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5590 (t0) REVERT: S2 286 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: V1 212 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7660 (ttt) REVERT: 2 202 PHE cc_start: 0.8045 (t80) cc_final: 0.7704 (t80) REVERT: 2 213 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8610 (m-10) REVERT: 2 271 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: 4L 4 ILE cc_start: 0.9195 (mm) cc_final: 0.8968 (mp) REVERT: A5 50 GLN cc_start: 0.8464 (tt0) cc_final: 0.8242 (tt0) REVERT: AL 194 ASP cc_start: 0.8411 (t0) cc_final: 0.8156 (t0) REVERT: AL 339 TYR cc_start: 0.8683 (m-80) cc_final: 0.8210 (m-80) REVERT: AL 372 ASP cc_start: 0.7229 (m-30) cc_final: 0.6963 (m-30) REVERT: AL 373 VAL cc_start: 0.8943 (t) cc_final: 0.8692 (t) outliers start: 173 outliers final: 128 residues processed: 1086 average time/residue: 0.6463 time to fit residues: 1204.7359 Evaluate side-chains 1085 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 943 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 58 PHE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain AN residue 127 THR Chi-restraints excluded: chain S6 residue 65 GLU Chi-restraints excluded: chain S6 residue 84 VAL Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 85 CYS Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 148 ASP Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 378 VAL Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 401 THR Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 500 ILE Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 174 ASP Chi-restraints excluded: chain V2 residue 61 SER Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain V2 residue 213 ASN Chi-restraints excluded: chain S7 residue 149 MET Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 144 SER Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 231 PHE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 137 LEU Chi-restraints excluded: chain 4 residue 154 MET Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 257 MET Chi-restraints excluded: chain 5 residue 312 PHE Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 390 LEU Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain A8 residue 24 SER Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain BL residue 50 THR Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 102 LEU Chi-restraints excluded: chain B6 residue 141 GLU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 19 VAL Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 46 SER Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 84 VAL Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 107 ASP Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain C2 residue 8 LEU Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain B1 residue 42 LEU Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 79 SER Chi-restraints excluded: chain S2 residue 149 MET Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 417 ILE Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 302 THR Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain 3 residue 70 GLU Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain A6 residue 40 ILE Chi-restraints excluded: chain A6 residue 51 MET Chi-restraints excluded: chain A6 residue 71 THR Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 473 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 chunk 457 optimal weight: 0.2980 chunk 230 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 486 optimal weight: 0.9990 chunk 521 optimal weight: 5.9990 chunk 378 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 601 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S8 211 GLN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 GLN ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 49 GLN S5 20 ASN B6 63 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 170 HIS S4 132 ASN A9 307 GLN ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN 2 82 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 83 GLN AL 160 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 69384 Z= 0.485 Angle : 1.538 50.704 93565 Z= 1.002 Chirality : 0.312 6.430 9932 Planarity : 0.004 0.060 11642 Dihedral : 11.494 160.054 10934 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.28 % Allowed : 15.02 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8026 helix: 1.34 (0.08), residues: 4219 sheet: -0.22 (0.26), residues: 417 loop : -0.29 (0.11), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPB6 42 HIS 0.015 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.026 0.001 TYRS7 167 ARG 0.014 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 950 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8527 (t80) cc_final: 0.8179 (t80) REVERT: AN 74 ASP cc_start: 0.7336 (t0) cc_final: 0.6895 (t0) REVERT: AN 90 TYR cc_start: 0.9052 (m-80) cc_final: 0.8670 (m-80) REVERT: S1 85 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8124 (p) REVERT: S3 60 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7958 (mm) REVERT: S3 174 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: V2 185 TYR cc_start: 0.8604 (m-10) cc_final: 0.8032 (m-80) REVERT: V2 188 ASP cc_start: 0.7708 (m-30) cc_final: 0.7399 (m-30) REVERT: S8 53 MET cc_start: 0.8740 (mmp) cc_final: 0.8341 (mmt) REVERT: S8 151 ASP cc_start: 0.7867 (m-30) cc_final: 0.7583 (m-30) REVERT: 1 162 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8810 (m-80) REVERT: 1 183 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7321 (mt) REVERT: 1 286 MET cc_start: 0.8299 (ttm) cc_final: 0.8033 (mtt) REVERT: 4 403 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7796 (mm-40) REVERT: 4 406 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: 5 32 ASP cc_start: 0.7908 (t0) cc_final: 0.7533 (t0) REVERT: 5 115 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8158 (tp) REVERT: 5 141 MET cc_start: 0.8844 (mmm) cc_final: 0.8577 (mmt) REVERT: 5 431 ILE cc_start: 0.8033 (mm) cc_final: 0.7778 (mt) REVERT: A8 142 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7418 (pptt) REVERT: BL 120 TYR cc_start: 0.8922 (m-80) cc_final: 0.8349 (m-80) REVERT: B6 41 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7951 (tp-100) REVERT: B7 9 MET cc_start: 0.7720 (mmt) cc_final: 0.7514 (mmm) REVERT: B8 118 TRP cc_start: 0.8857 (OUTLIER) cc_final: 0.8204 (t60) REVERT: B8 139 MET cc_start: 0.8675 (mmp) cc_final: 0.8389 (mmm) REVERT: B1 7 LYS cc_start: 0.7693 (mttp) cc_final: 0.7459 (pptt) REVERT: B1 31 GLU cc_start: 0.7825 (tt0) cc_final: 0.7624 (mt-10) REVERT: B1 42 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8669 (tt) REVERT: S4 102 ASN cc_start: 0.7999 (t0) cc_final: 0.7766 (p0) REVERT: S4 170 ILE cc_start: 0.9212 (mm) cc_final: 0.8955 (mt) REVERT: A9 412 LEU cc_start: 0.8422 (mm) cc_final: 0.7875 (pp) REVERT: B2 64 TRP cc_start: 0.8603 (t60) cc_final: 0.8057 (t60) REVERT: B2 81 LYS cc_start: 0.8417 (mtmm) cc_final: 0.7968 (pttp) REVERT: S2 247 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5542 (t0) REVERT: S2 286 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: V1 212 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: 2 202 PHE cc_start: 0.8025 (t80) cc_final: 0.7673 (t80) REVERT: 2 213 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: 2 271 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7457 (mt0) REVERT: 4L 4 ILE cc_start: 0.9207 (mm) cc_final: 0.8981 (mp) REVERT: A5 50 GLN cc_start: 0.8437 (tt0) cc_final: 0.8212 (tt0) REVERT: AL 339 TYR cc_start: 0.8644 (m-80) cc_final: 0.8134 (m-80) REVERT: AL 373 VAL cc_start: 0.8917 (t) cc_final: 0.8626 (t) REVERT: A6 85 MET cc_start: 0.8185 (mtt) cc_final: 0.7965 (mtp) outliers start: 160 outliers final: 123 residues processed: 1057 average time/residue: 0.6375 time to fit residues: 1159.6999 Evaluate side-chains 1059 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 921 time to evaluate : 5.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 58 PHE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain AN residue 127 THR Chi-restraints excluded: chain S1 residue 66 ILE Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 85 CYS Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 401 THR Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 500 ILE Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 174 ASP Chi-restraints excluded: chain V2 residue 61 SER Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain V2 residue 213 ASN Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 231 PHE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 4 residue 406 LYS Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 257 MET Chi-restraints excluded: chain 5 residue 312 PHE Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain A8 residue 24 SER Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain A8 residue 173 TRP Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 20 ASN Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain S5 residue 82 LEU Chi-restraints excluded: chain BL residue 50 THR Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 102 LEU Chi-restraints excluded: chain B6 residue 141 GLU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 107 ASP Chi-restraints excluded: chain B7 residue 19 VAL Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 46 SER Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 84 VAL Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 107 ASP Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain C2 residue 8 LEU Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain B1 residue 42 LEU Chi-restraints excluded: chain S4 residue 94 MET Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 189 ILE Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 417 ILE Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 302 THR Chi-restraints excluded: chain V1 residue 347 CYS Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 4L residue 57 SER Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 49 SER Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain 3 residue 70 GLU Chi-restraints excluded: chain AL residue 259 VAL Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain A6 residue 51 MET Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 121 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 696 optimal weight: 0.7980 chunk 733 optimal weight: 0.6980 chunk 668 optimal weight: 0.6980 chunk 713 optimal weight: 1.9990 chunk 732 optimal weight: 0.8980 chunk 429 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 559 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 644 optimal weight: 5.9990 chunk 674 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V2 175 ASN S8 211 GLN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 49 GLN S5 20 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 132 ASN A9 307 GLN ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 83 GLN AL 81 ASN AL 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 69384 Z= 0.487 Angle : 1.540 50.704 93565 Z= 1.003 Chirality : 0.312 6.418 9932 Planarity : 0.004 0.062 11642 Dihedral : 11.356 160.275 10934 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.39 % Allowed : 15.12 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.87 (0.10), residues: 8026 helix: 1.38 (0.08), residues: 4231 sheet: -0.21 (0.26), residues: 417 loop : -0.26 (0.11), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAM 103 HIS 0.013 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.030 0.001 TYRA6 37 ARG 0.014 0.000 ARGAN 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 935 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8533 (t80) cc_final: 0.8179 (t80) REVERT: AN 74 ASP cc_start: 0.7345 (t0) cc_final: 0.6917 (t0) REVERT: AN 90 TYR cc_start: 0.9050 (m-80) cc_final: 0.8688 (m-80) REVERT: S6 62 TYR cc_start: 0.8190 (m-80) cc_final: 0.7938 (m-80) REVERT: S1 85 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8126 (p) REVERT: S1 148 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: S3 46 LYS cc_start: 0.7671 (tppp) cc_final: 0.7439 (tppp) REVERT: S3 60 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7954 (mm) REVERT: S3 174 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: V2 185 TYR cc_start: 0.8600 (m-10) cc_final: 0.8044 (m-80) REVERT: V2 188 ASP cc_start: 0.7707 (m-30) cc_final: 0.7388 (m-30) REVERT: S8 53 MET cc_start: 0.8754 (mmp) cc_final: 0.8361 (mmt) REVERT: S8 151 ASP cc_start: 0.7851 (m-30) cc_final: 0.7574 (m-30) REVERT: 1 162 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: 1 183 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7266 (mt) REVERT: 1 286 MET cc_start: 0.8304 (ttm) cc_final: 0.8032 (mtt) REVERT: 4 403 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7817 (mm-40) REVERT: 4 406 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: 4 443 MET cc_start: 0.8095 (mmm) cc_final: 0.7445 (ttt) REVERT: 5 32 ASP cc_start: 0.7894 (t0) cc_final: 0.7530 (t0) REVERT: 5 115 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8117 (tp) REVERT: 5 422 MET cc_start: 0.8781 (mtt) cc_final: 0.8581 (mtt) REVERT: 5 431 ILE cc_start: 0.8032 (mm) cc_final: 0.7779 (mt) REVERT: A8 142 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7445 (pptt) REVERT: BL 120 TYR cc_start: 0.8908 (m-80) cc_final: 0.8434 (m-80) REVERT: B6 41 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7952 (tp-100) REVERT: B7 9 MET cc_start: 0.7824 (mmt) cc_final: 0.7592 (mmm) REVERT: B8 118 TRP cc_start: 0.8845 (OUTLIER) cc_final: 0.8203 (t60) REVERT: B8 139 MET cc_start: 0.8671 (mmp) cc_final: 0.8389 (mmm) REVERT: B1 7 LYS cc_start: 0.7675 (mttp) cc_final: 0.7443 (pptt) REVERT: S4 170 ILE cc_start: 0.9214 (mm) cc_final: 0.8956 (mt) REVERT: A9 412 LEU cc_start: 0.8420 (mm) cc_final: 0.7873 (pp) REVERT: B2 64 TRP cc_start: 0.8603 (t60) cc_final: 0.8063 (t60) REVERT: B2 81 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7971 (pttp) REVERT: S2 247 ASP cc_start: 0.5969 (OUTLIER) cc_final: 0.5502 (t0) REVERT: S2 286 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: V1 212 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7591 (ttt) REVERT: 2 202 PHE cc_start: 0.8056 (t80) cc_final: 0.7701 (t80) REVERT: 2 213 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: 2 271 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: 4L 4 ILE cc_start: 0.9202 (mm) cc_final: 0.8982 (mp) REVERT: 6 20 MET cc_start: 0.8240 (mmm) cc_final: 0.7647 (mmm) REVERT: A5 50 GLN cc_start: 0.8414 (tt0) cc_final: 0.8203 (tt0) REVERT: AL 201 MET cc_start: 0.7656 (mtt) cc_final: 0.7082 (mtt) REVERT: AL 339 TYR cc_start: 0.8634 (m-80) cc_final: 0.8142 (m-80) REVERT: AL 373 VAL cc_start: 0.8906 (t) cc_final: 0.8691 (t) REVERT: A6 85 MET cc_start: 0.8187 (mtt) cc_final: 0.7962 (mtp) outliers start: 168 outliers final: 128 residues processed: 1047 average time/residue: 0.6591 time to fit residues: 1187.9007 Evaluate side-chains 1062 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 919 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 35 ASP Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 58 PHE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain AN residue 127 THR Chi-restraints excluded: chain S1 residue 66 ILE Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 85 CYS Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 148 ASP Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 218 MET Chi-restraints excluded: chain S1 residue 240 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 401 THR Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 500 ILE Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 174 ASP Chi-restraints excluded: chain V2 residue 61 SER Chi-restraints excluded: chain V2 residue 72 MET Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 1 residue 231 PHE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 137 LEU Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 4 residue 406 LYS Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 257 MET Chi-restraints excluded: chain 5 residue 291 MET Chi-restraints excluded: chain 5 residue 312 PHE Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 5 residue 522 VAL Chi-restraints excluded: chain A8 residue 24 SER Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 20 ASN Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain S5 residue 82 LEU Chi-restraints excluded: chain AM residue 108 VAL Chi-restraints excluded: chain BL residue 50 THR Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 141 GLU Chi-restraints excluded: chain B6 residue 148 ASP Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B7 residue 19 VAL Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 46 SER Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 84 VAL Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 27 GLU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 107 ASP Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain C2 residue 8 LEU Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain B1 residue 42 LEU Chi-restraints excluded: chain S4 residue 94 MET Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 189 ILE Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 417 ILE Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 212 MET Chi-restraints excluded: chain V1 residue 302 THR Chi-restraints excluded: chain V1 residue 347 CYS Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 49 SER Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain 3 residue 70 GLU Chi-restraints excluded: chain AL residue 259 VAL Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain A6 residue 51 MET Chi-restraints excluded: chain AB residue 80 LEU Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 710 optimal weight: 0.0000 chunk 468 optimal weight: 5.9990 chunk 754 optimal weight: 0.9980 chunk 460 optimal weight: 0.9990 chunk 357 optimal weight: 9.9990 chunk 524 optimal weight: 0.9990 chunk 791 optimal weight: 0.9990 chunk 728 optimal weight: 3.9990 chunk 629 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 486 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S3 182 ASN ** V2 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 204 GLN S8 211 GLN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S5 20 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 132 ASN A9 307 GLN ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 83 GLN A5 118 GLN AL 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 69384 Z= 0.483 Angle : 1.538 50.708 93565 Z= 1.002 Chirality : 0.312 6.420 9932 Planarity : 0.004 0.061 11642 Dihedral : 11.191 160.601 10934 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 15.48 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.94 (0.10), residues: 8026 helix: 1.44 (0.08), residues: 4227 sheet: -0.19 (0.27), residues: 408 loop : -0.25 (0.11), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPB6 42 HIS 0.023 0.001 HISS5 21 PHE 0.026 0.001 PHE 2 288 TYR 0.026 0.001 TYR 5 394 ARG 0.015 0.000 ARGAN 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16052 Ramachandran restraints generated. 8026 Oldfield, 0 Emsley, 8026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 939 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AN 56 TYR cc_start: 0.8519 (t80) cc_final: 0.8167 (t80) REVERT: AN 74 ASP cc_start: 0.7313 (t0) cc_final: 0.6877 (t0) REVERT: AN 90 TYR cc_start: 0.9041 (m-80) cc_final: 0.8717 (m-80) REVERT: S6 62 TYR cc_start: 0.8178 (m-80) cc_final: 0.7945 (m-80) REVERT: S1 85 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8130 (p) REVERT: S1 148 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: S3 46 LYS cc_start: 0.7634 (tppp) cc_final: 0.7362 (tppp) REVERT: S3 60 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7984 (mm) REVERT: S3 174 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: V2 185 TYR cc_start: 0.8557 (m-10) cc_final: 0.8025 (m-80) REVERT: V2 188 ASP cc_start: 0.7688 (m-30) cc_final: 0.7382 (m-30) REVERT: V2 199 ASN cc_start: 0.8473 (m-40) cc_final: 0.8267 (m110) REVERT: S7 138 MET cc_start: 0.8895 (tpt) cc_final: 0.8596 (tpt) REVERT: S8 53 MET cc_start: 0.8738 (mmp) cc_final: 0.8348 (mmt) REVERT: 1 162 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: 1 183 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7246 (mt) REVERT: 1 286 MET cc_start: 0.8292 (ttm) cc_final: 0.8021 (mtt) REVERT: 4 403 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7833 (mm-40) REVERT: 4 406 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: 4 443 MET cc_start: 0.8108 (mmm) cc_final: 0.7446 (ttt) REVERT: 5 32 ASP cc_start: 0.7897 (t0) cc_final: 0.7536 (t0) REVERT: 5 115 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8074 (tp) REVERT: 5 267 GLU cc_start: 0.7310 (tt0) cc_final: 0.6984 (tt0) REVERT: 5 414 MET cc_start: 0.7670 (pmm) cc_final: 0.7374 (pmm) REVERT: 5 431 ILE cc_start: 0.8077 (mm) cc_final: 0.7843 (mt) REVERT: A8 142 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7470 (pptt) REVERT: AO 100 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7750 (tm-30) REVERT: BL 120 TYR cc_start: 0.8911 (m-80) cc_final: 0.8476 (m-80) REVERT: B6 41 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7933 (tp-100) REVERT: B4 108 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: B8 118 TRP cc_start: 0.8811 (OUTLIER) cc_final: 0.8265 (t60) REVERT: B8 139 MET cc_start: 0.8663 (mmp) cc_final: 0.8402 (mmm) REVERT: B1 7 LYS cc_start: 0.7679 (mttp) cc_final: 0.7448 (pptt) REVERT: B1 42 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8527 (tt) REVERT: S4 170 ILE cc_start: 0.9210 (mm) cc_final: 0.8948 (mt) REVERT: A9 412 LEU cc_start: 0.8430 (mm) cc_final: 0.7885 (pp) REVERT: B2 64 TRP cc_start: 0.8612 (t60) cc_final: 0.8020 (t60) REVERT: B2 81 LYS cc_start: 0.8398 (mtmm) cc_final: 0.7938 (pttp) REVERT: S2 247 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5470 (t0) REVERT: S2 286 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: V1 164 MET cc_start: 0.8683 (ttm) cc_final: 0.8395 (mtp) REVERT: 2 202 PHE cc_start: 0.8039 (t80) cc_final: 0.7710 (t80) REVERT: 2 213 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8554 (m-10) REVERT: 2 271 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: 4L 4 ILE cc_start: 0.9198 (mm) cc_final: 0.8973 (mp) REVERT: 6 20 MET cc_start: 0.8241 (mmm) cc_final: 0.7646 (mmm) REVERT: A5 50 GLN cc_start: 0.8364 (tt0) cc_final: 0.8162 (tt0) REVERT: AL 339 TYR cc_start: 0.8591 (m-80) cc_final: 0.8121 (m-80) REVERT: AL 372 ASP cc_start: 0.7122 (m-30) cc_final: 0.6834 (m-30) REVERT: AL 373 VAL cc_start: 0.8975 (t) cc_final: 0.8715 (t) REVERT: A6 85 MET cc_start: 0.8187 (mtt) cc_final: 0.7957 (mtp) outliers start: 146 outliers final: 118 residues processed: 1036 average time/residue: 0.6539 time to fit residues: 1166.9660 Evaluate side-chains 1053 residues out of total 7030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 920 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AN residue 40 THR Chi-restraints excluded: chain AN residue 58 PHE Chi-restraints excluded: chain AN residue 76 ASP Chi-restraints excluded: chain AN residue 110 ASP Chi-restraints excluded: chain AN residue 127 THR Chi-restraints excluded: chain S1 residue 66 ILE Chi-restraints excluded: chain S1 residue 84 ASN Chi-restraints excluded: chain S1 residue 85 CYS Chi-restraints excluded: chain S1 residue 132 MET Chi-restraints excluded: chain S1 residue 148 ASP Chi-restraints excluded: chain S1 residue 196 CYS Chi-restraints excluded: chain S1 residue 218 MET Chi-restraints excluded: chain S1 residue 240 CYS Chi-restraints excluded: chain S1 residue 251 SER Chi-restraints excluded: chain S1 residue 379 VAL Chi-restraints excluded: chain S1 residue 401 THR Chi-restraints excluded: chain S1 residue 409 ASP Chi-restraints excluded: chain S1 residue 481 LYS Chi-restraints excluded: chain S1 residue 500 ILE Chi-restraints excluded: chain S1 residue 580 ASP Chi-restraints excluded: chain S1 residue 709 MET Chi-restraints excluded: chain S3 residue 60 LEU Chi-restraints excluded: chain S3 residue 84 ASP Chi-restraints excluded: chain S3 residue 111 THR Chi-restraints excluded: chain S3 residue 174 ASP Chi-restraints excluded: chain S3 residue 182 ASN Chi-restraints excluded: chain V2 residue 61 SER Chi-restraints excluded: chain V2 residue 178 MET Chi-restraints excluded: chain S8 residue 82 ILE Chi-restraints excluded: chain S8 residue 124 CYS Chi-restraints excluded: chain S8 residue 125 GLU Chi-restraints excluded: chain S8 residue 138 GLU Chi-restraints excluded: chain S8 residue 163 CYS Chi-restraints excluded: chain S8 residue 167 CYS Chi-restraints excluded: chain 1 residue 76 LEU Chi-restraints excluded: chain 1 residue 104 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 162 PHE Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 1 residue 183 ILE Chi-restraints excluded: chain 4 residue 18 ASN Chi-restraints excluded: chain 4 residue 137 LEU Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 213 VAL Chi-restraints excluded: chain 4 residue 216 SER Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 317 LEU Chi-restraints excluded: chain 4 residue 400 SER Chi-restraints excluded: chain 4 residue 406 LYS Chi-restraints excluded: chain 5 residue 10 SER Chi-restraints excluded: chain 5 residue 113 ILE Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 291 MET Chi-restraints excluded: chain 5 residue 312 PHE Chi-restraints excluded: chain 5 residue 362 TYR Chi-restraints excluded: chain 5 residue 439 MET Chi-restraints excluded: chain 5 residue 461 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 5 residue 522 VAL Chi-restraints excluded: chain A8 residue 24 SER Chi-restraints excluded: chain A8 residue 50 GLN Chi-restraints excluded: chain A8 residue 106 THR Chi-restraints excluded: chain A8 residue 121 ASP Chi-restraints excluded: chain A8 residue 142 LYS Chi-restraints excluded: chain AO residue 140 ASP Chi-restraints excluded: chain S5 residue 37 CYS Chi-restraints excluded: chain S5 residue 52 ASP Chi-restraints excluded: chain BL residue 50 THR Chi-restraints excluded: chain BL residue 134 MET Chi-restraints excluded: chain B6 residue 60 LEU Chi-restraints excluded: chain B6 residue 141 GLU Chi-restraints excluded: chain B6 residue 153 SER Chi-restraints excluded: chain B4 residue 28 GLN Chi-restraints excluded: chain B7 residue 19 VAL Chi-restraints excluded: chain B7 residue 40 THR Chi-restraints excluded: chain B7 residue 46 SER Chi-restraints excluded: chain B7 residue 55 ASP Chi-restraints excluded: chain B5 residue 84 VAL Chi-restraints excluded: chain B5 residue 156 ASP Chi-restraints excluded: chain B9 residue 6 LEU Chi-restraints excluded: chain B9 residue 27 GLU Chi-restraints excluded: chain B9 residue 75 PHE Chi-restraints excluded: chain BM residue 47 THR Chi-restraints excluded: chain BM residue 81 VAL Chi-restraints excluded: chain BM residue 123 ASP Chi-restraints excluded: chain B8 residue 89 SER Chi-restraints excluded: chain B8 residue 118 TRP Chi-restraints excluded: chain B8 residue 168 VAL Chi-restraints excluded: chain AC residue 128 ASP Chi-restraints excluded: chain C2 residue 8 LEU Chi-restraints excluded: chain B1 residue 6 ASP Chi-restraints excluded: chain B1 residue 42 LEU Chi-restraints excluded: chain S4 residue 94 MET Chi-restraints excluded: chain S4 residue 96 SER Chi-restraints excluded: chain A9 residue 358 THR Chi-restraints excluded: chain A9 residue 368 VAL Chi-restraints excluded: chain A9 residue 401 SER Chi-restraints excluded: chain B2 residue 32 SER Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain S2 residue 189 ILE Chi-restraints excluded: chain S2 residue 247 ASP Chi-restraints excluded: chain S2 residue 286 GLU Chi-restraints excluded: chain S2 residue 317 ASN Chi-restraints excluded: chain S2 residue 361 ILE Chi-restraints excluded: chain S2 residue 378 THR Chi-restraints excluded: chain S2 residue 417 ILE Chi-restraints excluded: chain V1 residue 133 ASP Chi-restraints excluded: chain V1 residue 149 ASP Chi-restraints excluded: chain V1 residue 302 THR Chi-restraints excluded: chain V1 residue 347 CYS Chi-restraints excluded: chain V1 residue 440 CYS Chi-restraints excluded: chain V1 residue 472 VAL Chi-restraints excluded: chain 2 residue 18 THR Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 2 residue 213 PHE Chi-restraints excluded: chain 2 residue 271 GLN Chi-restraints excluded: chain A7 residue 50 HIS Chi-restraints excluded: chain A3 residue 56 LEU Chi-restraints excluded: chain A3 residue 69 LEU Chi-restraints excluded: chain 6 residue 43 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 3 residue 49 SER Chi-restraints excluded: chain 3 residue 69 VAL Chi-restraints excluded: chain 3 residue 70 GLU Chi-restraints excluded: chain AL residue 259 VAL Chi-restraints excluded: chain AL residue 280 ILE Chi-restraints excluded: chain AL residue 291 TRP Chi-restraints excluded: chain AL residue 359 GLU Chi-restraints excluded: chain AB residue 82 VAL Chi-restraints excluded: chain AB residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 794 random chunks: chunk 386 optimal weight: 6.9990 chunk 500 optimal weight: 0.0570 chunk 670 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 580 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 630 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 647 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 211 GLN ** 1 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 66 GLN S5 20 ASN ** B7 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 132 ASN A9 307 GLN ** S2 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 320 ASN ** A7 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 83 GLN AL 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112162 restraints weight = 92930.140| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.80 r_work: 0.3250 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 69384 Z= 0.480 Angle : 1.536 50.703 93565 Z= 1.001 Chirality : 0.312 6.409 9932 Planarity : 0.004 0.062 11642 Dihedral : 11.054 160.849 10934 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.01 % Allowed : 15.71 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.10), residues: 8026 helix: 1.51 (0.08), residues: 4230 sheet: -0.25 (0.27), residues: 405 loop : -0.22 (0.11), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPB6 42 HIS 0.012 0.001 HISS8 106 PHE 0.026 0.001 PHE 2 288 TYR 0.026 0.001 TYRA6 37 ARG 0.014 0.000 ARGAN 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18788.30 seconds wall clock time: 329 minutes 53.36 seconds (19793.36 seconds total)